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T

t_unit_code - Variable in class imaging.Nifti1Dataset
 
tan() - Method in class numerics.Complex
Returns the tangent.
tanh(double) - Static method in class numerics.Complex
 
tanh() - Method in class numerics.Complex
 
TargetCP_Image - Class in tractography
Connection probability image with targets.
TargetCP_Image(short[][][], double, double, double) - Constructor for class tractography.TargetCP_Image
Initializes the image with the dimensions of the seed space.
TargetProbsToASCII - Class in apps
Converts the results of tracking with target volumes to a text file.
TargetProbsToASCII() - Constructor for class apps.TargetProbsToASCII
 
tBar(Vector3D[]) - Static method in class numerics.SphericalDistributionFitter
 
tBarEigenSystem(RealMatrix) - Static method in class numerics.SphericalDistributionFitter
 
tBarEigenSystem(Vector3D[]) - Static method in class numerics.SphericalDistributionFitter
 
tBarEigenSystem(double[], boolean) - Static method in class numerics.SphericalDistributionFitter
Gets the eigen system of the scatter matrix from an array.
tBarEigenSystem(double[]) - Static method in class numerics.SphericalDistributionFitter
Gets the eigen system of the scatter matrix from an array.
TDIM - Variable in class imaging.Nifti1Dataset
 
TendInterpolator - Class in tractography
Does tensor deflection interpolation.
TendInterpolator(DT_TractographyImage) - Constructor for class tractography.TendInterpolator
Default constructor, doesn't use tend at all.
TendInterpolator(DT_TractographyImage, double, double) - Constructor for class tractography.TendInterpolator
Weight the tend term by a constant.
TendInterpolator(DT_TractographyImage, double[][][], double) - Constructor for class tractography.TendInterpolator
Weight the tend term independently in each voxel.
Tensor - Class in data.compartments
 
Tensor() - Constructor for class data.compartments.Tensor
constructor.
Tensor - Class in models.compartments
 
