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I

icosahedron - Static variable in class misc.SphericalPoints
These points are the vertices of an icosahedron.
identity(int, int) - Static method in class Jama.Matrix
Generate identity matrix
identity(int) - Static method in class numerics.RealMatrix
Returns a square identity matrix.
imag() - Method in class numerics.Complex
Returns the imaginary part.
imageExists(String) - Static method in class imaging.ImageHeader
 
imageFromBallStick(VoxelOrderDataSource, int[], double[], double[][][], double, double) - Static method in class apps.RGB_ScalarImage
Read image from Ball and stick input.
imageFromCompartmentModel(int[], double[], double[][][], double, double) - Static method in class apps.RGB_ScalarImage
Read image from fitting a compartment model.
imageFromPICoPDFs(VoxelOrderDataSource, int, int, int[], double[], double[][][], double, double) - Static method in class apps.RGB_ScalarImage
Read an image from PICoPDFs.
imageFromPICoPDFs(VoxelOrderDataSource, int, int, int[], double[], double[][][], double, double, int) - Static method in class apps.RGB_ScalarImage
Read an image from PICoPDFs.
imageFromSphFuncPDs(VoxelOrderDataSource, int[], double[], double[][][], double, double) - Static method in class apps.RGB_ScalarImage
Read image from ODF peak input.
imageFromTensorEigenSys(VoxelOrderDataSource, int[], double[], double[][][], double, double) - Static method in class apps.RGB_ScalarImage
Read an image from tensor eigen system input.
imageFromTensorEigenSys(VoxelOrderDataSource, int[], double[], double[][][], double, double, int) - Static method in class apps.RGB_ScalarImage
Read an image from tensor eigen system input.
ImageHeader - Class in imaging
Superclass for medical image headers, provides an interface for basic header information and a method to get the underlying data in voxel order.
ImageHeader() - Constructor for class imaging.ImageHeader
 
ImageInterpolator - Interface in tractography
Interface for interpolators.
ImageToVoxel - Class in apps
Converts Analyze / NIFTI / MHA files to voxel order.
ImageToVoxel(String[]) - Constructor for class apps.ImageToVoxel
 
imaginary() - Method in class numerics.Complex
Returns the imaginary part.
imaging - package imaging
 
ImagSH - Class in sphfunc
Purpose: Imaginary part of spherical harmonic function.
ImagSH(int, int) - Constructor for class sphfunc.ImagSH
Constructor requires order and the index.
ImagSH(int, int, double) - Constructor for class sphfunc.ImagSH
Constructor requires order and the index.
imPars - Static variable in class tools.CL_Initializer
The parameters of the imaging sequence corresponding to the input data.
ImportSH_Coeffs - Class in apps
Purpose: Converts the spherical harmonic (SH) output of several third party programs to the format expected in Camino.
ImportSH_Coeffs() - Constructor for class apps.ImportSH_Coeffs
 
in - Static variable in class apps.Shredder
 
IncompleteBeta - Class in numerics
Purpose: Contains implementation of the incomplete beta function.
IncompleteBeta() - Constructor for class numerics.IncompleteBeta
 
IncompleteBetaException - Exception in numerics
Purpose: Exception class used by the IncompleteBeta class.
init() - Method in class simulation.geometry.substrates.CellularLattice
initialiser.
init() - Method in class simulation.geometry.substrates.CylinderSubstrate
 
init() - Method in class simulation.geometry.substrates.EmptySubstrate
does nothing
init() - Method in class simulation.geometry.substrates.MeshSubstrate
not used, does nothing.
init() - Method in class simulation.geometry.substrates.SquashyInflammationSubstrate
initialise squashy cylinders of given radius at each centre specified by the P array
init() - Method in class simulation.geometry.substrates.Substrate
initialiser for substrate.
initBoundaryIntersectionArrays() - Method in class simulation.geometry.substrates.Substrate
sets the values of the min and max values to use when checking if a spin walks off the substrate.
initCandidates(Walker, double[], double[]) - Method in class simulation.geometry.substrates.Substrate
 
initDataSynthesizer() - Static method in class tools.CL_Initializer
Initializes the synthetic data source.
initDefaultVals() - Method in class apps.AddNoise
 
initDefaultVals() - Method in class apps.BinaryToText
 
initDefaultVals() - Method in class apps.ChunkStats
 
initDefaultVals() - Method in class apps.DT_EigenSystem
 
initDefaultVals() - Method in class apps.DT_FitMatrix
Output manager
initDefaultVals() - Method in class apps.DT_ShapeStatistics
 
