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N

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.
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