Tensor() - Constructor for class models.compartments.Tensor
constructor.
TensorCylinderAstrocylindersLM_Fitter - Class in fitters
Purpose: Fits the tensorcylinderastrocylinders model using one run of a Levenburg Marquardt.
TensorCylinderAstrocylindersLM_Fitter() - Constructor for class fitters.TensorCylinderAstrocylindersLM_Fitter
Default constructor required for derived classes.
TensorCylinderAstrocylindersLM_Fitter(DW_Scheme) - Constructor for class fitters.TensorCylinderAstrocylindersLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorCylinderAstrocylindersMultiRunLM_Fitter - Class in fitters
Purpose: Fits the tensorcylinderastrocylinders model using multiple runs of a Levenburg Marquardt.
TensorCylinderAstrocylindersMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.TensorCylinderAstrocylindersMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorCylinderAstrosticksLM_Fitter - Class in fitters
Purpose: Fits the tensorcylinderastrosticks model using one run of a Levenburg Marquardt.
TensorCylinderAstrosticksLM_Fitter() - Constructor for class fitters.TensorCylinderAstrosticksLM_Fitter
Default constructor required for derived classes.
TensorCylinderAstrosticksLM_Fitter(DW_Scheme) - Constructor for class fitters.TensorCylinderAstrosticksLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorCylinderAstrosticksMultiRunLM_Fitter - Class in fitters
Purpose: Fits the tensorcylinderastrosticks model using multiple runs of a Levenburg Marquardt.
TensorCylinderAstrosticksMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.TensorCylinderAstrosticksMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorCylinderDotLM_Fitter - Class in fitters
Purpose: Fits the tensorcylinderdot model using one run of a Levenburg Marquardt.
TensorCylinderDotLM_Fitter() - Constructor for class fitters.TensorCylinderDotLM_Fitter
Default constructor required for derived classes.
TensorCylinderDotLM_Fitter(DW_Scheme) - Constructor for class fitters.TensorCylinderDotLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorCylinderDotMultiRunLM_Fitter - Class in fitters
Purpose: Fits the tensorcylinderdot model using multiple runs of a Levenburg Marquardt.
TensorCylinderDotMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.TensorCylinderDotMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorCylinderLM_Fitter - Class in fitters
Purpose: Fits the tensor and cylinder model using one run of a Levenburg Marquardt.
TensorCylinderLM_Fitter() - Constructor for class fitters.TensorCylinderLM_Fitter
Default constructor required for derived classes.
TensorCylinderLM_Fitter(DW_Scheme) - Constructor for class fitters.TensorCylinderLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorCylinderMultiRunLM_Fitter - Class in fitters
Purpose: Fits the tensorcylinder model using multiple runs of a Levenburg Marquardt.
TensorCylinderMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.TensorCylinderMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorCylinderSphereLM_Fitter - Class in fitters
Purpose: Fits the tensorcylindersphere model using one run of a Levenburg Marquardt.
TensorCylinderSphereLM_Fitter() - Constructor for class fitters.TensorCylinderSphereLM_Fitter
Default constructor required for derived classes.
TensorCylinderSphereLM_Fitter(DW_Scheme) - Constructor for class fitters.TensorCylinderSphereLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorCylinderSphereMultiRunLM_Fitter - Class in fitters
Purpose: Fits the tensorcylindersphere model using multiple runs of a Levenburg Marquardt.
TensorCylinderSphereMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.TensorCylinderSphereMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorGDRCylindersAstrocylindersLM_Fitter - Class in fitters
Purpose: Fits the tensor and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
TensorGDRCylindersAstrocylindersLM_Fitter() - Constructor for class fitters.TensorGDRCylindersAstrocylindersLM_Fitter
Default constructor required for derived classes.
TensorGDRCylindersAstrocylindersLM_Fitter(DW_Scheme) - Constructor for class fitters.TensorGDRCylindersAstrocylindersLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorGDRCylindersAstrocylindersMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballcylinderastrosticks model using multiple runs of a Levenburg Marquardt.
TensorGDRCylindersAstrocylindersMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.TensorGDRCylindersAstrocylindersMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorGDRCylindersAstrosticksLM_Fitter - Class in fitters
Purpose: Fits the tensor and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
TensorGDRCylindersAstrosticksLM_Fitter() - Constructor for class fitters.TensorGDRCylindersAstrosticksLM_Fitter
Default constructor required for derived classes.
TensorGDRCylindersAstrosticksLM_Fitter(DW_Scheme) - Constructor for class fitters.TensorGDRCylindersAstrosticksLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorGDRCylindersAstrosticksMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballcylinderastrosticks model using multiple runs of a Levenburg Marquardt.
TensorGDRCylindersAstrosticksMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.TensorGDRCylindersAstrosticksMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorGDRCylindersDotLM_Fitter - Class in fitters
Purpose: Fits the tensor and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
TensorGDRCylindersDotLM_Fitter() - Constructor for class fitters.TensorGDRCylindersDotLM_Fitter
Default constructor required for derived classes.
TensorGDRCylindersDotLM_Fitter(DW_Scheme) - Constructor for class fitters.TensorGDRCylindersDotLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorGDRCylindersDotMultiRunLM_Fitter - Class in fitters
Purpose: Fits the ballcylinderastrosticks model using multiple runs of a Levenburg Marquardt.
TensorGDRCylindersDotMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.TensorGDRCylindersDotMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorGDRCylindersLM_Fitter - Class in fitters
Purpose: Fits the tensor and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
TensorGDRCylindersLM_Fitter() - Constructor for class fitters.TensorGDRCylindersLM_Fitter
Default constructor required for derived classes.
TensorGDRCylindersLM_Fitter(DW_Scheme) - Constructor for class fitters.TensorGDRCylindersLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorGDRCylindersMultiRunLM_Fitter - Class in fitters
Purpose: Fits the TensorGDRCylinders model using multiple runs of a Levenburg Marquardt.
TensorGDRCylindersMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.TensorGDRCylindersMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorGDRCylindersSphereLM_Fitter - Class in fitters
Purpose: Fits the tensor and gamma distributed radii cylinders and sphere model using one run of a Levenburg Marquardt.
TensorGDRCylindersSphereLM_Fitter() - Constructor for class fitters.TensorGDRCylindersSphereLM_Fitter
Default constructor required for derived classes.
TensorGDRCylindersSphereLM_Fitter(DW_Scheme) - Constructor for class fitters.TensorGDRCylindersSphereLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorGDRCylindersSphereMultiRunLM_Fitter - Class in fitters
Purpose: Fits the TensorGDRCylindersSphere model using multiple runs of a Levenburg Marquardt.
TensorGDRCylindersSphereMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.TensorGDRCylindersSphereMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorModelFitter - Class in inverters
Purpose: General abstract class for a simple-diffusion based model fitter.
TensorModelFitter() - Constructor for class inverters.TensorModelFitter
 
