- N - Static variable in class tools.CL_Initializer
-
The number of non-zero measurements.
- name - Variable in enum inverters.InversionIndex
-
The name of the index.
- name - Variable in enum inverters.ModelIndex
-
The name of the index.
- name - Variable in enum tractography.DataModel
-
The name of the model.
- name - Variable in enum tractography.PICoPDF
-
The name of the PDF.
- NC_ProbFibreTracker - Class in tractography
-
Does Probabilistic tractography using neighbour-choice interpolation.
- NC_ProbFibreTracker(TractographyImage, double, double, Random) - Constructor for class tractography.NC_ProbFibreTracker
-
- nDims - Variable in class imaging.MetaImageHeader
-
NDims, number of dimensions.
- negate() - Method in class numerics.Complex
-
Negates the complex number.
- negate() - Method in class numerics.RealMatrix
-
Negates the matrix.
- negated() - Method in class numerics.Vector3D
-
Get the negated version of this vector
- NeighbourChoiceInterpolator - Class in tractography
-
Provides interpolated tracking directions at any point within the dataset.
- NeighbourChoiceInterpolator(TractographyImage, Random) - Constructor for class tractography.NeighbourChoiceInterpolator
-
- newDepVals(double[]) - Method in class inverters.BallStickFitter
-
Initializes the fitting procedure with a new set of measurements (dependent variables).
- newDepVals(double[]) - Method in class inverters.DiffDataFitter
-
Initialises a new fitting procedure with the same independent variables
(b-vectors), but a new set of measurements (dependent variables).
- newDepVals(double[]) - Method in class mesd.MESD_Fitter
-
Initialises a new fitting procedure with the same independent variables
(sampled directions), but a new set of measurements (dependent
variables).
- NewtonRaphsonSolver - Class in numerics
-
Solves nonlinear equations by the Newton-Raphson method.
- NewtonRaphsonSolver() - Constructor for class numerics.NewtonRaphsonSolver
-
- nextCandidate() - Method in class simulation.geometry.substrates.Substrate
-
get the next substrate object in the candidate list
- nextGamma() - Method in class numerics.GammaRandom
-
returns a sample drawn from the gamma distribution given by
k and beta.
- nextTract() - Method in class tractography.TractSource
-
- nextVector() - Method in class numerics.ACG_Distribution
-
- nextVector() - Method in interface numerics.AxialDistribution
-
Gets the next Vector from the distribution.
- nextVector() - Method in class numerics.BinghamDistribution
-
- nextVector(Vector3D[], double, double, double, Random) - Static method in class numerics.BinghamDistribution
-
- nextVector() - Method in class numerics.WatsonDistribution
-
- nextVector(double) - Method in class numerics.WatsonDistribution
-
- nextVector(double, double, double, Random) - Static method in class numerics.WatsonDistribution
-
- nextVector(Vector3D, double) - Method in class numerics.WatsonDistribution
-
- nextVector(Vector3D, double, Random) - Static method in class numerics.WatsonDistribution
-
- nextVoxel() - Method in class data.BootstrapDataSynthesizer
-
- nextVoxel() - Method in class data.compartments.CompartmentModel
-
interface for data synthesis.
- nextVoxel() - Method in interface data.DataSource
-
Returns the data in the next voxel.
- nextVoxel() - Method in class data.DataSynthesizer
-
- nextVoxel() - Method in class data.DataSynthFromInput
-
- nextVoxel() - Method in class data.MatlabArrayDataSource
-
- nextVoxel() - Method in class data.ScannerOrderDataSource
-
- nextVoxel() - Method in class data.ScannerOrderScaledDataSource
-
- nextVoxel() - Method in class data.SyntheticBootstrapper
-
- nextVoxel() - Method in class data.VoxelOrderDataSource
-
- nextVoxel() - Method in class data.VoxelOrderScaledDataSource
-
- nextVoxel() - Method in class data.WildBootstrapDataSynth
-
Gets the next bootstrap sample of the raw data from this data source.
- nextVoxel() - Method in class models.compartments.CompartmentModel
-
interface for data synthesis.
- nextVoxel() - Method in class simulation.DiffusionSimulation
-
initialises a simulation and runs the main loop before
constructing a
- NI1_EXT - Static variable in class imaging.Nifti1Dataset
-
- Nifti1Dataset - Class in imaging
-
This class is adapted from the NIFTI Java code provided by Kate Fissell at
the University of Pittsburgh.
- Nifti1Dataset(String) - Constructor for class imaging.Nifti1Dataset
-
Constructor for a dataset existing on disk.
- Nifti1Dataset() - Constructor for class imaging.Nifti1Dataset
-
Constructor for creation of a new dataset.
