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E

e1() - Method in class numerics.BinghamDistribution
Eigenvector corresponding to the smallest eigenvalue of T.
e2() - Method in class numerics.BinghamDistribution
Eigenvector corresponding to the second eigenvalue of T.
e3() - Method in class numerics.BinghamDistribution
Eigenvector corresponding to the largest eigenvalue of T.
Edge - Class in tractography
 
Edge(int, int, int, double, double) - Constructor for class tractography.Edge
 
eig() - Method in class Jama.Matrix
Eigenvalue Decomposition
eigenSystem() - Method in class misc.DT
Eigensystem computed using the Jama.EigenvalueDecomposition class.
EigenSystem3D - Class in numerics
Purpose: Container for eigenvectors and eigenvalues.
EigenSystem3D(Vector3D[], double[]) - Constructor for class numerics.EigenSystem3D
 
EigenSystem3D(double[][]) - Constructor for class numerics.EigenSystem3D
Convert a sorted eigen system where the eigenvalues are (in decreasing order) seig([0][0], [0][1], [0][2]).
EigenvalueDecomposition - Class in Jama
Eigenvalues and eigenvectors of a real matrix.
EigenvalueDecomposition(Matrix) - Constructor for class Jama.EigenvalueDecomposition
Check for symmetry, then construct the eigenvalue decomposition
eigenvalues(double, double) - Static method in class apps.SphFuncPICoCalibrationData
Calculates eigenvalues of prolate DT with specified FA and trace.
eigenValues() - Method in class misc.DT
Returns an array containing the three eigenvalues of the diffusion tensor.
eigenvalues - Variable in class numerics.EigenSystem3D
 
eigenvectors() - Method in class numerics.ACG_Distribution
 
eigenvectors - Variable in class numerics.EigenSystem3D
 
EightNeighbourInterpolator - Class in tractography
Purpose: To provide linearly interpolated measurements using eight-neighbour interpolation at any point within the dataset.
EightNeighbourInterpolator(int, int, int, double, double, double) - Constructor for class tractography.EightNeighbourInterpolator
Construct an interpolator.
EightNeighbourInterpolator(int[], double[]) - Constructor for class tractography.EightNeighbourInterpolator
Construct an interpolator.
ElasticReflector - Class in simulation.dynamics
reflects a step off a barrier with a given normal.
ElasticReflector(Substrate) - Constructor for class simulation.dynamics.ElasticReflector
constructor
elecPointSetScheme(int, int, double) - Static method in class imaging.B_VectorScheme
For backwards compatibility, allow construction at run time (no scheme file) given the number of zero and non-zero measurements and a fixed b-value.
ElectrostaticSubsets - Class in apps
Orders electrostatic points into subsets following the method in Cook et al (ISMRM 2005, p.
ElectrostaticSubsets(String[]) - Constructor for class apps.ElectrostaticSubsets
 
EmptySubstrate - Class in simulation.geometry.substrates
this is for debugging purposes.
EmptySubstrate(SimulationParams) - Constructor for class simulation.geometry.substrates.EmptySubstrate
 
EmptySubstrate(double[]) - Constructor for class simulation.geometry.substrates.EmptySubstrate
test constructor, size only
EndianCorrectInputStream - Class in imaging
Input stream provided with NiftiDataset class.
EndianCorrectInputStream(String, boolean) - Constructor for class imaging.EndianCorrectInputStream
Constructor for a disk file.
EndianCorrectInputStream(InputStream, boolean) - Constructor for class imaging.EndianCorrectInputStream
Constructor for an InputStream.
EndianCorrectOutputStream - Class in imaging
Output stream provided with NiftiDataset class.
EndianCorrectOutputStream(String, boolean) - Constructor for class imaging.EndianCorrectOutputStream
Constructor for a disk file.
EndianCorrectOutputStream(OutputStream, boolean) - Constructor for class imaging.EndianCorrectOutputStream
Constructor for an OutputStream.
EndianNeutralDataInputStream - Class in tools
 
