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D

D - Static variable in class simulation.DiffusionSimulation
the dimensionality of the simulation.
data - package data
 
data - Variable in class misc.ScalarImage
 
data - Variable in class sphfunc.SphericalPointSet
The data array containing the points is publicly available, it has dimensions [number of points][3] and contains the x y and z coordinates of each point.
data - Static variable in class tools.CL_Initializer
The data source to process.
data.compartments - package data.compartments
 
data_type_string - Variable in class imaging.Nifti1Dataset
 
dataByteOffset - Variable in class imaging.MetaImageHeader
Offset of data in elementDataFile.
dataDims - Static variable in class tools.CL_Initializer
Dimensions of voxel grid
dataFile - Variable in class imaging.MetaImageHeader
data file.
DataModel - Enum in tractography
Data model types: "cylsymmdt", "ballsticks".
DataSource - Interface in data
Purpose: General interface for source of multi-component voxel data, e.g., diffusion-weighted image data.
DataSourceException - Exception in data
Purpose: Exception class used by the DataSource interface.
DataSourceException() - Constructor for exception data.DataSourceException
 
DataSourceException(String) - Constructor for exception data.DataSourceException
 
DataStats - Class in apps
Purpose: Computes simple statistics of data files.
DataStats() - Constructor for class apps.DataStats
 
DataSynthesizer - Class in data
Purpose: Source of synthetic data.
DataSynthesizer(ModelPDF, DW_Scheme, double) - Constructor for class data.DataSynthesizer
Constructor requires the DW_Scheme, the test function and the signal to noise level.
DataSynthesizer(ModelPDF, DW_Scheme, double, int) - Constructor for class data.DataSynthesizer
Constructor includes the number of voxels in the synthetic data source.
DataSynthesizer(ModelPDF, DW_Scheme, double, int, int) - Constructor for class data.DataSynthesizer
Constructor includes the number of voxels in the synthetic data source.
DataSynthesizer(ModelPDF, DW_Scheme, double, int, Random) - Constructor for class data.DataSynthesizer
Constructor includes the number of voxels in the synthetic data source and the actual Random object to use.
DataSynthFromBallStickInput - Class in data
Purpose: Class for synthesizing diffusion weighted data from ball and stick model parameters read from an input stream.
DataSynthFromBallStickInput(String, String, DW_Scheme, double) - Constructor for class data.DataSynthFromBallStickInput
 
DataSynthFromBallStickInput(String, String, DW_Scheme, double, int) - Constructor for class data.DataSynthFromBallStickInput
 
DataSynthFromDT_Input - Class in data
Purpose: Class for synthesizing diffusion weighted data from diffusion tensor parameters read from an input stream.
DataSynthFromDT_Input(String, String, DW_Scheme, double) - Constructor for class data.DataSynthFromDT_Input
The constructor requires the name of the data file and the details of the acquisition sequence to use for data synthesis.
DataSynthFromDT_Input(String, String, DW_Scheme, double, int) - Constructor for class data.DataSynthFromDT_Input
The constructor requires the name of the data file and the details of the acquisition sequence to use for data synthesis.
DataSynthFromInput - Class in data
Purpose: General class for synthesizing diffusion weighted data from model parameters read from an input stream.
DataSynthFromInput() - Constructor for class data.DataSynthFromInput
Default constructor does nothing.
DataSynthFromInput(String, String, DW_Scheme, double) - Constructor for class data.DataSynthFromInput
The constructor requires the name of the data file and the details of the acquisition sequence to use for data synthesis.
DataSynthFromInput(String, String, DW_Scheme, double, int) - Constructor for class data.DataSynthFromInput
This constructor allows the random number generator seed to be specified.
DataSynthFromMultiTensorInput - Class in data
Purpose: Class for synthesizing diffusion weighted data from multi-tensor parameters read from an input stream.
DataSynthFromMultiTensorInput(String, String, DW_Scheme, int, double) - Constructor for class data.DataSynthFromMultiTensorInput
 
DataSynthFromMultiTensorInput(String, String, DW_Scheme, int, double, int) - Constructor for class data.DataSynthFromMultiTensorInput
 
