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F

f(double, double) - Method in class numerics.NumericalIntegration
abstract method to evaluate the function to be integrated
f1 - Static variable in class tools.CL_Initializer
The f-test thresholds.
f2 - Static variable in class tools.CL_Initializer
 
f3 - Static variable in class tools.CL_Initializer
 
F_TestThresholdSelector - Class in apps
Purpose: Loads F-test data for interactive threshold selection.
F_TestThresholdSelector(double[][][][], int, double, double) - Constructor for class apps.F_TestThresholdSelector
 
F_TestThresholdSelector(double[][][][], int, double, double, double, double, double) - Constructor for class apps.F_TestThresholdSelector
 
fa() - Method in class misc.DT
Compute the fractional anisotropy of the diffusion tensor.
FacetCylinder - Class in simulation.geometry.elements
Cylinder implementation with polygonal cross-section.
FacetCylinder(Vector3D, Vector3D, double, int, double) - Constructor for class simulation.geometry.elements.FacetCylinder
constructor.
FacetCylinder(Vector3D, double, int, double) - Constructor for class simulation.geometry.elements.FacetCylinder
constructor with default alignment
FACT_TendFibreTracker - Class in tractography
Purpose: To perform Tractography operations.
FACT_TendFibreTracker(DT_TractographyImage, double, double, double) - Constructor for class tractography.FACT_TendFibreTracker
Construct a tracker with additional options set.
FACT_TendFibreTracker(DT_TractographyImage, double, double[][][], double) - Constructor for class tractography.FACT_TendFibreTracker
Construct a tracker with additional options set.
factor - Static variable in class simulation.geometry.substrates.Substrate
cheat factor for curved surfaces
fAndBetaToDT(double[]) - Static method in class inverters.TensorModelFitter
Computes the DT from F and Beta.
FanningGrid - Class in apps
Outputs a ball and stick model fanning structure
FanningGrid(String[]) - Constructor for class apps.FanningGrid
 
FibreTracker - Class in tractography
Abstract superclass for classes that perform streamline tractography.
FILEBUFFERSIZE - Static variable in class apps.Shredder
 
FILEBUFFERSIZE - Static variable in class data.ExternalDataSource
Size of read in file buffer.
FILEBUFFERSIZE - Static variable in class data.OutputManager
 
FileInput - Class in tools
A simple input class to read values from a file of characters.
FileInput(String) - Constructor for class tools.FileInput
Construct FileInput object given a file name.
FileOutput - Class in tools
A simple output class to write values to a file of characters.
FileOutput(String) - Constructor for class tools.FileOutput
Construct FileOutput object given a file name.
findA(Vector3D[]) - Static method in class numerics.ACG_Fitter
Finds the covariance matrix A of the ACG distribution.
firstDeriv(double[], double[], double[][], double[], double, double, double, double) - Method in class numerics.TwoFibreWatsonFitter
 
fit(double[]) - Method in class fitters.Fitter
Fits the model to one voxel's worth of data.
fit(double[]) - Method in class fitters.MCMC_Fitter
 
fit(double[]) - Method in class inverters.EvenSphHarmFitter
Fits the spherical harmonic series using the inverse matrix.
fit(double[]) - Method in class inverters.EvenSphHarmSignalFitter
Fits the spherical harmonic series using the inverse matrix.
FitAlgorithm - Enum in fitters
 
