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B

B_VectorScheme - Class in imaging
This class stores a list of b-values.
B_VectorScheme(double[][], double[]) - Constructor for class imaging.B_VectorScheme
 
background() - Method in class inverters.DiffusionInversion
Operations to perform in background voxels.
background() - Method in class inverters.MultiTensorInversion
Need to read off one item from the voxel classification when a background voxel is found.
background() - Method in class inverters.RestoreDT_Inversion
In background voxels this inverter needs to output the outlier map.
background() - Method in class inverters.WeightedLinearDT_Inversion
In background voxels this inverter needs to output zero if there is a noise map.
BACKGROUNDTHRESHOLD - Static variable in class tools.CL_Initializer
Threshold on the q=0 measurements to detect background.
BACKWARD - Static variable in class tractography.FibreTracker
 
Ball - Class in data.compartments
implents the compartment interface for an isotropic Ball compartment
Ball() - Constructor for class data.compartments.Ball
constructor.
Ball - Class in models.compartments
implents the compartment interface for an isotropic Ball compartment
Ball() - Constructor for class models.compartments.Ball
constructor.
BallAndStickLM_GaussianFitter - Class in fitters
Purpose: Fits the ball and stick model using one run of a Levenburg Marquardt and assuming a Gaussian noise model.
BallAndStickLM_GaussianFitter() - Constructor for class fitters.BallAndStickLM_GaussianFitter
Default constructor required for derived classes.
BallAndStickLM_GaussianFitter(DW_Scheme) - Constructor for class fitters.BallAndStickLM_GaussianFitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallAndStickLM_OffGaussFitter - Class in fitters
Purpose: Fits the ball and stick model using one run of a Levenburg Marquardt using the offset chi-sq objective function to compensate for Rician noise bias.
BallAndStickLM_OffGaussFitter() - Constructor for class fitters.BallAndStickLM_OffGaussFitter
Default constructor required for derived classes.
BallAndStickLM_OffGaussFitter(DW_Scheme, double) - Constructor for class fitters.BallAndStickLM_OffGaussFitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallAndStickLM_RicianFitter - Class in fitters
Purpose: Fits the ball and stick model using one run of a Levenburg Marquardt using the Rician objective function.
BallAndStickLM_RicianFitter() - Constructor for class fitters.BallAndStickLM_RicianFitter
Default constructor required for derived classes.
BallAndStickLM_RicianFitter(DW_Scheme, double) - Constructor for class fitters.BallAndStickLM_RicianFitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallAndStickModel - Class in models
Purpose: Implements Behrens' ball-and-stick model Description: Model parameters are: {unweighted signal S0, intra-stick volume fraction f, ball diffusivity, stick diffusivity, theta, phi}.
BallAndStickModel() - Constructor for class models.BallAndStickModel
 