initDefaultVals() - Method in class apps.DT_ToCamino
 
initDefaultVals() - Method in class apps.DT_ToNii
 
initDefaultVals() - Method in class apps.ElectrostaticSubsets
 
initDefaultVals() - Method in class apps.EstimateSNR
 
initDefaultVals() - Method in class apps.Executable
initialise the default values of class-level fields, as they would be at declaration.
initDefaultVals() - Method in class apps.FanningGrid
 
initDefaultVals() - Method in class apps.FracAnis
 
initDefaultVals() - Method in class apps.FSL_ToScheme
 
initDefaultVals() - Method in class apps.GenerateDTLUT
 
initDefaultVals() - Method in class apps.ImageToVoxel
Output manager
initDefaultVals() - Method in class apps.InversionStats
 
initDefaultVals() - Method in class apps.MeanDiff
Output manager
initDefaultVals() - Method in class apps.ModelFit
 
initDefaultVals() - Method in class apps.OrderElectrostaticPoints
 
initDefaultVals() - Method in class apps.OrientationBiasMap
 
initDefaultVals() - Method in class apps.PICoPDFs
Output manager
initDefaultVals() - Method in class apps.PointSetToScheme
 
initDefaultVals() - Method in class apps.ProcessStreamlines
initialise the default values of class-level fields, as they would be at declaration.
initDefaultVals() - Method in class apps.QBallMX
Output manager
initDefaultVals() - Method in class apps.ScannerToVoxel
Output manager
initDefaultVals() - Method in class apps.Shredder
 
initDefaultVals() - Method in class apps.SphFuncAnisotropy
 
initDefaultVals() - Method in class apps.SphFuncBitMap
 
initDefaultVals() - Method in class apps.SphFuncKurtosis
 
initDefaultVals() - Method in class apps.SphFuncPD_Stats
 
initDefaultVals() - Method in class apps.SphFuncSkewness
 
initDefaultVals() - Method in class apps.SphHarmFitter
 
initDefaultVals() - Method in class apps.SphPDF_Fit
 
initDefaultVals() - Method in class apps.Split4D_NiiImage
 
initDefaultVals() - Method in class apps.StreamlineTractography
 
initDefaultVals() - Method in class apps.SubsetScheme
 
initDefaultVals() - Method in class apps.SyntheticData
 
initDefaultVals() - Method in class apps.TraceD
 
initDefaultVals() - Method in class apps.VoxelClassify
 
initDefaultVals() - Method in class apps.VoxelToScanner
Output manager
initialiseSpatialOptimisation(int[]) - Method in class simulation.geometry.substrates.Substrate
initialises the map of substrate objects to subvoxels in the spatial optimisation grid.
initialiseWalkers() - Method in class simulation.DiffusionSimulation
sets all walkers in initial conditions
initializeRandom() - Method in class misc.OrderedAcqMinimizer
Randomly order the points.
initializeSphericalPointSet(int) - Method in class tractography.BayesDiracRandomizer
 
initImagingScheme() - Static method in class tools.CL_Initializer
Initializes the DW_Scheme object containing the acqusition information.
initLattice() - Method in class simulation.geometry.substrates.CellularLattice
abstract method for initialising cell activation.
initLattice() - Method in class simulation.geometry.substrates.PercCellularLattice
initialises a lattice of cells with each location being occupied with propbability p_perc or unoccupied with probability (1-p_perc)
initLattice() - Method in class simulation.geometry.substrates.StripedCellularLattice
initialises D dimensional lattice in stripes of proscribed thickness
initMaskSource() - Static method in class tools.CL_Initializer
Initializes the data source for the background mask.
initMaxEnt() - Static method in class tools.CL_Initializer
Initializes the reconstruction direction set for maximum entropy deconvolution.
initOptions(String[]) - Method in class apps.AddNoise
 
initOptions(String[]) - Method in class apps.BinaryToText
 
initOptions(String[]) - Method in class apps.ChunkStats
 
initOptions(String[]) - Method in class apps.ClassifiedModelFit
 
initOptions(String[]) - Method in class apps.DT_EigenSystem
 
initOptions(String[]) - Method in class apps.DT_FitMatrix
 
initOptions(String[]) - Method in class apps.DT_ShapeStatistics
 
initOptions(String[]) - Method in class apps.DT_ToCamino
 
initOptions(String[]) - Method in class apps.DT_ToNii
 
initOptions(String[]) - Method in class apps.ElectrostaticSubsets
 
initOptions(String[]) - Method in class apps.EstimateSNR
 
initOptions(String[]) - Method in class apps.Executable
default commandline parsing and initialisation
initOptions(String[]) - Method in class apps.FanningGrid
 