TensorOrientationViewer - Class in apps
Simple tool to visualize principal directions of tensor data.
TensorOrientationViewer(RGB_ScalarImage, double) - Constructor for class apps.TensorOrientationViewer
Creates and displays the viewer.
TensorStickAstrocylindersLM_Fitter - Class in fitters
Purpose: Fits the tensorstick and astrocylinders model using one run of a Levenburg Marquard.
TensorStickAstrocylindersLM_Fitter() - Constructor for class fitters.TensorStickAstrocylindersLM_Fitter
Default constructor required for derived classes.
TensorStickAstrocylindersLM_Fitter(DW_Scheme) - Constructor for class fitters.TensorStickAstrocylindersLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorStickAstrocylindersMultiRunLM_Fitter - Class in fitters
Purpose: Fits the tensorstickastrocylinders model using multiple runs of a Levenburg Marquardt.
TensorStickAstrocylindersMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.TensorStickAstrocylindersMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorStickAstrosticksLM_Fitter - Class in fitters
Purpose: Fits the tensorstick and astrosticks model using one run of a Levenburg Marquardt.
TensorStickAstrosticksLM_Fitter() - Constructor for class fitters.TensorStickAstrosticksLM_Fitter
Default constructor required for derived classes.
TensorStickAstrosticksLM_Fitter(DW_Scheme) - Constructor for class fitters.TensorStickAstrosticksLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorStickAstrosticksMultiRunLM_Fitter - Class in fitters
Purpose: Fits the tensorstickastrosticks model using multiple runs of a Levenburg Marquardt.
TensorStickAstrosticksMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.TensorStickAstrosticksMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorStickDotLM_Fitter - Class in fitters
Purpose: Fits the tensorstick and dot model using one run of a Levenburg Marquardt.
TensorStickDotLM_Fitter() - Constructor for class fitters.TensorStickDotLM_Fitter
Default constructor required for derived classes.
TensorStickDotLM_Fitter(DW_Scheme) - Constructor for class fitters.TensorStickDotLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorStickDotMultiRunLM_Fitter - Class in fitters
Purpose: Fits the tensorstickdot model using multiple runs of a Levenburg Marquardt.
TensorStickDotMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.TensorStickDotMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorStickLM_Fitter - Class in fitters
Purpose: Fits the tensor and stick model using one run of a Levenburg Marquardt.
TensorStickLM_Fitter() - Constructor for class fitters.TensorStickLM_Fitter
Default constructor required for derived classes.
TensorStickLM_Fitter(DW_Scheme) - Constructor for class fitters.TensorStickLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorStickMultiRunLM_Fitter - Class in fitters
Purpose: Fits the tensor and stick model using multiple runs of a Levenburg Marquardt.
TensorStickMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.TensorStickMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorStickSphereLM_Fitter - Class in fitters
Purpose: Fits the tensorstick and sphere model using one run of a Levenburg Marquardt.
TensorStickSphereLM_Fitter() - Constructor for class fitters.TensorStickSphereLM_Fitter
Default constructor required for derived classes.
TensorStickSphereLM_Fitter(DW_Scheme) - Constructor for class fitters.TensorStickSphereLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
TensorStickSphereMultiRunLM_Fitter - Class in fitters
Purpose: Fits the tensorsticksphere model using multiple runs of a Levenburg Marquardt.
TensorStickSphereMultiRunLM_Fitter(DW_Scheme, int, int) - Constructor for class fitters.TensorStickSphereMultiRunLM_Fitter
Constructor implements the mapping between model and optimized parameters in the Codec object.
testAmendment(Walker, double[], double[], double[], double, double[], double[], double[]) - Method in class simulation.geometry.substrates.Substrate
test access to the amender.
testAnnoyingCase() - Static method in class simulation.geometry.elements.BasicCylinder
 
testArbOrientation() - Static method in class simulation.geometry.elements.BasicCylinder
 
testBarrierReflection() - Static method in class simulation.geometry.substrates.CellularLattice
 
testBipolarRotSymm(EigenSystem3D, Vector3D, Vector3D[]) - Static method in class numerics.WatsonFitter
Test of rotational symmetry for a bipolar distribution.
testBoundaryCrossing() - Static method in class simulation.geometry.substrates.CellularLattice
 
testBoxIntersection1() - Static method in class simulation.geometry.elements.Triangle
checks intersection between triangle completely contained in cubic region
testBoxIntersection2() - Static method in class simulation.geometry.elements.Triangle
checks intersection between triangle with two vertices inside cubic region
testBoxIntersection3() - Static method in class simulation.geometry.elements.Triangle
checks intersection between triangle with one vertex inside cubic region
testBoxIntersection4() - Static method in class simulation.geometry.elements.Triangle
checks intersection between triangle with no vertices inside box that does nonetheless intersect the region
testBoxIntersection5() - Static method in class simulation.geometry.elements.Triangle
checks intersection between triangle with no vertices inside box that does nonetheless intersect the region
testCompartmetnParsing() - Static method in class tools.CL_Initializer
 