BallAndStickMultiRunLM_GaussianFitter - Class in fitters
Purpose: Fits the ball and stick model using multiple runs of a Levenburg Marquardt and assuming a Gaussian noise model.
BallAndStickMultiRunLM_GaussianFitter(DW_Scheme, int, int) - Constructor for class fitters.BallAndStickMultiRunLM_GaussianFitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallCylinderAstrocylindersLM_Fitter - Class in fitters
Purpose: Fits the ballcylinderastrocylinders model using one run of a Levenburg Marquardt.
BallCylinderAstrocylindersLM_Fitter() - Constructor for class fitters.BallCylinderAstrocylindersLM_Fitter
Default constructor required for derived classes.
BallCylinderAstrocylindersLM_Fitter(DW_Scheme) - Constructor for class fitters.BallCylinderAstrocylindersLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallCylinderAstrocylindersMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballcylinderastrocylinders model using multiple runs of a Levenburg Marquardt.
BallCylinderAstrocylindersMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BallCylinderAstrocylindersMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallCylinderAstrosticksLM_Fitter - Class in fitters
Purpose: Fits the ballcylinderastrosticks model using one run of a Levenburg Marquardt and assuming a Gaussian noise model.
BallCylinderAstrosticksLM_Fitter() - Constructor for class fitters.BallCylinderAstrosticksLM_Fitter
Default constructor required for derived classes.
BallCylinderAstrosticksLM_Fitter(DW_Scheme) - Constructor for class fitters.BallCylinderAstrosticksLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallCylinderAstrosticksMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballcylinderastrosticks model using multiple runs of a Levenburg Marquardt.
BallCylinderAstrosticksMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BallCylinderAstrosticksMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallCylinderDotLM_Fitter - Class in fitters
Purpose: Fits the ballcylinder and dot model using one run of a Levenburg Marquardt.
BallCylinderDotLM_Fitter() - Constructor for class fitters.BallCylinderDotLM_Fitter
Default constructor required for derived classes.
BallCylinderDotLM_Fitter(DW_Scheme) - Constructor for class fitters.BallCylinderDotLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallCylinderDotMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballcylinderdot model using multiple runs of a Levenburg Marquardt.
BallCylinderDotMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BallCylinderDotMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallCylinderLM_Fitter - Class in fitters
Purpose: Fits the ball and cylinder model using one run of a Levenburg Marquardt.
BallCylinderLM_Fitter() - Constructor for class fitters.BallCylinderLM_Fitter
Default constructor required for derived classes.
BallCylinderLM_Fitter(DW_Scheme) - Constructor for class fitters.BallCylinderLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallCylinderMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ball and cylinder model using multiple runs of a Levenburg Marquardt.
BallCylinderMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BallCylinderMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallCylinderSphereLM_Fitter - Class in fitters
Purpose: Fits the ballcylinderspherer model using one run of a Levenburg Marquardt.
BallCylinderSphereLM_Fitter() - Constructor for class fitters.BallCylinderSphereLM_Fitter
Default constructor required for derived classes.
BallCylinderSphereLM_Fitter(DW_Scheme) - Constructor for class fitters.BallCylinderSphereLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallCylinderSphereMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballcylindersphere model using multiple runs of a Levenburg Marquardt.
BallCylinderSphereMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BallCylinderSphereMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallGDRCylindersAstrocylindersLM_Fitter - Class in fitters
Purpose: Fits the ball and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
BallGDRCylindersAstrocylindersLM_Fitter() - Constructor for class fitters.BallGDRCylindersAstrocylindersLM_Fitter
Default constructor required for derived classes.
BallGDRCylindersAstrocylindersLM_Fitter(DW_Scheme) - Constructor for class fitters.BallGDRCylindersAstrocylindersLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallGDRCylindersAstrocylindersMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballcylinderastrosticks model using multiple runs of a Levenburg Marquardt.
BallGDRCylindersAstrocylindersMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BallGDRCylindersAstrocylindersMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallGDRCylindersAstrosticksLM_Fitter - Class in fitters
Purpose: Fits the ball and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
BallGDRCylindersAstrosticksLM_Fitter() - Constructor for class fitters.BallGDRCylindersAstrosticksLM_Fitter
Default constructor required for derived classes.
BallGDRCylindersAstrosticksLM_Fitter(DW_Scheme) - Constructor for class fitters.BallGDRCylindersAstrosticksLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallGDRCylindersAstrosticksMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballcylinderastrosticks model using multiple runs of a Levenburg Marquardt.
BallGDRCylindersAstrosticksMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BallGDRCylindersAstrosticksMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallGDRCylindersDotLM_Fitter - Class in fitters
Purpose: Fits the ball and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
BallGDRCylindersDotLM_Fitter() - Constructor for class fitters.BallGDRCylindersDotLM_Fitter
Default constructor required for derived classes.
BallGDRCylindersDotLM_Fitter(DW_Scheme) - Constructor for class fitters.BallGDRCylindersDotLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallGDRCylindersDotMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballcylinderastrosticks model using multiple runs of a Levenburg Marquardt.
BallGDRCylindersDotMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BallGDRCylindersDotMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallGDRCylindersLM_Fitter - Class in fitters
Purpose: Fits the ball and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
BallGDRCylindersLM_Fitter() - Constructor for class fitters.BallGDRCylindersLM_Fitter
Default constructor required for derived classes.
BallGDRCylindersLM_Fitter(DW_Scheme) - Constructor for class fitters.BallGDRCylindersLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallGDRCylindersMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballgdrcylinders model using multiple runs of a Levenburg Marquardt.
BallGDRCylindersMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BallGDRCylindersMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallGDRCylindersSphereLM_Fitter - Class in fitters
Purpose: Fits the ball and gamma distributed radii cylinders and sphere model using one run of a Levenburg Marquardt.
BallGDRCylindersSphereLM_Fitter() - Constructor for class fitters.BallGDRCylindersSphereLM_Fitter
Default constructor required for derived classes.
BallGDRCylindersSphereLM_Fitter(DW_Scheme) - Constructor for class fitters.BallGDRCylindersSphereLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallGDRCylindersSphereMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballgdrcylinderssphere model using multiple runs of a Levenburg Marquardt.
BallGDRCylindersSphereMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BallGDRCylindersSphereMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStick - Class in data
Purpose: Simple model for the diffusion displacement density function .
BallStick(double, double, double[]) - Constructor for class data.BallStick
constructor for specified diffusivity, volume fraction and orientation
BallStickAstrocylindersLM_Fitter - Class in fitters
Purpose: Fits the ballstick and astrocylinders model using one run of a Levenburg Marquardt.
BallStickAstrocylindersLM_Fitter() - Constructor for class fitters.BallStickAstrocylindersLM_Fitter
Default constructor required for derived classes.
BallStickAstrocylindersLM_Fitter(DW_Scheme) - Constructor for class fitters.BallStickAstrocylindersLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickAstrocylindersLM_Fitter(DW_Scheme, String[], double[]) - Constructor for class fitters.BallStickAstrocylindersLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickAstrocylindersMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballstickastrocylinders model using multiple runs of a Levenburg Marquardt.
BallStickAstrocylindersMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BallStickAstrocylindersMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickAstrosticksLM_Fitter - Class in fitters
Purpose: Fits the ballstick and astrosticks model using one run of a Levenburg Marquardt.
BallStickAstrosticksLM_Fitter() - Constructor for class fitters.BallStickAstrosticksLM_Fitter
Default constructor required for derived classes.
BallStickAstrosticksLM_Fitter(DW_Scheme) - Constructor for class fitters.BallStickAstrosticksLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickAstrosticksLM_Fitter(DW_Scheme, String[], double[]) - Constructor for class fitters.BallStickAstrosticksLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickAstrosticksMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballstickastrosticks model using multiple runs of a Levenburg Marquardt.
BallStickAstrosticksMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BallStickAstrosticksMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickDotLM_Fitter - Class in fitters
Purpose: Fits the ballstickdot model using one run of a Levenburg Marquardt.
BallStickDotLM_Fitter() - Constructor for class fitters.BallStickDotLM_Fitter
Default constructor required for derived classes.
BallStickDotLM_Fitter(DW_Scheme) - Constructor for class fitters.BallStickDotLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickDotLM_Fitter(DW_Scheme, String[], double[]) - Constructor for class fitters.BallStickDotLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickDotMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballstickdot model using multiple runs of a Levenburg Marquardt.
BallStickDotMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BallStickDotMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickFitter - Class in inverters
Fits the Behrens ball and stick model to diffusion-weighted data.
BallStickFitter(DW_Scheme) - Constructor for class inverters.BallStickFitter
 
