- 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.