testDiffusionSimulation() - Static method in class simulation.DiffusionSimulation
 
testFunction - Static variable in class tools.CL_Initializer
Standard test function index.
testFunctionData - Static variable in class tools.CL_Initializer
If a non-standard test function was specified, the parameters are read from the command line into this array.
testGetCell() - Static method in class simulation.geometry.substrates.CellularLattice
 
testGirdleRotSymm(EigenSystem3D, Vector3D, Vector3D[]) - Static method in class numerics.WatsonFitter
Test rotational symmetry for a girdle distribution.
TestMatrix - Class in Jama.test
TestMatrix tests the functionality of the Jama Matrix class and associated decompositions.
TestMatrix() - Constructor for class Jama.test.TestMatrix
 
testPeriodicBoundaries() - Static method in class simulation.geometry.substrates.CellularLattice
 
testReplacePositionVector(double[]) - Method in class simulation.dynamics.Walker
set the position directly.
testStepAmendment() - Static method in class simulation.geometry.substrates.Substrate
test of step amending code.
testStepIntersection() - Static method in class simulation.geometry.elements.Triangle
 
testWindingNumbers() - Static method in class simulation.geometry.substrates.CellularLattice
 
thetaPhi(Vector3D) - Static method in class numerics.Vector3D
 
ThreeTensorAxiSymFitter - Class in inverters
Purpose: Non-linear least squares fitter of a three tensor model with prolate axisymmetric tensors to DW-MR data.
ThreeTensorAxiSymFitter() - Constructor for class inverters.ThreeTensorAxiSymFitter
Default constructor does nothing.
ThreeTensorAxiSymFitter(double[][], double[], double[], int) - Constructor for class inverters.ThreeTensorAxiSymFitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
ThreeTensorAxiSymFixMP_Fitter - Class in inverters
Purpose: Non-linear least squares fitter of a three-tensor model to DW-MR data with fixed mixing parameters and axisymmetric tensors.
ThreeTensorAxiSymFixMP_Fitter() - Constructor for class inverters.ThreeTensorAxiSymFixMP_Fitter
Default constructor does nothing.
ThreeTensorAxiSymFixMP_Fitter(double[][], double[], double[], int) - Constructor for class inverters.ThreeTensorAxiSymFixMP_Fitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
ThreeTensorCholFitter - Class in inverters
Purpose: Non-linear least squares fitter of a three-tensor model to DW-MR data.
ThreeTensorCholFitter() - Constructor for class inverters.ThreeTensorCholFitter
Default constructor does nothing.
ThreeTensorCholFitter(double[][], double[], double[], int) - Constructor for class inverters.ThreeTensorCholFitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
ThreeTensorCholFixMP_Fitter - Class in inverters
Purpose: Non-linear least squares fitter of a three-tensor model to DW-MR data with fixed mixing parameters.
ThreeTensorCholFixMP_Fitter() - Constructor for class inverters.ThreeTensorCholFixMP_Fitter
Default constructor does nothing.
ThreeTensorCholFixMP_Fitter(double[][], double[], double[], int) - Constructor for class inverters.ThreeTensorCholFixMP_Fitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
ThreeTensorFitter - Class in inverters
Purpose: Non-linear least squares fitter of a three tensor model to DW-MR data.
ThreeTensorFitter() - Constructor for class inverters.ThreeTensorFitter
Default constructor does nothing.
ThreeTensorFitter(double[][], double[], double[], int) - Constructor for class inverters.ThreeTensorFitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
ThreeTensorInversion - Class in inverters
Purpose: Fit the three-tensor model.
ThreeTensorInversion(DW_Scheme) - Constructor for class inverters.ThreeTensorInversion
This constructor requires the details of the sequence used to generate the data that will be processed.
ThreeTensorInversion(DW_Scheme, ModelIndex, ModelIndex) - Constructor for class inverters.ThreeTensorInversion
This constructor requires the details of the sequence and the indexes of the choices of ThreeTensorFitter and DT_Inverter.
ThreeTensorOneAxiSymFitter - Class in inverters
Purpose: Non-linear least squares fitter of a three tensor model with one prolate axisymmetric tensor to DW-MR data.
ThreeTensorOneAxiSymFitter() - Constructor for class inverters.ThreeTensorOneAxiSymFitter
Default constructor does nothing.
ThreeTensorOneAxiSymFitter(double[][], double[], double[], int) - Constructor for class inverters.ThreeTensorOneAxiSymFitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
ThreeTensorOneAxiSymFixMP_Fitter - Class in inverters
Purpose: Non-linear least squares fitter of a three-tensor model to DW-MR data with fixed mixing parameters and one axisymmetric tensor.
ThreeTensorOneAxiSymFixMP_Fitter() - Constructor for class inverters.ThreeTensorOneAxiSymFixMP_Fitter
Default constructor does nothing.
ThreeTensorOneAxiSymFixMP_Fitter(double[][], double[], double[], int) - Constructor for class inverters.ThreeTensorOneAxiSymFixMP_Fitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
threeTensorStats(double[][]) - Static method in class apps.SequenceStats
Computes the statistics for three tensors and outputs them.
ThreeTensorTwoAxiSymFitter - Class in inverters
Purpose: Non-linear least squares fitter of a three tensor model with two prolate axisymmetric tensors to DW-MR data.
ThreeTensorTwoAxiSymFitter() - Constructor for class inverters.ThreeTensorTwoAxiSymFitter
Default constructor does nothing.
ThreeTensorTwoAxiSymFitter(double[][], double[], double[], int) - Constructor for class inverters.ThreeTensorTwoAxiSymFitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
ThreeTensorTwoAxiSymFixMP_Fitter - Class in inverters
Purpose: Non-linear least squares fitter of a three-tensor model to DW-MR data with fixed mixing parameters and two axisymmetric tensors.
ThreeTensorTwoAxiSymFixMP_Fitter() - Constructor for class inverters.ThreeTensorTwoAxiSymFixMP_Fitter
Default constructor does nothing.
ThreeTensorTwoAxiSymFixMP_Fitter(double[][], double[], double[], int) - Constructor for class inverters.ThreeTensorTwoAxiSymFixMP_Fitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
THREETENVALSPERVOXEL - Static variable in class tools.CL_Initializer
The number of values per voxel in three-tensor data.
ThresholdB0 - Class in apps
Purpose: Creates a background mask.
ThresholdB0() - Constructor for class apps.ThresholdB0
 