initOptions(String[]) - Method in class apps.FracAnis
 
initOptions(String[]) - Method in class apps.FSL_ToScheme
 
initOptions(String[]) - Method in class apps.GenerateDTLUT
 
initOptions(String[]) - Method in class apps.ImageToVoxel
 
initOptions(String[]) - Method in class apps.InversionStats
Runs the main program given the command line arguments.
initOptions(String[]) - Method in class apps.MeanDiff
 
initOptions(String[]) - Method in class apps.ModelFit
 
initOptions(String[]) - Method in class apps.OrderElectrostaticPoints
 
initOptions(String[]) - Method in class apps.OrientationBiasMap
default commandline parsing and initialisation
initOptions(String[]) - Method in class apps.PICoPDFs
 
initOptions(String[]) - Method in class apps.PointSetToScheme
 
initOptions(String[]) - Method in class apps.ProcessStreamlines
Command line parsing
initOptions(String[]) - Method in class apps.QBallMX
 
initOptions(String[]) - Static method in class apps.Reorient
 
initOptions(String[]) - Method in class apps.ScannerToVoxel
 
initOptions(String[]) - Method in class apps.Shredder
 
initOptions(String[]) - Method in class apps.SphFuncAnisotropy
 
initOptions(String[]) - Method in class apps.SphFuncBitMap
 
initOptions(String[]) - Method in class apps.SphFuncKurtosis
 
initOptions(String[]) - Method in class apps.SphFuncPD_Stats
 
initOptions(String[]) - Method in class apps.SphFuncSkewness
 
initOptions(String[]) - Method in class apps.SphHarmFitter
 
initOptions(String[]) - Method in class apps.SphPDF_Fit
 
initOptions(String[]) - Method in class apps.Split4D_NiiImage
 
initOptions(String[]) - Method in class apps.StreamlineTractography
 
initOptions(String[]) - Method in class apps.SubsetScheme
 
initOptions(String[]) - Method in class apps.SyntheticData
 
initOptions(String[]) - Method in class apps.TraceD
 
initOptions(String[]) - Method in class apps.VoxelClassify
 
initOptions(String[]) - Method in class apps.VoxelToScanner
 
initSphFuncDataSource() - Static method in class tools.CL_Initializer
Initializes an external data source for spherical function parameters.
initTensorDataSource() - Static method in class tools.CL_Initializer
Initializes an external data source for tensor data
initVariables() - Method in class apps.AddNoise
 
initVariables() - Method in class apps.BinaryToText
 
initVariables() - Method in class apps.ChunkStats
 
initVariables() - Method in class apps.ClassifiedModelFit
 
initVariables() - Method in class apps.DT_EigenSystem
 
initVariables() - Method in class apps.DT_FitMatrix
 
initVariables() - Method in class apps.DT_ShapeStatistics
 
initVariables() - Method in class apps.DT_ToCamino
 
initVariables() - Method in class apps.DT_ToNii
 
initVariables() - Method in class apps.ElectrostaticSubsets
 
initVariables() - Method in class apps.EstimateSNR
 
initVariables() - Method in class apps.Executable
abstract initialisation method for commands
initVariables() - Method in class apps.FanningGrid
 
initVariables() - Method in class apps.FracAnis
 
initVariables() - Method in class apps.FSL_ToScheme
 
initVariables() - Method in class apps.GenerateDTLUT
 
initVariables() - Method in class apps.ImageToVoxel
 
initVariables() - Method in class apps.InversionStats
 
initVariables() - Method in class apps.LinearRecon
 
initVariables() - Method in class apps.MeanDiff
 
initVariables() - Method in class apps.ModelFit
 
initVariables() - Method in class apps.OrderElectrostaticPoints
 
initVariables() - Method in class apps.OrientationBiasMap
 
initVariables() - Method in class apps.PICoPDFs
 
initVariables() - Method in class apps.PointSetToScheme
 
initVariables() - Method in class apps.ProcessStreamlines
Initialize class variables
initVariables() - Method in class apps.QBallMX
 