- NIFTI_FIRST_STATCODE - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_BETA - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_BINOM - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_CHI - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_CHISQ - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_CHISQ_NONC - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_CORREL - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_DISPVECT - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_ESTIMATE - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_EXTVAL - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_FTEST - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_FTEST_NONC - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_GAMMA - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_GENMATRIX - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_INVGAUSS - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_LABEL - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_LAPLACE - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_LOGISTIC - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_NEURONAME - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_NONE - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_NORMAL - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_POINTSET - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_POISSON - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_PVAL - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_QUATERNION - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_SYMMATRIX - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_TRIANGLE - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_TTEST - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_TTEST_NONC - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_UNIFORM - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_VECTOR - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_WEIBULL - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_INTENT_ZSCORE - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_LAST_STATCODE - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_SLICE_ALT_DEC - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_SLICE_ALT_INC - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_SLICE_SEQ_DEC - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_SLICE_SEQ_INC - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_TYPE_COMPLEX128 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_TYPE_COMPLEX256 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_TYPE_COMPLEX64 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_TYPE_FLOAT128 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_TYPE_FLOAT32 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_TYPE_FLOAT64 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_TYPE_INT16 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_TYPE_INT32 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_TYPE_INT64 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_TYPE_INT8 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_TYPE_RGB24 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_TYPE_UINT16 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_TYPE_UINT32 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_TYPE_UINT64 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_TYPE_UINT8 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_UNITS_HZ - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_UNITS_METER - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_UNITS_MICRON - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_UNITS_MM - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_UNITS_MSEC - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_UNITS_PPM - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_UNITS_SEC - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_UNITS_UNKNOWN - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_UNITS_USEC - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_XFORM_ALIGNED_ANAT - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_XFORM_MNI_152 - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_XFORM_SCANNER_ANAT - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_XFORM_TALAIRACH - Static variable in class imaging.Nifti1Dataset
-
- NIFTI_XFORM_UNKNOWN - Static variable in class imaging.Nifti1Dataset
-
- NII_HDR_SIZE - Static variable in class imaging.Nifti1Dataset
-
- NII_MAGIC_STRING - Static variable in class imaging.Nifti1Dataset
-
- nImages - Variable in class imaging.AnalyzeHeader
-
- NO_FLIP - Static variable in class apps.PD_OrientationViewer
-
- NOCOMPS - Static variable in class simulation.SimulationParams
-
flag for compartmental signal: default (no compartmental segregation
- NoiseModel - Enum in fitters
-
- noiseModel - Static variable in class tools.CL_Initializer
-
type of noise model for fitting
- noiseType - Static variable in class tools.CL_Initializer
-
Specifies the type of noise to add.
- noiseVarianceMapFile - Static variable in class tools.CL_Initializer
-
Name of the noise variance map file for inversions that compute it.
- NonInterpolatedFibreTracker - Class in tractography
-
Purpose: To perform Tractography operations.
- NonInterpolatedFibreTracker(TractographyImage, double) - Constructor for class tractography.NonInterpolatedFibreTracker
-
Construct a tracker with additional options set.
- NonIntProbFibreTracker - Class in tractography
-
Purpose: To perform Tractography operations.
- NonIntProbFibreTracker(TractographyImage, double, Random) - Constructor for class tractography.NonIntProbFibreTracker
-
Construct a tracker with additional options set.
- NonLinearDT_Inversion - Class in inverters
-
Purpose:
Fit the diffusion tensor.
- NonLinearDT_Inversion(DW_Scheme) - Constructor for class inverters.NonLinearDT_Inversion
-
This constructor takes only the imaging sequence parameters and creates a
fitter that does not use the Hessian of the objective function.
- NonLinearDT_Inversion(DW_Scheme, ModelIndex) - Constructor for class inverters.NonLinearDT_Inversion
-
This constructor takes the imaging sequence parameters and an index
specifying the type of fitting to use.
- nonStandardTestFunction - Static variable in class tools.CL_Initializer
-
Indicates whether or not the user specified a non-standard test function.
- norm1() - Method in class Jama.Matrix
-
One norm
- norm2() - Method in class Jama.Matrix
-
Two norm
- norm2() - Method in class Jama.SingularValueDecomposition
-
Two norm
- normal() - Method in class simulation.geometry.elements.Line
-
access to the normal to the line
- normalized() - Method in class numerics.Vector3D
-
- normalizeData(double[]) - Method in class imaging.DW_Scheme
-
Normalizes a voxel set of measurements acquired with this
sequence by the geometric mean of the b=0 measurements.
- normalizeData(double[], int[]) - Method in class imaging.DW_Scheme
-
Normalizes a voxel set of measurements acquired with this sequence by the geometric mean
of a specified set of measurements.
- normalizeData(double[], double) - Method in class imaging.DW_Scheme
-
Normalizes a voxel set of measurements acquired with this
sequence.
- normalizeGradDirs(double[][]) - Static method in class imaging.DW_Scheme
-
Returns gradient directions as vectors normalized to unit length if non-zero.