fitAlgorithm - Static variable in class tools.CL_Initializer
type of fitting algorithm
fitEstimatedParams(Vector3D, Vector3D, double) - Method in class numerics.TwoFibreACGFitter
Runs the minimization and returns the answer.
fitEstimatedParams(double[], double[], double) - Method in class numerics.TwoFibreACGFitter
Runs the minimization and returns the answer.
fitEstimatedParams(Vector3D[], double[], double) - Method in class numerics.TwoFibreBinghamFitter
Runs the minimization and returns the answer.
fitEstimatedParams(Vector3D, Vector3D, double, double, double, double, double, double, int) - Method in class numerics.TwoFibreFixedPropWatsonFitter
Make estimates of the initial parameters and attempt a minimisation with each.
fitEstimatedParams(Vector3D, Vector3D, int) - Method in class numerics.TwoFibreFixedPropWatsonFitter
Two cones are defined for each mean axis, centered on the mean axis.
fitEstimatedParams(double, int) - Method in class numerics.TwoFibreWatsonFitter
Make estimates of the initial parameters and attempt a minimisation with each.
fitKappa(Vector3D[]) - Static method in class numerics.WatsonFitter
Fits kappa for a sample of vectors.
fitKappa(EigenSystem3D, Vector3D[]) - Static method in class numerics.WatsonFitter
Fits kappa for a sample of vectors.
fitKappa(EigenSystem3D) - Static method in class numerics.WatsonFitter
Fits kappa to a scatter matrix.
fitKappa(double) - Static method in class numerics.WatsonFitter
Fits kappa to an eigenvalue.
FitModel - Enum in fitters
list of models for fitting.
fitModel - Static variable in class tools.CL_Initializer
type of tissue model for fitting
Fitter - Class in fitters
Purpose: General base class for objects that fit a model to data.
Fitter() - Constructor for class fitters.Fitter
 
fitters - package fitters
 
FixedLengthStepGenerator - Class in simulation.dynamics
Generates steps of random orientation and fixed length
FixedLengthStepGenerator(SimulationParams) - Constructor for class simulation.dynamics.FixedLengthStepGenerator
constructor.
fixedStartPoint - Static variable in class tools.CL_Initializer
Start point for compartment model fitting from commandline
FixedSTD_GaussianPerturbation - Class in fitters
* Class for starting point perturbations using a gaussian standard distribution Description: Perturbs the parameters using a gaussian standard distribution which is controlled by a single parameter: the standard deviation (0.1 by default).
FixedSTD_GaussianPerturbation() - Constructor for class fitters.FixedSTD_GaussianPerturbation
Creates a gaussian perturbation with std 0.1
FixedSTD_GaussianPerturbation(double) - Constructor for class fitters.FixedSTD_GaussianPerturbation
Creates a gaussian perturbation with std
fixedWidthDoubletoString(double, int, int) - Static method in class Jama.examples.MagicSquareExample
Format double with Fw.d.
fixedWidthIntegertoString(int, int) - Static method in class Jama.examples.MagicSquareExample
Format integer with Iw.
FLIP_X - Static variable in class apps.PD_OrientationViewer
 
FLIP_Y - Static variable in class apps.PD_OrientationViewer
 
FLIP_Z - Static variable in class apps.PD_OrientationViewer
 
flipDouble(double) - Method in class imaging.EndianCorrectInputStream
flipDouble will flip the byte order of a double
flipDouble(double) - Method in class imaging.EndianCorrectOutputStream
flipDouble will flip the byte order of a double
flipFloat(float) - Method in class imaging.EndianCorrectInputStream
flipFloat will flip the byte order of a float
flipFloat(float) - Method in class imaging.EndianCorrectOutputStream
flipFloat will flip the byte order of a float
flipInt(int) - Method in class imaging.EndianCorrectInputStream
flipInt will flip the byte order of an int
flipInt(int) - Method in class imaging.EndianCorrectOutputStream
flipInt will flip the byte order of an int
flipLong(long) - Method in class imaging.EndianCorrectInputStream
flipLong will flip the byte order of a long
flipLong(long) - Method in class imaging.EndianCorrectOutputStream
flipLong will flip the byte order of a long
flipShort(short) - Method in class imaging.EndianCorrectInputStream
flipShort will byte flip a short
flipShort(short) - Method in class imaging.EndianCorrectOutputStream
flipShort will byte flip a short
flipX - Static variable in class apps.PICoPDFs
 