DataSynthFromThreeTensorInput - Class in data
Purpose: Class for synthesizing diffusion weighted data from three-tensor parameters read from an input stream.
DataSynthFromThreeTensorInput(String, String, DW_Scheme, double) - Constructor for class data.DataSynthFromThreeTensorInput
The constructor requires the name of the data file and the details of the acquisition sequence to use for data synthesis.
DataSynthFromThreeTensorInput(String, String, DW_Scheme, double, int) - Constructor for class data.DataSynthFromThreeTensorInput
The constructor requires the name of the data file and the details of the acquisition sequence to use for data synthesis.
DataSynthFromTwoTensorInput - Class in data
Purpose: Class for synthesizing diffusion weighted data from two-tensor parameters read from an input stream.
DataSynthFromTwoTensorInput(String, String, DW_Scheme, double) - Constructor for class data.DataSynthFromTwoTensorInput
The constructor requires the name of the data file and the details of the acquisition sequence to use for data synthesis.
DataSynthFromTwoTensorInput(String, String, DW_Scheme, double, int) - Constructor for class data.DataSynthFromTwoTensorInput
The constructor requires the name of the data file and the details of the acquisition sequence to use for data synthesis.
datatype - Variable in class imaging.AnalyzeHeader
 
dataType - Variable in class imaging.MetaImageHeader
ElementType, ie datatype.
DB - Class in tools
Purpose: Contains printIfVerbose used for debugging.
DB() - Constructor for class tools.DB
Default constructor.
DB(int) - Constructor for class tools.DB
Constructs a DB object given a verbosity level.
DB(int, String) - Constructor for class tools.DB
Constructs a DB object given a verbosity level and filename for output.
db_name - Variable in class imaging.Nifti1Dataset
 
decimalDF - Static variable in class tools.ArrayOps
 
decodeDatatype(short) - Method in class imaging.Nifti1Dataset
Decode the nifti datatype codes
decodeIntent(short) - Method in class imaging.Nifti1Dataset
Decode the nifti intent codes
decodeSliceOrder(short) - Method in class imaging.Nifti1Dataset
Decode the nifti slice order codes
decodeUnits(short) - Method in class imaging.Nifti1Dataset
Decode the nifti unit codes
decodeXform(short) - Method in class imaging.Nifti1Dataset
Decode the nifti xform codes
DeconvToCamenoFormat - Class in apps
Purpose: Converts the output of Donald Tournier's sig2fod program to the format expected in the Cameno suite.
DeconvToCamenoFormat() - Constructor for class apps.DeconvToCamenoFormat
 
depth - Variable in class imaging.AnalyzeHeader
 
derivAt(Point3D) - Method in class misc.ScalarImage
 
descrip - Variable in class imaging.Nifti1Dataset
 
description - Variable in class imaging.AnalyzeHeader
 
det() - Method in class Jama.LUDecomposition
Determinant
det() - Method in class Jama.Matrix
Matrix determinant
det() - Method in class numerics.RealMatrix
Computes the determinant.
determinant() - Method in class misc.DT
Computes the determinant.
dfridr(float, float, float[]) - Method in class numerics.NumDeriv
Computes the derivative at x.
DIFF_CONST - Static variable in class simulation.DiffusionSimulation
the self-diffusion constant of water at room temperature
DIFF_CONST - Static variable in class tools.CL_Initializer
simulation diffusivity
DiffDataFitter - Class in inverters
Purpose: Marquardt fitter especially for fitting models to diffusion data.
DiffDataFitter() - Constructor for class inverters.DiffDataFitter
 
differentiable - Variable in class numerics.SVAnalyticalFunction
 
differentiated() - Method in class numerics.SVAnalyticalFunction
 
differentiated() - Method in class numerics.WatsonD
 
DiffTensorFitter - Class in inverters
Purpose: Non-linear least squares fitter of diffusion tensor to DW-MR data.
DiffTensorFitter() - Constructor for class inverters.DiffTensorFitter
Default constructor.
DiffTensorFitter(double[][], double[], double[], int) - Constructor for class inverters.DiffTensorFitter
The number of unweighted acquisitions that are made (nob0s) is required to estimate the noise levels of each data item.
DiffTensorUnConFitter - Class in inverters
Purpose: Non-linear least squares fitter of diffusion tensor to DW-MR data.
DiffTensorUnConFitter() - Constructor for class inverters.DiffTensorUnConFitter
Default constructor.
DiffTensorUnConFitter(double[][], double[], double[], int) - Constructor for class inverters.DiffTensorUnConFitter
The constructor requires a list of independent values (indepVals, the gradient directions) and associated dependent values (depVals, the data).
DiffusionInversion - Class in inverters
Purpose: General abstract class for inversion techniques for diffusion MRI data.
DiffusionInversion() - Constructor for class inverters.DiffusionInversion
 