EndianNeutralDataInputStream(InputStream, boolean) - Constructor for class tools.EndianNeutralDataInputStream
 
entries - Variable in class numerics.RealMatrix
The array of matrix entries.
entry(int, int) - Method in class numerics.RealMatrix
Returns a single entry of the matrix.
EntryPoint - Class in apps
Unified entrypoint for all camino commands, incorporating generic main method structure and command checking.
EntryPoint() - Constructor for class apps.EntryPoint
 
eof() - Method in class tools.FileInput
Return true if the end of file has been reached.
equals(Complex) - Method in class numerics.Complex
 
equals(Object) - Method in class numerics.Point3D
 
equals(Object) - Method in class numerics.Vector3D
 
equals(Object) - Method in class tractography.Tract
 
equals(Object) - Method in class tractography.Voxel
 
equivalent(PDList, double) - Method in class sphfunc.PDList
Compares this PDList to another to see if they are the same to within the specified tolerance on the dot product between unit vectors.
erf(double) - Static method in class numerics.ErrorFunction
evaluates the error function for a real argumant using the MacClaurin series representation.
ErrorFunction - Class in numerics
Contains static method for evaluation of the error function (erf(z)) using the MacClaurin series representation.
ErrorFunction() - Constructor for class numerics.ErrorFunction
 
ErrorFunctionException - Exception in numerics
The exception thrown due to errors in calculating the error function
ErrorFunctionException() - Constructor for exception numerics.ErrorFunctionException
 
ErrorFunctionException(String) - Constructor for exception numerics.ErrorFunctionException
 
ErrorFunctionException(Throwable) - Constructor for exception numerics.ErrorFunctionException
 
ErrorFunctionException(String, Throwable) - Constructor for exception numerics.ErrorFunctionException
 
EstimateSNR - Class in apps
Estimates SNR using different methods explained in the paper "Measurement of signal-to-noise ratios in MR images: Influence of multichannel coils, parallel imaging, and reconstruction filters" by Olaf Dietrich et al, JMRI 26:376-385 (2007).
EstimateSNR(String[]) - Constructor for class apps.EstimateSNR
 
EulerFibreTracker - Class in tractography
Superclass for trackers that use Euler's method to track through the data.
EulerFibreTracker(TractographyImage, double, double) - Constructor for class tractography.EulerFibreTracker
Construct an EulerFibreTracker with additional options set.
EULERGAMMA - Static variable in class numerics.GammaFunctions
Euler's constant.
evaluate(double[]) - Method in class numerics.PolynomialFunction
Evaluate the function.
evaluate(double[]) - Method in class numerics.PolynomialFunction1D
 
evaluate(double[]) - Method in class numerics.PolynomialFunction2D
 
evaluate(double) - Method in class numerics.SVAnalyticalFunction
 
evaluate(double) - Method in class numerics.WatsonD
 
evenFuncsUpTo(int) - Static method in class numerics.SphericalHarmonics
Computes the number of even spherical harmonic functions up to a specified order.
EvenSHS - Class in sphfunc
Purpose: Real antipodally symmetric function represented as a spherical harmonic series.
EvenSHS(double[], int) - Constructor for class sphfunc.EvenSHS
The constructor takes an array containing the spherical harmonic coefficients in the format output by EvenSphHarmFitter.fit.
EvenSphHarmFitter - Class in inverters
Purpose: Fits an even spherical harmonic series to diffusion MRI data.
EvenSphHarmFitter() - Constructor for class inverters.EvenSphHarmFitter
Default constructor required for inheritance.
EvenSphHarmFitter(DW_Scheme, int) - Constructor for class inverters.EvenSphHarmFitter
The constructor computes the inversion matrix from the imaging parameters for the sequence used in the data acquisition.
EvenSphHarmSignalFitter - Class in inverters
Purpose: Fits an even spherical harmonic series to diffusion MRI signal as a function of direction.
EvenSphHarmSignalFitter(DW_Scheme, int) - Constructor for class inverters.EvenSphHarmSignalFitter
The constructor computes the inversion matrix from the imaging parameters for the sequence used in the data acquisition.
exceptionTest() - Static method in class tools.CL_Initializer
routine that throws an exeption, to test exception handling.
Executable - Class in apps
first stab at a base-level executable class.
Executable(String[]) - Constructor for class apps.Executable
constructor taking commandline args
execute(OutputManager) - Method in class apps.AddNoise
 
