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Package Hierarchies:
apps
,
data
,
data.compartments
,
fitters
,
imaging
,
inverters
,
Jama
,
Jama.examples
,
Jama.test
,
Jama.util
,
mesd
,
misc
,
models
,
models.compartments
,
numerics
,
optimizers
,
simulation
,
simulation.dynamics
,
simulation.geometry
,
simulation.geometry.elements
,
simulation.geometry.substrates
,
simulation.measurement
,
sphfunc
,
tools
,
tractography
Class Hierarchy
java.lang.Object
numerics.
ACG_Distribution
(implements numerics.
AxialDistribution
)
simulation.measurement.
AgnosticScan
(implements simulation.measurement.
SyntheticScan
)
tools.
ArrayOps
data.
BallStick
(implements data.
ModelPDF
)
simulation.geometry.elements.
BasicCylinder
(implements simulation.geometry.elements.
Cylinder
, simulation.geometry.elements.
SubstrateObject
)
simulation.geometry.elements.
SquashyCylinder
sphfunc.
BasisSumFactory
tractography.
BayesDiracRandomizer
tractography.
BayesDiracBallStickRandomizer
tractography.
BayesDiracCylSymmTensorRandomizer
numerics.
BesselFunctions
numerics.
BinghamDistribution
(implements numerics.
AxialDistribution
)
data.
BootstrapDataSynthesizer
(implements data.
DataSource
)
data.
BootstrapDataSynthFromInput
(implements data.
DataSource
)
data.
BootstrapDataSynthFromSimulationInput
(implements data.
DataSource
)
simulation.geometry.elements.
BoundingBox
Jama.
CholeskyDecomposition
(implements java.io.Serializable)
tools.
CL_Initializer
fitters.
Codec
apps.
CombineTwoFibreLUTs
data.compartments.
CompartmentFactory
models.compartments.
CompartmentFactory
numerics.
Complex
(implements java.lang.Cloneable)
java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
java.awt.Container
javax.swing.JComponent (implements java.io.Serializable)
javax.swing.JPanel (implements javax.accessibility.Accessible)
apps.
F_TestThresholdSelector
apps.
PD_OrientationViewer
apps.
BallSticksOrientationViewer
apps.
CompartmentModelOrientationViewer
apps.
PICoPDF_OrientationViewer
apps.
SphFuncPeaksOrientationViewer
apps.
TensorOrientationViewer
optimizers.
ConjGradMinimizer
optimizers.
ConjGradMinimizerTest
numerics.
TwoFibreACGFitter
numerics.
TwoFibreBinghamFitter
tractography.
ConnectionProbabilityImage
apps.
ConnectivityMapping
tractography.
ConnectivitySegmentedImage
apps.
CountSeeds
tractography.
CP_StatMap
tractography.
MaxCP
tractography.
MeanCP
tractography.
MedianCP
tractography.
MinCP
tractography.
SumCP
apps.
CP_Stats
simulation.geometry.elements.
CylinderFactory
data.
CylinderModel
(implements data.
ModelPDF
)
simulation.dynamics.
CylindricalSurfaceStepGenerator
(implements simulation.dynamics.
StepGenerator
)
apps.
DataStats
data.
DataSynthesizer
(implements data.
DataSource
)
data.
DataSynthFromInput
(implements data.
DataSource
)
data.
DataSynthFromBallStickInput
data.
DataSynthFromDT_Input
data.
DataSynthFromMultiTensorInput
data.
DataSynthFromThreeTensorInput
data.
DataSynthFromTwoTensorInput
tools.
DB
apps.
DeconvToCamenoFormat
inverters.
DiffusionInversion
inverters.
BallStickInversion
inverters.
DT_Inversion
inverters.
LinearDT_Inversion
inverters.
NonLinearDT_Inversion
inverters.
RestoreDT_Inversion
inverters.
WeightedLinearDT_Inversion
inverters.