BallStickInversion - Class in inverters
Fits the ball and stick partial volume model to diffusion-weighted data.
BallStickInversion(DW_Scheme) - Constructor for class inverters.BallStickInversion
 
BallStickLM_Fitter - Class in fitters
Purpose: Fits the ball and stick model using one run of a Levenburg Marquardt.
BallStickLM_Fitter() - Constructor for class fitters.BallStickLM_Fitter
Default constructor required for derived classes.
BallStickLM_Fitter(DW_Scheme) - Constructor for class fitters.BallStickLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickLM_Fitter(DW_Scheme, String[], double[]) - Constructor for class fitters.BallStickLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickLM_GaussianFitter - Class in fitters
Purpose: Fits the ball and stick model using one run of a Levenburg Marquardt and assuming a Gaussian noise model.
BallStickLM_GaussianFitter() - Constructor for class fitters.BallStickLM_GaussianFitter
Default constructor required for derived classes.
BallStickLM_GaussianFitter(DW_Scheme) - Constructor for class fitters.BallStickLM_GaussianFitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickLM_GaussianFitter(DW_Scheme, String[], double[]) - Constructor for class fitters.BallStickLM_GaussianFitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickMCMC_Fitter - Class in fitters
Purpose: Fits the ball and stick model using MCMC and with a specified noise model.
BallStickMCMC_Fitter() - Constructor for class fitters.BallStickMCMC_Fitter
Default constructor required for derived classes.
BallStickMCMC_Fitter(DW_Scheme) - Constructor for class fitters.BallStickMCMC_Fitter
Basic constructor extracts model particulars and calls full constructor.
BallStickMCMC_Fitter(DW_Scheme, String[], double[]) - Constructor for class fitters.BallStickMCMC_Fitter
Constructor sets up various required objects for MCMC.
BallStickMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ball and stick model using multiple runs of a Levenburg Marquardt and a specified noise model.
BallStickMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BallStickMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickMultiRunLM_GaussianFitter - Class in fitters
Purpose: Fits the ball and stick model using multiple runs of a Levenburg Marquardt and assuming a Gaussian noise model.
BallStickMultiRunLM_GaussianFitter(DW_Scheme, int, int) - Constructor for class fitters.BallStickMultiRunLM_GaussianFitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallSticksOrientationViewer - Class in apps
Simple tool to visualize principal directions of ball and stick data.
BallSticksOrientationViewer(RGB_ScalarImage, double) - Constructor for class apps.BallSticksOrientationViewer
Creates and displays the viewer.
BallStickSphereLM_Fitter - Class in fitters
Purpose: Fits the ballstick and sphere model using one run of a Levenburg Marquardt.
BallStickSphereLM_Fitter() - Constructor for class fitters.BallStickSphereLM_Fitter
Default constructor required for derived classes.
BallStickSphereLM_Fitter(DW_Scheme) - Constructor for class fitters.BallStickSphereLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickSphereLM_Fitter(DW_Scheme, String[], double[]) - Constructor for class fitters.BallStickSphereLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickSphereMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballsticksphere model using multiple runs of a Levenburg Marquardt.
BallStickSphereMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BallStickSphereMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BallStickTractographyImage - Class in tractography
Defines image for tractography from tensor data.
BallStickTractographyImage(Vector3D[][][][], int[][][], double[]) - Constructor for class tractography.BallStickTractographyImage
Constructs an image directly from an array of vectors.
BallStickTractographyImage(VoxelOrderDataSource, int[], double[]) - Constructor for class tractography.BallStickTractographyImage
Constructs an image from the data sources.
BALLSTICKVALSPERVOXEL - Static variable in class tools.CL_Initializer
The number of values per voxel for the ball and stick model.
basePointSet - Static variable in class mesd.MESD_Inversion
Specifies the index of the base point set, ie the one used for the numerical integration during the first minimization.
BasicCylinder - Class in simulation.geometry.elements
implements a cylindrical geometry.
BasicCylinder(double[], double, double) - Constructor for class simulation.geometry.elements.BasicCylinder
constructor without specifying direction.
BasicCylinder(double[], double[], double, double) - Constructor for class simulation.geometry.elements.BasicCylinder
constructor that specifies orientation.
basisFunction(int) - Method in class sphfunc.EvenSHS
 
basisFunction(int) - Method in class sphfunc.LinearBasisSum
Returns the basis function with weight c[i].
basisFunction(int) - Method in class sphfunc.TuchRBF_Sum
 
BasisSumFactory - Class in sphfunc
Purpose: Creates Basis Sum object on request Description: Factory for creating LinearBasisSum Objects.
BasisSumFactory() - Constructor for class sphfunc.BasisSumFactory
 
basisType - Static variable in class tools.CL_Initializer
The type of basis function used for linear reconstructions.
BayesDiracBallStickRandomizer - Class in tractography
Samples orientations x from a Bayesian PDF P(x|data, model).
BayesDiracBallStickRandomizer(float[][][][], DW_Scheme, Random) - Constructor for class tractography.BayesDiracBallStickRandomizer
 
BayesDiracBallStickRandomizer(float[][][][], DW_Scheme, int, Random) - Constructor for class tractography.BayesDiracBallStickRandomizer
 
BayesDiracCylSymmTensorRandomizer - Class in tractography
Samples orientations x from a Bayesian PDF P(x|data, model).
BayesDiracCylSymmTensorRandomizer(float[][][][], DW_Scheme, Random) - Constructor for class tractography.BayesDiracCylSymmTensorRandomizer
 
BayesDiracCylSymmTensorRandomizer(float[][][][], DW_Scheme, int, Random) - Constructor for class tractography.BayesDiracCylSymmTensorRandomizer
 
BayesDiracRandomizer - Class in tractography
Samples orientations x from a Bayesian PDF P(x|data, model).
BayesDiracRandomizer(float[][][][], DW_Scheme, Random) - Constructor for class tractography.BayesDiracRandomizer
 