times(double) - Method in class Jama.Matrix
Multiply a matrix by a scalar, C = s*A
times(Matrix) - Method in class Jama.Matrix
Linear algebraic matrix multiplication, A * B
times(Complex) - Method in class numerics.Complex
Multiplies complex numbers.
times(double) - Method in class numerics.Complex
Multiplies by a scalar.
timesEquals(double) - Method in class Jama.Matrix
Multiply a matrix by a scalar in place, A = s*A
TINYNUM - Static variable in class simulation.geometry.substrates.CellularLattice
tolerence for floating point equality
tmax - Variable in class simulation.geometry.elements.SquashyCylinder.Chord
 
tmin - Variable in class simulation.geometry.elements.SquashyCylinder.Chord
 
toArray() - Method in class tractography.Tract
Flattens tract into an array.
toffset - Variable in class imaging.Nifti1Dataset
 
toFile(Writer) - Method in class simulation.geometry.elements.BasicCylinder
 
toFile(Writer) - Method in interface simulation.geometry.elements.Cylinder
spits out cylinder cross section to a file
toFile(Writer) - Method in class simulation.geometry.elements.FacetCylinder
write out cross section to file
toFile(Writer) - Method in class simulation.geometry.elements.MyelinatedCylinder
spits out cylinder cross section
toggleAutoUpdate() - Method in class apps.F_TestThresholdSelector
Toggles automatic updating.
toJamaMatrix() - Method in class numerics.Vector3D
 
toMatrix() - Method in class misc.DT
 
tools - package tools
 
toOOGLVECT() - Method in class tractography.Tract
Output as OOGL vector, suitable for display in Geomview.
toRealMatrix() - Method in class numerics.Vector3D
 
toString() - Method in class data.GaussianMixture
 
toString() - Method in class imaging.AnalyzeHeader
 
toString() - Method in class imaging.B_VectorScheme
Returns the String representation of this object.
toString() - Method in enum imaging.MetaImageHeader.DataType
 
toString() - Method in enum imaging.MetaImageHeader.ObjectType
 
toString() - Method in class imaging.Nifti1Dataset
 
toString() - Method in class imaging.RectGradSteTanScheme
Returns the String representation of this object.
toString() - Method in class imaging.RectGradTRSE_Scheme
 
toString() - Method in enum inverters.InversionIndex
 
toString() - Method in enum inverters.ModelIndex
 
toString() - Method in class misc.DT
Returns a string containing the diffusion tensor matrix.
toString() - Method in class numerics.ACG_Distribution
 
toString() - Method in class numerics.BinghamDistribution
 
toString() - Method in class numerics.Complex
 
toString() - Method in class numerics.EigenSystem3D
String representation is 3x4 matrix of eigenvalues and eigenvectors.
toString() - Method in class numerics.Point3D
 