DiffusionSimulation - Class in simulation
top level class in diffusion simulation.
DiffusionSimulation(SimulationParams, SimulableScheme) - Constructor for class simulation.DiffusionSimulation
debug file writers
DiffusionSimulation(SimulationParams) - Constructor for class simulation.DiffusionSimulation
 
dim - Variable in class imaging.Nifti1Dataset
 
DIM5 - Variable in class imaging.Nifti1Dataset
 
DIM6 - Variable in class imaging.Nifti1Dataset
 
DIM7 - Variable in class imaging.Nifti1Dataset
 
dim_info - Variable in class imaging.Nifti1Dataset
 
dimension() - Method in class tractography.LookupTable
Dimensionality of the LUT.
dimSize - Variable in class imaging.MetaImageHeader
Number of voxels in each dimension.
directional() - Method in class tractography.TargetCP_Image
 
dirStatsWithRotations(double[][], int, int, double) - Static method in class apps.SequenceStats
Computes the mean, standard deviation, maximum and minimum of the angle between directions and the closest matching principal direction of the test function.
displace(Vector3D) - Method in class numerics.Point3D
 
distance(Point3D) - Method in class numerics.Point3D
 
DISTRIBUTED - Static variable in class simulation.geometry.substrates.ParallelCylinderSubstrate
 
DistributedRadiusCylinderSubstrate - Class in simulation.geometry.substrates
implements a class of substrate whereby the radii of cylinders are drawn from a specified distribution.
DistributedRadiusCylinderSubstrate(SimulationParams) - Constructor for class simulation.geometry.substrates.DistributedRadiusCylinderSubstrate
constructor.
divide(Complex) - Method in class numerics.Complex
Complex division.
doNumIntTests - Static variable in class mesd.MESD_Inversion
Specifies whether to do the numerical integration tests and increase point set sizes automatically or whether to just stick with the result from the base point set.
Dot - Class in data.compartments
Implements the compartment interface for an isotropic restricted compartment, Spherical boundary compartment with zero radius.
Dot() - Constructor for class data.compartments.Dot
constructor needs array of params.
Dot - Class in models.compartments
Implements the compartment interface for an isotropic restricted compartment, Spherical boundary compartment with zero radius.
Dot() - Constructor for class models.compartments.Dot
constructor needs array of params.
dot(Vector3D) - Method in class numerics.Vector3D
Gives scalar (dot) product of this with another vector.
DOUBLE - Static variable in class data.ExternalDataSource
 
dPhi - Variable in class simulation.dynamics.Walker
space to stop phase shifts in each scan direction
drawCrossSection(BufferedWriter) - Method in class simulation.geometry.elements.SquashyCylinder
outputs coords around the circumference of the cross-section (chords not included).
drawCrossSection() - Method in class simulation.geometry.substrates.DistributedRadiusCylinderSubstrate
writes the cross sections of each cylinder to a file
drawCrossSection() - Method in class simulation.geometry.substrates.SquashyInflammationSubstrate
writes the cross sections of each cylinder to a file.
drawGraph() - Method in class tractography.Graph
 
ds_is_nii - Variable in class imaging.Nifti1Dataset
 
DT - Class in misc
Purpose: Encapsulates a diffusion tensor.
DT(double, double, double, double, double, double) - Constructor for class misc.DT
Constructor requires the six components.
DT(double[]) - Constructor for class misc.DT
Constructor from an array containing the six components.
dt - Variable in class simulation.DiffusionSimulation
time increment associated with a timestep
DT1_E1 - Static variable in class apps.SphFuncPICoCalibrationData
 
DT1_E1_PHI - Static variable in class apps.SphFuncPICoCalibrationData
 
DT1_E1_THETA - Static variable in class apps.SphFuncPICoCalibrationData
 
DT1_E2 - Static variable in class apps.SphFuncPICoCalibrationData
 
DT1_E2_PHI - Static variable in class apps.SphFuncPICoCalibrationData
 
DT1_E2_THETA - Static variable in class apps.SphFuncPICoCalibrationData
 
DT1_E3 - Static variable in class apps.SphFuncPICoCalibrationData
 
DT1_E3_PHI - Static variable in class apps.SphFuncPICoCalibrationData
 
DT1_E3_THETA - Static variable in class apps.SphFuncPICoCalibrationData
 
DT2_E1 - Static variable in class apps.SphFuncPICoCalibrationData
 
DT2_E1_PHI - Static variable in class apps.SphFuncPICoCalibrationData
 
DT2_E1_THETA - Static variable in class apps.SphFuncPICoCalibrationData
 
DT2_E2 - Static variable in class apps.SphFuncPICoCalibrationData
 
DT2_E2_PHI - Static variable in class apps.SphFuncPICoCalibrationData
 
DT2_E2_THETA - Static variable in class apps.SphFuncPICoCalibrationData
 
DT2_E3 - Static variable in class apps.SphFuncPICoCalibrationData
 
DT2_E3_PHI - Static variable in class apps.SphFuncPICoCalibrationData
 
DT2_E3_THETA - Static variable in class apps.SphFuncPICoCalibrationData
 
dt2mix - Static variable in class tools.CL_Initializer
Specifies the mixing parameter for StandardTestFunctions.dt2.
dt2rotangle - Static variable in class tools.CL_Initializer
Specifies the angle of rotation for StandardTestFunctions.dt2.
DT_ALL - Static variable in class imaging.AnalyzeHeader
 