initVariables() - Static method in class apps.Reorient
 
initVariables() - Method in class apps.ScannerToVoxel
 
initVariables() - Method in class apps.Shredder
 
initVariables() - Method in class apps.SphFuncAnisotropy
 
initVariables() - Method in class apps.SphFuncBitMap
 
initVariables() - Method in class apps.SphFuncKurtosis
 
initVariables() - Method in class apps.SphFuncPD_Stats
 
initVariables() - Method in class apps.SphFuncSkewness
 
initVariables() - Method in class apps.SphHarmFitter
 
initVariables() - Method in class apps.SphPDF_Fit
 
initVariables() - Method in class apps.Split4D_NiiImage
 
initVariables() - Method in class apps.StreamlineTractography
 
initVariables() - Method in class apps.SubsetScheme
 
initVariables() - Method in class apps.SyntheticData
 
initVariables() - Method in class apps.TraceD
 
initVariables() - Method in class apps.VoxelClassify
 
initVariables() - Method in class apps.VoxelToScanner
 
initVectors() - Method in class simulation.geometry.elements.Triangle
recalculate the normal and the u and v vectors used for triangle intersection
inputDataType - Static variable in class tools.CL_Initializer
The type of the input data
inputFile - Static variable in class tools.CL_Initializer
Name of the input data file.
inputModel - Static variable in class tools.CL_Initializer
The type of model represented by the input data.
inside(double[]) - Method in class simulation.geometry.elements.BasicCylinder
decides whether a point Q is inside the cylinder or not by comparing the shortest disance of the point to the central axis to the radius of the cylinder
inside(double[]) - Method in class simulation.geometry.elements.FacetCylinder
checks if a position is inside or outside the cylinder.
inside(double[]) - Method in class simulation.geometry.elements.MyelinatedCylinder
checks if a postion is inside the cylinder.
inside(double[]) - Method in interface simulation.geometry.elements.SubstrateObject
checks if a point is inside or outside the object
inside(double[]) - Method in class simulation.geometry.elements.Triangle
 
INT - Static variable in class data.ExternalDataSource
 
integerDF - Static variable in class tools.ArrayOps
 
integrate() - Method in class numerics.NumericalIntegration
 
integrate(int) - Method in class numerics.NumericalIntegration
performs an integration with a given index
integrationErrorStats() - Method in class mesd.MESD_Fitter
This method looks at the max.
intelByteOrder - Variable in class imaging.AnalyzeHeader
 
intelByteOrder - Variable in class imaging.MetaImageHeader
BinaryDataByteOrderMSB = !intelByteOrder.
intent - Variable in class imaging.Nifti1Dataset
 
intent_code - Variable in class imaging.Nifti1Dataset
 
intent_name - Variable in class imaging.Nifti1Dataset
 
intErrThresh - Static variable in class mesd.MESD_Inversion
The threshold on the error of the integral above which the minimisation needs to be performed again.
intErrThreshUpper - Static variable in class mesd.MESD_Inversion
A second threshold is used to semi-acceptance of a result once integration has been performed using the largest point set.
intersectsBoundary - Variable in class simulation.geometry.substrates.Substrate
flag to say whether an intersection is with the cell boundary or not
intersectsCubicRegion(double[], double[]) - Method in class simulation.geometry.elements.BasicCylinder
checks if cylinder intersects a specified axis-aligned cubic region.
intersectsCubicRegion(double[], double[]) - Method in class simulation.geometry.elements.FacetCylinder
 
intersectsCubicRegion(double[], double[]) - Method in class simulation.geometry.elements.MyelinatedCylinder
checks if cylinder intersects axis-aligned cubic region
intersectsCubicRegion(double[], double[]) - Method in interface simulation.geometry.elements.SubstrateObject
checks if the object intersects a cubic region.
intersectsCubicRegion(double[], double[]) - Method in class simulation.geometry.elements.Triangle
checks if triangle intersects an axis-aligned cubic region
interval - Static variable in class tools.CL_Initializer
Number of steps between samples in Markov Chain Monte Carlo algorithm .
intracellular(Walker) - Method in class simulation.geometry.substrates.CellularLattice
 
intracellular(Walker) - Method in class simulation.geometry.substrates.CylinderSubstrate
 
intracellular(Walker) - Method in class simulation.geometry.substrates.EmptySubstrate
 
intracellular(Walker) - Method in class simulation.geometry.substrates.MeshSubstrate
performs the ray test to check if a point is inside the object or not.
intracellular(Walker) - Method in class simulation.geometry.substrates.SquashyInflammationSubstrate
tests if a position is intracellular or not.
intracellular(Walker) - Method in class simulation.geometry.substrates.StickyCylinderSubstrate
override intracellular check to account for being stuck to the surface which would otherwise cause annoying floating-point precision related difficulties and spurious crossings
intracellular(Walker) - Method in class simulation.geometry.substrates.Substrate
checks if a walker is in intracellular (true) or extracellular (false) space
INTRACELLULAR - Static variable in class simulation.SimulationParams
flag for intracellular walkers only
INTRAONLY - Static variable in class simulation.SimulationParams
flag for compartmental signal: intracellular only
inverse() - Method in class Jama.Matrix
Matrix inverse or pseudoinverse
inverse() - Method in class misc.DT
Computes the inverse diffusion tensor.
inverse() - Method in class numerics.Complex
Reciprocates the complex number.
inverse() - Method in class numerics.RealMatrix
Inverts a matrix inefficiently by computing the determinant and adjoint.
InversionIndex - Enum in inverters
Codes for model-based inversions.
inversionIndices - Static variable in class tools.CL_Initializer
Index specifying the inversion.
InversionStats - Class in apps
Purpose: Computes statistics of properties of the inversion outputs.
InversionStats(String[]) - Constructor for class apps.InversionStats
 