- normalizePoints(double[][]) - Static method in class apps.PointSetToScheme
-
Normalizes points to unit length.
- normC() - Method in class numerics.BinghamDistribution
-
- normF() - Method in class Jama.Matrix
-
Frobenius norm
- normInf() - Method in class Jama.Matrix
-
Infinity norm
- normMoment(int) - Method in class sphfunc.SphericalFunction
-
Computes the normalised order-th moment of the function over
the sphere.
- normMoment(int, double[][]) - Method in class sphfunc.SphericalFunction
-
Computes the normalised order-th moment of the function over
the sphere.
- nullScheme() - Static method in class imaging.DW_Scheme
-
This static method simply returns a default scheme for
various applications that require a scheme object without
actually using it.
- numBasisFunctions() - Method in class sphfunc.LinearBasisSum
-
Returns the number of coeffs (terms in the sum).
- numberOfPDs(int, int, int) - Method in class tractography.TractographyImage
-
- numberOfPoints() - Method in class tractography.Tract
-
- numberOfRegions() - Method in class tractography.FreeFormROI
-
- numberOfRegions() - Method in class tractography.PointListROI
-
- numberOfRegions() - Method in interface tractography.RegionOfInterest
-
- numberOfTracts() - Method in class tractography.TractCollection
-
- NumDeriv - Class in numerics
-
Purpose:
General Levenburg Marquardt Non-linear least squares fitter.
- NumDeriv() - Constructor for class numerics.NumDeriv
-
- numDTs - Variable in enum inverters.InversionIndex
-
Number of diffusion tensors returned by the inversion.
- numDTs - Variable in enum inverters.ModelIndex
-
Number of diffusion tensors returned by the inversion.
- numElements - Static variable in class tools.CL_Initializer
-
number of elements in a voxel
- NumericalIntegration - Class in numerics
-
Camino fibre reconstruction and tracking toolkit
NumericalIntegration (numerics)
Abstract class providing numerical integration on a sphere via the use of
Gaussian Quadrature.
- NumericalIntegration(boolean) - Constructor for class numerics.NumericalIntegration
-
- NumericalIntegration(boolean, int, int) - Constructor for class numerics.NumericalIntegration
-
- NumericalIntegration(boolean, int, int, double) - Constructor for class numerics.NumericalIntegration
-
- numerics - package numerics
-
- numGreatCircleCentralMoment(double[], double) - Method in class sphfunc.SphericalFunction
-
returns the great circle central moment of order pow given a
vector normal to the plane of the great circle
- numGreatCircleIntegral(double[]) - Method in class sphfunc.SphericalFunction
-
returns the great circle integral given a vector
normal to the plane of the great circle
- numGreatCirclePowerIntegral(double[], double) - Method in class sphfunc.SphericalFunction
-
returns the great circle integral of the function
raised to power pow given a vector
normal to the plane of the great circle
- numIndex - Variable in enum inverters.InversionIndex
-
Numerical index for this inversion.
- numIndex - Variable in enum inverters.ModelIndex
-
Numerical index for this inversion.
- numLambdas() - Static method in class sphfunc.MaxEntProfile
-
Returns the number of lambdas defining the profile.
- numMeasurements() - Method in class imaging.DW_Scheme
-
Gets the number of measurements in each voxel.
- numMeasurements() - Method in class imaging.GradientWaveform_Scheme
-
overrides the number of measurements method
- NUMMFRSTATS - Static variable in class apps.SequenceStats
-
The number of statistics in MFR trials.
- numParams - Variable in enum data.compartments.CompartmentType
-
- numParams - Variable in enum models.compartments.CompartmentType
-
- numParams() - Method in class models.ParametricModel
-
- numParams - Variable in enum tractography.PICoPDF
-
Number of parameters for this PDF.
- numPDsIO - Static variable in class tools.CL_Initializer
-
Number of principal directions in the input or output stream.
- numPoints() - Static method in class sphfunc.RBF_Sum
-
Returns the number of functions in the basis.
- NUMSINGLEDTSTATS - Static variable in class apps.SequenceStats
-
The number of statistics in single DT trials.
- numSticks - Variable in class simulation.dynamics.StickyWalker
-
counts the number of times we get stuck to the surface
- NUMTHREETENSORSTATS - Static variable in class apps.SequenceStats
-
The number of statistics in three tensor trials.
- NUMTWOTENSORSTATS - Static variable in class apps.SequenceStats
-
The number of statistics in two tensor trials.
- numVoxels - Static variable in class tools.CL_Initializer
-
The number of voxels to process.
- numZeroMeasurements() - Method in class imaging.DW_Scheme
-
Gets the number of zero (b=0) measurements in each voxel.
- numZeroMeasurements() - Method in class imaging.GradientWaveform_Scheme
-
overrides the number of zeros measurements method to
use local count.