- 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.