- 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