- 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