LinearADC_Inversion
inverters.
LinearInversion
mesd.
MESD_Inversion
inverters.
MultiTensorInversion
inverters.
ThreeTensorInversion
inverters.
TwoTensorInversion
simulation.
DiffusionSimulation
(implements data.
DataSource
)
misc.
DT
(implements java.lang.Cloneable)
tractography.
DT_LookupTableGenerator
tractography.
OneTensorLUTGenerator
tractography.
TwoTensorLUTGenerator
imaging.
DW_Scheme
imaging.
B_VectorScheme
imaging.
GradientWaveform_Scheme
(implements imaging.
SimulableScheme
)
imaging.
StejskalTannerScheme
(implements imaging.
SimulableScheme
)
imaging.
RectGradSteTanScheme
imaging.
TRSE_Scheme
(implements imaging.
SimulableScheme
)
imaging.
RectGradTRSE_Scheme
(implements imaging.
SimulableScheme
)
misc.
DynamicScalarImage
(implements misc.
VoxelwiseStatisticalImage
)
tractography.
Edge
numerics.
EigenSystem3D
Jama.
EigenvalueDecomposition
(implements java.io.Serializable)
tractography.
EightNeighbourInterpolator
tractography.
DT_LinearInterpolator
(implements tractography.
ImageInterpolator
)
tractography.
NeighbourChoiceInterpolator
(implements tractography.
ImageInterpolator
, tractography.
ProbabilisticInterpolator
)
tractography.
VectorLinearInterpolator
(implements tractography.
ImageInterpolator
)
simulation.dynamics.
ElasticReflector
(implements simulation.dynamics.
StepAmender
)
simulation.dynamics.
StickAndDiffuse
tools.
EndianNeutralDataInputStream
(implements java.io.DataInput)
apps.
EntryPoint
numerics.
ErrorFunction
inverters.
EvenSphHarmFitter
inverters.
EvenSphHarmSignalFitter
apps.
Executable
apps.
AddNoise
apps.
BinaryToText
apps.
ChunkStats
apps.
DT_EigenSystem
apps.
DT_FitMatrix
apps.
DT_ShapeStatistics
apps.
DT_ToCamino
apps.
DT_ToNii
apps.
ElectrostaticSubsets
apps.
EstimateSNR
apps.
FanningGrid
apps.
FracAnis
apps.
FSL_ToScheme
apps.
GenerateDTLUT
apps.
ImageToVoxel
apps.
InversionStats
apps.
MultiFibreReconStats
apps.
ConsistencyFraction
apps.
MeanDiff
apps.
ModelFit
apps.
ClassifiedModelFit
apps.
LinearRecon
apps.
OrderElectrostaticPoints
apps.
OrientationBiasMap
apps.
PICoPDFs
apps.
PointSetToScheme
apps.
ProcessStreamlines
apps.
QBallMX
apps.
ScannerToVoxel
apps.
Shredder
apps.
SphFuncAnisotropy
apps.
SphFuncBitMap
apps.
SphFuncKurtosis
apps.
SphFuncPD_Stats
apps.
SphFuncSkewness
apps.
SphHarmFitter
apps.
SphPDF_Fit
apps.
Split4D_NiiImage
apps.
StreamlineTractography
apps.
SubsetScheme
apps.
SyntheticData
apps.
TraceD
apps.
VoxelClassify
apps.
VoxelToScanner
data.
ExternalDataSource
(implements data.
DataSource
)
data.
ScannerOrderDataSource
data.
ScannerOrderScaledDataSource
data.
VoxelOrderDataSource
data.
VoxelOrderDW_DataSource
data.
VoxelOrderScaledDataSource
simulation.geometry.elements.
FacetCylinder
(implements simulation.geometry.elements.
Cylinder
, simulation.geometry.elements.
SubstrateObject
)
tractography.
FibreTracker
tractography.
EulerFibreTracker
tractography.