toString() - Method in class numerics.PolynomialFunction1D
 
toString() - Method in class numerics.PolynomialFunction2D
 
toString() - Method in class numerics.RealMatrix
 
toString() - Method in class numerics.SVAnalyticalFunction
 
toString() - Method in class numerics.Vector3D
 
toString() - Method in class numerics.WatsonD
 
toString() - Method in class simulation.dynamics.Walker
outputs walker fields as string
toString() - Method in class simulation.geometry.elements.Triangle
returns the details of the triangle as a string
toString() - Method in class sphfunc.EvenSHS
Constructs a string containing the coefficients of the series.
toString() - Method in class sphfunc.PD
 
toString(double[]) - Static method in class tools.ArrayOps
Converts an array to a string representation with a specified number of decimal places
toString() - Method in enum tractography.DataModel
 
toString() - Method in enum tractography.PICoPDF
 
toString() - Method in class tractography.Tract
 
toString() - Method in class tractography.TractCollection
 
toString() - Method in class tractography.Voxel
 
toString() - Method in class tractography.VoxelList
 
totalPoints() - Method in class tractography.TractCollection
 
totalStreamlines() - Method in class tractography.ConnectionProbabilityImage
 
totalStreamlines() - Method in class tractography.TargetCP_Image
 
totalTimeStuck - Variable in class simulation.dynamics.StickyWalker
total time stuck
toTract() - Method in class tractography.VoxelList
Makes a Tract with a point at the centre of each voxel in the list.
toVoxelList(double[]) - Method in class tractography.Tract
List of voxel coordinates of the tract.
toVoxelList(double, double, double) - Method in class tractography.Tract
List of voxel coordinates of the tract.
trace - Static variable in class apps.SphFuncPICoCalibrationData
 
trace() - Method in class Jama.Matrix
Matrix trace.
trace() - Method in class misc.DT
Computes the trace of the diffusion tensor.
trace() - Method in class numerics.RealMatrix
Computes the trace of the matrix.
TraceD - Class in apps
Purpose: Computes the trace of each diffusion tensor.
TraceD(String[]) - Constructor for class apps.TraceD
Output manager
trackFromSeed(Point3D) - Method in class tractography.FibreTracker
Track paths from a single seed point within the ROI.
trackFromSeed(Point3D, int) - Method in class tractography.FibreTracker
Track paths from a single seed point within the ROI.
trackFromSeed(Point3D) - Method in class tractography.NC_ProbFibreTracker
Track a path from a single seed point, and wrap result in a #TractCollection.
trackFromSeed(Point3D, int) - Method in class tractography.NC_ProbFibreTracker
Track a path from a single seed point, following a specified PD.
trackPaths(RegionOfInterest) - Method in class tractography.FibreTracker
Track paths from seed points placed at the centre of all voxels within the ROI.
Tract - Class in tractography
Purpose: To contain a list of points describing one streamline.
Tract(int, double) - Constructor for class tractography.Tract
Construct a Tract with a specified capacity and growth factor.
Tract() - Constructor for class tractography.Tract
Construct a Tract with a capacity of 100 and a growth factor of 100%.
TractCollection - Class in tractography
Purpose: To hold a collection of Tract objects.
TractCollection() - Constructor for class tractography.TractCollection
Default constructor.
TractCollection(int, double) - Constructor for class tractography.TractCollection
Construct a TractCollection with a specified capacity and growth factor.
TractCounter - Class in apps
Counts the number of streamlines in a file.
TractCounter() - Constructor for class apps.TractCounter
 
tractography - package tractography
 
TractographyImage - Class in tractography
Superclass for tractography images.
TractographyImage(int[], double[], int) - Constructor for class tractography.TractographyImage
Basic constructor initialises dimensions only.
TractographyImage(Vector3D[][][][], double[], int) - Constructor for class tractography.TractographyImage
Matlab constructor.
TractShredder - Class in apps
Like shredder, but used to sample periodically from a set of streamlines
TractShredder() - Constructor for class apps.TractShredder
 
TractSource - Class in tractography
Provides an interface for input of Tract objects.
TractSource(String, String, double[]) - Constructor for class tractography.TractSource
Construct a source from the file or stdin.
TractSource(String, String, double, double, double) - Constructor for class tractography.TractSource
 