BayesDiracRandomizer(float[][][][], DW_Scheme, int, Random) - Constructor for class tractography.BayesDiracRandomizer
 
BayesDiracTractographyImage - Class in tractography
Bayesian tractography image using Dirac priors for "nuisance parameters", see Friman et al, TMI 25:965-978 (2006).
BayesDiracTractographyImage(float[][][][], double[], int[][][], DW_Scheme, DataModel, int, Random) - Constructor for class tractography.BayesDiracTractographyImage
Matlab constructor.
BesselFunctions - Class in numerics
Purpose: Contains implementation of the various Bessel functions.
BesselFunctions() - Constructor for class numerics.BesselFunctions
 
besselI0(double) - Static method in class numerics.BesselFunctions
Zeroth-order modified Bessel function of the first kind.
besselI1(double) - Static method in class numerics.BesselFunctions
First-order modified Bessel function of the first kind.
besselIn(int, double) - Static method in class numerics.BesselFunctions
nth-order modified Bessel function of the first kind.
besselJ0(double) - Static method in class numerics.BesselFunctions
Zeroth-order Bessel function of the first kind.
besselJ1(double) - Static method in class numerics.BesselFunctions
First-order Bessel function of the first kind.
betacf(double, double, double) - Static method in class numerics.IncompleteBeta
Evaluates the continued fraction for the incomplete beta function by modified Lentz's method.
betai(double, double, double) - Static method in class numerics.IncompleteBeta
Computes the incomplete beta function I_x(a, b).
bgMask - Static variable in class tools.CL_Initializer
The background mask.
bgMaskFile - Static variable in class tools.CL_Initializer
Name of the background mask file.
bgMaskType - Static variable in class tools.CL_Initializer
The type of the background mask
BiexponLM_GaussianFitter - Class in fitters
Purpose: Fits the biexponential model (two cylindrically symmetric tensors) using one run of a Levenburg Marquardt and assuming a Gaussian noise model.
BiexponLM_GaussianFitter() - Constructor for class fitters.BiexponLM_GaussianFitter
Default constructor required for derived classes.
BiexponLM_GaussianFitter(DW_Scheme) - Constructor for class fitters.BiexponLM_GaussianFitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BiexponMultiRunLM_GaussianFitter - Class in fitters
Purpose: Fits the biexponential model using multiple runs of a Levenburg Marquardt and assuming a Gaussian noise model.
BiexponMultiRunLM_GaussianFitter(DW_Scheme, int, int) - Constructor for class fitters.BiexponMultiRunLM_GaussianFitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
big_endian - Variable in class imaging.Nifti1Dataset
 
binaryData - Variable in class imaging.MetaImageHeader
BinaryData, which is always true.
BinaryToText - Class in apps
Purpose: Converts binary data to text.
BinaryToText(String[]) - Constructor for class apps.BinaryToText
 
bingc(double, double) - Static method in class numerics.BinghamFitter
Automatically chooses which type of numerical method to use.
bingc(double, double, double[], double[]) - Static method in class numerics.BinghamFitter
Get the normalization constant and its derivatives.
BINGHAM - Static variable in class tractography.DT_LookupTableGenerator
 
BinghamDistribution - Class in numerics
Bingham Distribution.
BinghamDistribution(Vector3D[], double, double, double, Random) - Constructor for class numerics.BinghamDistribution
 
BinghamFitter - Class in numerics
Translation of John Kent's code that implements his paper "Asymptotic Expansions for the Bingham Distribution" (Applied Statistics 36(2):139-144, 1987).
bitpix - Variable in class imaging.AnalyzeHeader
 
BiZeppelinLM_Fitter - Class in fitters
Purpose: Fits the biexponential model (two cylindrically symmetric tensors) using one run of a Levenburg Marquardt.
BiZeppelinLM_Fitter() - Constructor for class fitters.BiZeppelinLM_Fitter
Default constructor required for derived classes.
BiZeppelinLM_Fitter(DW_Scheme) - Constructor for class fitters.BiZeppelinLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
BiZeppelinMultiRunLM_Fitter - Class in fitters
Purpose: Fits the biexponential model using multiple runs of a Levenburg Marquardt.
BiZeppelinMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.BiZeppelinMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
bngpar(double, double) - Static method in class numerics.BinghamFitter
Gets the Bingham parameters k1, k2 (concentration parameters) and bingC (normalization constant).
bootstrap - Static variable in class tools.CL_Initializer
The number of bootstraps used in bootstrapping.
BootstrapDataSynthesizer - Class in data
Source of bootstrap data.
BootstrapDataSynthesizer(String[], int, int, String) - Constructor for class data.BootstrapDataSynthesizer
 