flipX() - Method in class imaging.B_VectorScheme
Negates the X component of the gradient directions.
flipX() - Method in class imaging.DW_Scheme
Negates the X component of the gradient directions.
flipX() - Method in class imaging.GradientWaveform_Scheme
returns a new copy of the current scheme with gradients flipped in the x-direction
flipX() - Method in class imaging.RectGradSteTanScheme
Negates the X component of the gradient directions.
flipX() - Method in class imaging.RectGradTRSE_Scheme
Negates the X component of the gradient directions.
flipY - Static variable in class apps.PICoPDFs
 
flipY() - Method in class imaging.B_VectorScheme
Negates the Y component of the gradient directions.
flipY() - Method in class imaging.DW_Scheme
Negates the Y component of the gradient directions.
flipY() - Method in class imaging.GradientWaveform_Scheme
returns a new copy of the current scheme with gradients flipped in the y-direction
flipY() - Method in class imaging.RectGradSteTanScheme
Negates the Y component of the gradient directions.
flipY() - Method in class imaging.RectGradTRSE_Scheme
Negates the Y component of the gradient directions.
flipZ - Static variable in class apps.PICoPDFs
 
flipZ() - Method in class imaging.B_VectorScheme
Negates the Z component of the gradient directions.
flipZ() - Method in class imaging.DW_Scheme
Negates the Z component of the gradient directions.
flipZ() - Method in class imaging.GradientWaveform_Scheme
returns a new copy of the current scheme with gradients flipped in the z-direction
flipZ() - Method in class imaging.RectGradSteTanScheme
Negates the Z component of the gradient directions.
flipZ() - Method in class imaging.RectGradTRSE_Scheme
Negates the Z component of the gradient directions.
FLOAT - Static variable in class data.ExternalDataSource
 
FORWARD - Static variable in class tractography.FibreTracker
 
FracAnis - Class in apps
Purpose: Computes the fractional anisotropy of each diffusion tensor.
FracAnis(String[]) - Constructor for class apps.FracAnis
Output manager
free - Variable in class simulation.dynamics.StickyWalker
are we in the bulk or stuck to a the surface?
FreeFormROI - Class in tractography
A free form voxel-based ROI for tractography.
FreeFormROI(short[][][], double[]) - Constructor for class tractography.FreeFormROI
Create an ROI from an integer volume.
FreeFormROI(short[][][], double, double, double) - Constructor for class tractography.FreeFormROI
Create an ROI from an integer volume.
FreeFormROI(short[][][], short, double[]) - Constructor for class tractography.FreeFormROI
Create an ROI from an integer volume.
FreeFormROI(short[][][], short, double, double, double) - Constructor for class tractography.FreeFormROI
Create an ROI from an integer volume.
freq_dim - Variable in class imaging.Nifti1Dataset
 
fsAndBetasFromSingleDT(DT) - Static method in class inverters.TensorModelFitter
Computes the Fs and betas defining two axisymmetric tensors derived from a single DT to use as a starting point for fitting the two-tensor model.
fsAndBetasThreeFromSingleDT(DT) - Static method in class inverters.TensorModelFitter
Computes the Fs and betas defining three axisymmetric tensors derived from a single DT to use as a starting point for fitting the three tensor model.
FSL_ToScheme - Class in apps
Converts FSL b-vectors and b-values to Camino scheme file format.
FSL_ToScheme(String[]) - Constructor for class apps.FSL_ToScheme
 
ftAt(double[], double) - Method in class data.BallStick
 
ftAt(double[], double) - Method in class data.CylinderModel
 
ftAt(double[], double) - Method in class data.GaussianMixture
 
ftAt(double[], double) - Method in interface data.ModelPDF
Returns the value of the FT of the function at the specified wavenumber.
ftAtB_Vec(double[], double) - Method in class data.BallStick
 
ftAtB_Vec(double[], double) - Method in class data.CylinderModel
 
ftAtB_Vec(double[], double) - Method in class data.GaussianMixture
 
ftAtB_Vec(double[], double) - Method in interface data.ModelPDF
Returns the value of the FT of the function at the specified gradient direction and b-value.
funcsUpTo(int) - Static method in class numerics.SphericalHarmonics
Computes the number of spherical harmonic functions up to a specified order.
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