- 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.