DT_ALL - Static variable in class imaging.Nifti1Dataset
 
DT_BINARY - Static variable in class imaging.AnalyzeHeader
 
DT_BINARY - Static variable in class imaging.Nifti1Dataset
 
DT_COMPLEX - Static variable in class imaging.AnalyzeHeader
 
DT_DOUBLE - Static variable in class imaging.AnalyzeHeader
 
DT_EigenSystem - Class in apps
Purpose: Computes the eigensystem of each diffusion tensor.
DT_EigenSystem(String[]) - Constructor for class apps.DT_EigenSystem
Output manager
DT_FitMatrix - Class in apps
Purpose: Creates a matrix for fitting the diffusion tensor via a linear transform.
DT_FitMatrix(String[]) - Constructor for class apps.DT_FitMatrix
 
DT_FLOAT - Static variable in class imaging.AnalyzeHeader
 
DT_Inversion - Class in inverters
Purpose: Fits the diffusion tensor.
DT_Inversion() - Constructor for class inverters.DT_Inversion
 
DT_LinearInterpolator - Class in tractography
Provides interpolated measurements of the diffusion tensor at any point within the dataset.
DT_LinearInterpolator(DT_TractographyImage) - Constructor for class tractography.DT_LinearInterpolator
Construct an interpolator.
DT_LookupTableGenerator - Class in tractography
Fits some distribution to samples of tensors with added noise.
DT_NONE - Static variable in class imaging.AnalyzeHeader
 
DT_NONE - Static variable in class imaging.Nifti1Dataset
 
DT_RGB - Static variable in class imaging.AnalyzeHeader
 
DT_ShapeStatistics - Class in apps
Computes indices of tensor shape.
DT_ShapeStatistics(String[]) - Constructor for class apps.DT_ShapeStatistics
 
DT_SIGNED_CHAR - Static variable in class imaging.AnalyzeHeader
8-bit signed char, equivalent to Java byte.
DT_SIGNED_INT - Static variable in class imaging.AnalyzeHeader
 
DT_SIGNED_SHORT - Static variable in class imaging.AnalyzeHeader
16-bit signed integer (-32768-32767).
DT_ToCamino - Class in apps
Converts a NIFTI, ITK or Analyze tensor volume to Camino format.
DT_ToCamino(String[]) - Constructor for class apps.DT_ToCamino
 
DT_ToNii - Class in apps
Converts Camino dts to Nifti format.
DT_ToNii(String[]) - Constructor for class apps.DT_ToNii
 
DT_TractographyImage - Class in tractography
Defines image for tractography from tensor data.
DT_TractographyImage(DT[][][][], double[][][][], int[][][], int[], double[]) - Constructor for class tractography.DT_TractographyImage
Constructs an image directly from an array of DTs and an array of mixing parameters.
DT_TractographyImage(VoxelOrderDataSource, int, int[], double[]) - Constructor for class tractography.DT_TractographyImage
Constructs an image from the data sources.
DT_UNKNOWN - Static variable in class imaging.AnalyzeHeader
 
DT_UNSIGNED_CHAR - Static variable in class imaging.AnalyzeHeader
8-bit unsigned char (0-255) datatype.
DT_UNSIGNED_INT - Static variable in class imaging.AnalyzeHeader
32-bit unsigned int datatype.
DT_UNSIGNED_SHORT - Static variable in class imaging.AnalyzeHeader
16-bit unsigned short datatype.
duration - Static variable in class simulation.SimulationParams
duration of simulation in seconds
DW_Scheme - Class in imaging
Top level class for diffusion-weighted imaging schemes.
dyadic(double[]) - Static method in class apps.InversionStats
Computes the dyadic of a direction.
DynamicScalarImage - Class in misc
Scalar image that allows computation of the mean, min, and max values in each voxel.
DynamicScalarImage(int[], double[]) - Constructor for class misc.DynamicScalarImage
Construct an image, default interpolation is nearest neighbour.
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