BootstrapDataSynthesizer(String[], int, int, String, int) - Constructor for class data.BootstrapDataSynthesizer
 
BootstrapDataSynthesizer(String[], int, int, String, Random) - Constructor for class data.BootstrapDataSynthesizer
 
BootstrapDataSynthFromInput - Class in data
Source of bootstrap data.
BootstrapDataSynthFromInput(DataSynthFromInput, int, DW_Scheme, int, double, Random) - Constructor for class data.BootstrapDataSynthFromInput
 
BootstrapDataSynthFromInput(DataSynthFromInput, int, DW_Scheme, int, double, int) - Constructor for class data.BootstrapDataSynthFromInput
 
BootstrapDataSynthFromSimulationInput - Class in data
Source of bootstrap data.
BootstrapDataSynthFromSimulationInput(DiffusionSimulation, int, int, int, Random) - Constructor for class data.BootstrapDataSynthFromSimulationInput
 
BootstrapDataSynthFromSimulationInput(DiffusionSimulation, int, int, int, int) - Constructor for class data.BootstrapDataSynthFromSimulationInput
 
BootstrapTractographyImage - Class in tractography
Superclass to bootstrap images.
BootstrapTractographyImage(int[], double[], int, int[][][], DW_Scheme, Random) - Constructor for class tractography.BootstrapTractographyImage
 
border - Static variable in class simulation.DiffusionSimulation
likely border in which to clone bits of substrate
border - Variable in class simulation.geometry.substrates.Substrate
boundary widths in each direction
BoundingBox - Class in simulation.geometry.elements
An optimally oriented bounding box that minimally surrounds a Substrate object a bounding box is defined by three vectors defining a coordinate system centred on the substrate origin, and max and min values of each of them for points on the object.
boundingBoxIntersects(double[], double[]) - Method in class simulation.geometry.elements.BasicCylinder
checks if bounding box is intersected by a step
boundingBoxIntersects(double[], double[]) - Method in class simulation.geometry.elements.FacetCylinder
TODO: always returns true checks if a step will intersect the bounding box
boundingBoxIntersects(double[], double[]) - Method in class simulation.geometry.elements.MyelinatedCylinder
checks if bounding box is intersected by a step
boundingBoxIntersects(double[], double[]) - Method in interface simulation.geometry.elements.SubstrateObject
checks if a step will intersect the bounding box for the object.
boundingBoxIntersects(double[], double[]) - Method in class simulation.geometry.elements.Triangle
 
brownianSimulation - Static variable in class tools.CL_Initializer
Indicates whether to synthesise data using simulation
BS_DT_TractographyImage - Class in tractography
Each call to #getPDs(int, int, int) returns a new bootstrap estimate of the PDs.
BS_DT_TractographyImage(int[], double[], int[][][], ModelIndex[], DW_Scheme, Random) - Constructor for class tractography.BS_DT_TractographyImage
Construct an image.
bsDataFiles - Static variable in class tools.CL_Initializer
List of files containing repeated measurements of the same data for use in bootstrapping.
BufferedInflaterInputStream - Class in tools
This class is useful to reduce the decompression overhead that comes from reading from a InflaterInputStream a few bytes at a time.
BufferedInflaterInputStream(InflaterInputStream, int) - Constructor for class tools.BufferedInflaterInputStream
Create a stream from a compressed input stream.
BUFFERSIZE - Static variable in class apps.RGB_ScalarImage
 
BUFFERSIZE - Static variable in class apps.SphFuncBitMap
Buffer size in input and output stream.
buffsize - Variable in class simulation.SimulationParams
size of traj file output buffer (one meg by default)
buildEnergyMatrix() - Method in class misc.OrderedAcqMinimizer
 
burnInTime - Static variable in class tools.CL_Initializer
Burn-in period of Markov Chain Monte Carlo algorithm .
bValue - Static variable in class tools.CL_Initializer
Fixed b-value for schemes created at run time.
BYTE - Static variable in class data.ExternalDataSource
Codes for different possible data types.
bytesPerVoxel(short) - Method in class imaging.Nifti1Dataset
Return bytes per voxel for each nifti-1 datatype
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