execute(OutputManager) - Method in class apps.BinaryToText
 
execute(OutputManager) - Method in class apps.ChunkStats
 
execute(OutputManager) - Method in class apps.DT_EigenSystem
 
execute(OutputManager) - Method in class apps.DT_FitMatrix
 
execute(OutputManager) - Method in class apps.DT_ShapeStatistics
 
execute(OutputManager) - Method in class apps.DT_ToCamino
 
execute(OutputManager) - Method in class apps.DT_ToNii
 
execute(OutputManager) - Method in class apps.ElectrostaticSubsets
 
execute(OutputManager) - Method in class apps.EstimateSNR
 
execute(OutputManager) - Method in class apps.Executable
abstract method execution for commands
execute(OutputManager) - Method in class apps.FanningGrid
 
execute(OutputManager) - Method in class apps.FracAnis
 
execute(OutputManager) - Method in class apps.FSL_ToScheme
 
execute(OutputManager) - Method in class apps.GenerateDTLUT
 
execute(OutputManager) - Method in class apps.ImageToVoxel
 
execute(OutputManager) - Method in class apps.InversionStats
 
execute(OutputManager) - Method in class apps.MeanDiff
 
execute(OutputManager) - Method in class apps.ModelFit
 
execute(OutputManager) - Method in class apps.OrderElectrostaticPoints
 
execute(OutputManager) - Method in class apps.OrientationBiasMap
 
execute(OutputManager) - Method in class apps.PICoPDFs
 
execute(OutputManager) - Method in class apps.PointSetToScheme
 
execute(OutputManager) - Method in class apps.ProcessStreamlines
abstract method execution for commands
execute(OutputManager) - Method in class apps.QBallMX
 
execute(OutputManager) - Static method in class apps.Reorient
 
execute(OutputManager) - Method in class apps.ScannerToVoxel
 
execute(OutputManager) - Method in class apps.Shredder
 
execute(OutputManager) - Method in class apps.SphFuncAnisotropy
 
execute(OutputManager) - Method in class apps.SphFuncBitMap
 
execute(OutputManager) - Method in class apps.SphFuncKurtosis
 
execute(OutputManager) - Method in class apps.SphFuncPD_Stats
 
execute(OutputManager) - Method in class apps.SphFuncSkewness
 
execute(OutputManager) - Method in class apps.SphHarmFitter
 
execute(OutputManager) - Method in class apps.SphPDF_Fit
 
execute(OutputManager) - Method in class apps.Split4D_NiiImage
 
execute(OutputManager) - Method in class apps.StreamlineTractography
 
execute(OutputManager) - Method in class apps.SubsetScheme
 
execute(OutputManager) - Method in class apps.SyntheticData
 
execute(OutputManager) - Method in class apps.TraceD
 
execute(OutputManager) - Method in class apps.VoxelClassify
 
execute(OutputManager) - Method in class apps.VoxelToScanner
 
exists() - Method in class imaging.Nifti1Dataset
Check if a valid dataset (header+data) exists.
existsDat() - Method in class imaging.Nifti1Dataset
Check if a valid dataset data file exists.
existsHdr() - Method in class imaging.Nifti1Dataset
Check if a valid dataset header file exists.
EXT_KEY_SIZE - Static variable in class imaging.Nifti1Dataset
 
extension - Variable in class imaging.Nifti1Dataset
 
extents - Variable in class imaging.Nifti1Dataset
 
ExternalDataSource - Class in data
Purpose: Base class for data sources of data from files and input streams.
EXTRACELLULAR - Static variable in class simulation.SimulationParams
flag for extracellular walkers only
EXTRAONLY - Static variable in class simulation.SimulationParams
flag for compartmental signal: extracellular only
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