TractStatisticFilter - Class in tractography
Computes a statistic from streamlines, either from the streamline itself or by the values of a scalar image along the streamline.
TractStatisticFilter(ScalarImage) - Constructor for class tractography.TractStatisticFilter
Construct an filter that uses the scalar image to define the tract statistic.
TractStatisticFilter(double[][][], double[]) - Constructor for class tractography.TractStatisticFilter
For Matlab.
TractStatisticFilter(int[], double[]) - Constructor for class tractography.TractStatisticFilter
Constructor for filters that do not use scalars.
TractStatisticImage - Class in tractography
Gathers statistics from a TractStatisticFilter and creates an image using the tracts.
TractStatisticImage(ScalarImage) - Constructor for class tractography.TractStatisticImage
Construct an image that uses the scalar image to define the tract statistic.
TractStatisticImage(double[][][], double[]) - Constructor for class tractography.TractStatisticImage
For Matlab.
TractStatisticImage(int[], double[]) - Constructor for class tractography.TractStatisticImage
Constructs an image without scalars.
TractStatistics - Class in apps
Generates statistics of streamline tracts, either of the tracts themselves or of scalar values along the tracts.
TractStatistics() - Constructor for class apps.TractStatistics
 
trajectories - Static variable in class simulation.SimulationParams
are we generating trajectories?
trajFile - Static variable in class simulation.SimulationParams
name of trajectories file
transform(RealMatrix) - Method in class misc.DT
Applies a similarity transform to the diffusion tensor using the linear transformation matrix supplied.
transform(RealMatrix) - Method in class numerics.Point3D
Transform a point by a 4D Affine matrix.
transform(RealMatrix) - Method in class tractography.Tract
 
transformation - Variable in class imaging.MetaImageHeader
TransformMatrix, a 3x3 rotation matrix.
transformFile - Static variable in class tools.CL_Initializer
Name of a file containing an affine image transformation.
transformFileX - Static variable in class tools.CL_Initializer
Names of files containing an image warp.
transformFileY - Static variable in class tools.CL_Initializer
 
transformFileZ - Static variable in class tools.CL_Initializer
 
transformPoint(RealMatrix, double[]) - Static method in class numerics.Rotations
Applies a 3D transformation matrix to a point.
transpose() - Method in class Jama.Matrix
Matrix transpose.
transpose() - Method in class numerics.RealMatrix
Computes the transpose.
Triangle - Class in simulation.geometry.elements
 
Triangle(double[], double[], double[], double) - Constructor for class simulation.geometry.elements.Triangle
define a triangle from three vertices.
triangular() - Method in class numerics.RealMatrix
Tests whether a matrix is triangular.
triBoxOverlap() - Method in class simulation.geometry.elements.Triangle
 
TRSE_Scheme - Class in imaging
Scheme file for twice-refocused pulse sequences, which use four diffusion-weighting pulses, which begin at time t_delN and last for delN seconds.
truncate(double[], double[]) - Method in class inverters.EvenSphHarmFitter
Determines the level of truncation of the series using a series of f-tests between models from truncations at different orders.
truncateToMaxLength(double) - Method in class tractography.Tract
Reduce the length of a Tract to the specified maximum length in mm.
truncateToMaxPoints(int) - Method in class tractography.Tract
Reduce the length of a tract to the specified maximum number of points.
TUCH_RBF - Static variable in class sphfunc.BasisSumFactory
Creates a TuchRBF_Sum object
TuchRBF - Class in sphfunc
Purpose: Implements the radial basis function used in Dave Tuch's original q-ball implementation..
TuchRBF(double[], double) - Constructor for class sphfunc.TuchRBF
Constructor requires parameters of the function.
TuchRBF_Sum - Class in sphfunc
Purpose: Function of the sphere represented using Dave Tuch's spherical radial basis function.
TuchRBF_Sum(double[]) - Constructor for class sphfunc.TuchRBF_Sum
 
TwoFibreACGFitter - Class in numerics
Purpose: Fits two ACG distributions to a collection of axes.
TwoFibreACGFitter(Vector3D[]) - Constructor for class numerics.TwoFibreACGFitter
 
TwoFibreBinghamFitter - Class in numerics
Purpose: Fits two Bingham distributions to a collection of axes.
TwoFibreBinghamFitter(Vector3D[]) - Constructor for class numerics.TwoFibreBinghamFitter
 
TwoFibreBipolarWatsonFitter - Class in numerics
Purpose: Fits two Watson distributions to a collection of axes.
TwoFibreBipolarWatsonFitter(Vector3D[]) - Constructor for class numerics.TwoFibreBipolarWatsonFitter
 
TwoFibreFixedPropWatsonFitter - Class in numerics
Purpose: Fits two Watson distributions to a collection of axes.
TwoFibreFixedPropWatsonFitter(Vector3D[], double) - Constructor for class numerics.TwoFibreFixedPropWatsonFitter
 
