- 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