invert(double[]) - Method in class inverters.BallStickInversion
Does the inversion.
invert(double[]) - Method in class inverters.DiffusionInversion
Does the inversion.
invert(double[]) - Method in class inverters.LinearADC_Inversion
Fits the apparent diffusion coefficient using the inverse matrix.
invert(double[]) - Method in class inverters.LinearDT_Inversion
Fits the diffusion tensor using the inverse matrix.
invert(double[]) - Method in class inverters.LinearInversion
Fits the diffusion tensor using the inverse matrix.
invert(double[]) - Method in class inverters.MultiTensorInversion
Fits the model.
invert(double[]) - Method in class inverters.NonLinearDT_Inversion
Fits the diffusion tensor.
invert(double[]) - Method in class inverters.RestoreDT_Inversion
Fits the diffusion tensor.
invert(double[]) - Method in class inverters.ThreeTensorInversion
Fits the model.
invert(double[]) - Method in class inverters.TwoTensorInversion
Fits the model.
invert(double[]) - Method in class inverters.WeightedLinearDT_Inversion
Fits the diffusion tensor.
invert(double[]) - Method in class mesd.MESD_Inversion
Computes the MESD.
inverters - package inverters
 
invX2P1(double) - Static method in class inverters.TensorModelFitter
One of the standard functions for constraining optimization parameters (eg a mixing parameter) to [0, 1].
ipThreshold() - Method in class tractography.FibreTracker
 
isBG(double) - Static method in class apps.ModelFit
Check whether the next voxel is background
ISCodes - Class in sphfunc
Purpose: Implements a simple database of icosahedral spherical codes of increasing degree.
ISCodes() - Constructor for class sphfunc.ISCodes
 
ISCodesException - Exception in sphfunc
Purpose: Exception class used in ISCodes database.
isExpanding() - Method in class simulation.geometry.elements.SquashyCylinder
checks if cylinder is expanding or not
isFullRank() - Method in class Jama.QRDecomposition
Is the matrix full rank?
isIn(PD) - Method in class sphfunc.PDList
Tests to see if the PD is already in the list to within the specified threshold.
isNonsingular() - Method in class Jama.LUDecomposition
Is the matrix nonsingular?
isSPD() - Method in class Jama.CholeskyDecomposition
Is the matrix symmetric and positive definite?
isZero() - Method in class numerics.Complex
Tests for equality with zero.
ITEMSPERVOX - Static variable in class inverters.DT_Inversion
The number of data items per voxel in the output format from this inversion.
ITEMSPERVOX - Static variable in class inverters.LinearADC_Inversion
The number of data items returned by the inversion.
ITEMSPERVOX - Static variable in class inverters.ThreeTensorInversion
The number of elements of the output array.
ITEMSPERVOX - Static variable in class inverters.TwoTensorInversion
The number of elements of the output array.
itemsPerVoxel() - Method in class inverters.BallStickInversion
Specifies the number of elements of the output array from the inversion.
itemsPerVoxel() - Method in class inverters.DiffusionInversion
Specifies the number of elements of the output array from the inversion.
itemsPerVoxel() - Method in class inverters.DT_Inversion
 
itemsPerVoxel() - Method in class inverters.EvenSphHarmFitter
Specifies the number of elements in the output array.
itemsPerVoxel() - Method in class inverters.LinearADC_Inversion
 
itemsPerVoxel() - Method in class inverters.LinearInversion
Returns the length of the arrays returned by invert.
itemsPerVoxel() - Method in class inverters.MultiTensorInversion
 
itemsPerVoxel() - Method in class inverters.ThreeTensorInversion
 
itemsPerVoxel() - Method in class inverters.TwoTensorInversion
 
itemsPerVoxel() - Method in class mesd.MESD_Inversion
 
iTransform(RealMatrix) - Method in class misc.DT
Applies a similarity transform to the diffusion tensor using the linear transformation matrix supplied.
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