TwoFibreWatsonFitter - Class in numerics
Purpose: Fits two Watson distributions to a collection of axes.
TwoFibreWatsonFitter(Vector3D[]) - Constructor for class numerics.TwoFibreWatsonFitter
 
TwoTensorAxiSymFitter - Class in inverters
Purpose: Non-linear least squares fitter of a two prolate axisymmetric tensor model to DW-MR data.
TwoTensorAxiSymFitter() - Constructor for class inverters.TwoTensorAxiSymFitter
Default constructor does nothing.
TwoTensorAxiSymFitter(double[][], double[], double[], int) - Constructor for class inverters.TwoTensorAxiSymFitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
TwoTensorAxiSymFixMP_Fitter - Class in inverters
Purpose: Non-linear least squares fitter of a two prolate axisymmetric tensor model to DW-MR data with fixed mixing parameter.
TwoTensorAxiSymFixMP_Fitter() - Constructor for class inverters.TwoTensorAxiSymFixMP_Fitter
Default constructor does nothing.
TwoTensorAxiSymFixMP_Fitter(double[][], double[], double[], int) - Constructor for class inverters.TwoTensorAxiSymFixMP_Fitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
TwoTensorCholFitter - Class in inverters
Purpose: Non-linear least squares fitter of a two tensor model to DW-MR data.
TwoTensorCholFitter() - Constructor for class inverters.TwoTensorCholFitter
Default constructor does nothing.
TwoTensorCholFitter(double[][], double[], double[], int) - Constructor for class inverters.TwoTensorCholFitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
TwoTensorCholFixMP_Fitter - Class in inverters
Purpose: Non-linear least squares fitter of a two tensor model to DW-MR data with fixed mixing parameter.
TwoTensorCholFixMP_Fitter() - Constructor for class inverters.TwoTensorCholFixMP_Fitter
Default constructor does nothing.
TwoTensorCholFixMP_Fitter(double[][], double[], double[], int) - Constructor for class inverters.TwoTensorCholFixMP_Fitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
TwoTensorFitter - Class in inverters
Purpose: Non-linear least squares fitter of a two tensor model to DW-MR data.
TwoTensorFitter() - Constructor for class inverters.TwoTensorFitter
Default constructor does nothing.
TwoTensorFitter(double[][], double[], double[], int) - Constructor for class inverters.TwoTensorFitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
TwoTensorInversion - Class in inverters
Purpose: Fit the two-tensor model.
TwoTensorInversion(DW_Scheme) - Constructor for class inverters.TwoTensorInversion
This constructor requires the details of the sequence used to generate the data that will be processed.
TwoTensorInversion(DW_Scheme, ModelIndex, ModelIndex) - Constructor for class inverters.TwoTensorInversion
This constructor requires the details of the sequence and the indexes of the choices of TwoTensorFitter and DT_Inverter.
TwoTensorLUTGenerator - Class in tractography
Fits some distribution to samples of tensors with added noise.
TwoTensorLUTGenerator(DW_Scheme, double, double, double, double, Random) - Constructor for class tractography.TwoTensorLUTGenerator
 
TwoTensorOneAxiSymFitter - Class in inverters
Purpose: Non-linear least squares fitter of a two tensor model with one prolate axisymmetric tensor to DW-MR data.
TwoTensorOneAxiSymFitter() - Constructor for class inverters.TwoTensorOneAxiSymFitter
Default constructor does nothing.
TwoTensorOneAxiSymFitter(double[][], double[], double[], int) - Constructor for class inverters.TwoTensorOneAxiSymFitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
TwoTensorOneAxiSymFixMP_Fitter - Class in inverters
Purpose: Non-linear least squares fitter of a two tensor model with one prolate axisymmetric tensor to DW-MR data with fixed mixing parameter.
TwoTensorOneAxiSymFixMP_Fitter() - Constructor for class inverters.TwoTensorOneAxiSymFixMP_Fitter
Default constructor does nothing.
TwoTensorOneAxiSymFixMP_Fitter(double[][], double[], double[], int) - Constructor for class inverters.TwoTensorOneAxiSymFixMP_Fitter
The constructor requires a list of independent values (indepVals) and associated dependent values (depVals) - these are the data.
twoTensorStats(double[][], double) - Static method in class apps.SequenceStats
Computes the statistics for two tensors and outputs them.
TWOTENVALSPERVOXEL - Static variable in class tools.CL_Initializer
The number of values per voxel in two-tensor data.
typeString(int) - Static method in class data.ExternalDataSource
Converts the data type integer code to a string
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