LinIntDTEulerFibreTracker
tractography.
LinIntVectorEulerFibreTracker
tractography.
NC_ProbFibreTracker
tractography.
NonInterpolatedFibreTracker
tractography.
FACT_TendFibreTracker
tractography.
NonIntProbFibreTracker
tractography.
RK4FibreTracker
tractography.
LinIntVectorRK4FibreTracker
tools.
FileInput
tools.
FileOutput
fitters.
Fitter
fitters.
BallAndStickLM_GaussianFitter
fitters.
BallAndStickLM_OffGaussFitter
fitters.
BallAndStickLM_RicianFitter
fitters.
BallAndStickMultiRunLM_GaussianFitter
fitters.
CompartmentFitter
fitters.
BallCylinderAstrocylindersLM_Fitter
fitters.
BallCylinderAstrocylindersMultiRunLM_Fitter
fitters.
BallCylinderAstrosticksLM_Fitter
fitters.
BallCylinderAstrosticksMultiRunLM_Fitter
fitters.
BallCylinderDotLM_Fitter
fitters.
BallCylinderDotMultiRunLM_Fitter
fitters.
BallCylinderLM_Fitter
fitters.
BallCylinderMultiRunLM_Fitter
fitters.
BallCylinderSphereLM_Fitter
fitters.
BallCylinderSphereMultiRunLM_Fitter
fitters.
BallGDRCylindersAstrocylindersLM_Fitter
fitters.
BallGDRCylindersAstrocylindersMultiRunLM_Fitter
fitters.
BallGDRCylindersAstrosticksLM_Fitter
fitters.
BallGDRCylindersAstrosticksMultiRunLM_Fitter
fitters.
BallGDRCylindersDotLM_Fitter
fitters.
BallGDRCylindersDotMultiRunLM_Fitter
fitters.
BallGDRCylindersLM_Fitter
fitters.
BallGDRCylindersMultiRunLM_Fitter
fitters.
BallGDRCylindersSphereLM_Fitter
fitters.
BallGDRCylindersSphereMultiRunLM_Fitter
fitters.
BallStickAstrocylindersLM_Fitter
fitters.
BallStickAstrocylindersMultiRunLM_Fitter
fitters.
BallStickAstrosticksLM_Fitter
fitters.
BallStickAstrosticksMultiRunLM_Fitter
fitters.
BallStickDotLM_Fitter
fitters.
BallStickDotMultiRunLM_Fitter
fitters.
BallStickLM_Fitter
fitters.
BallStickMultiRunLM_Fitter
fitters.
BallStickLM_GaussianFitter
fitters.
BallStickMultiRunLM_GaussianFitter
fitters.
BallStickSphereLM_Fitter
fitters.
BallStickSphereMultiRunLM_Fitter
fitters.
BiexponLM_GaussianFitter
fitters.
BiexponMultiRunLM_GaussianFitter
fitters.
BiZeppelinLM_Fitter
fitters.
BiZeppelinMultiRunLM_Fitter
fitters.
MCMC_Fitter
fitters.
BallStickMCMC_Fitter
fitters.
MMWMD_BasicMCMC_Fitter
fitters.
MMWMD_FixedMCMC_Fitter
fitters.
MMWMD_InVivoMCMC_Fitter
fitters.
ZeppelinCylinderDotMCMC_GaussianFitter
fitters.
MMWMD_BasicLM_DirectFitter
fitters.
MMWMD_BasicMultiRunLM_DirectFitter
fitters.
MMWMD_FixedLM_DirectFitter
fitters.
MMWMD_FixedMultiRunLM_DirectFitter
fitters.
MMWMD_InVivoLM_DirectFitter
fitters.
MMWMD_InVivoMultiRunLM_DirectFitter
fitters.
MMWMD_InVivoLM_GaussianFitter
fitters.
TensorCylinderAstrocylindersLM_Fitter
fitters.
TensorCylinderAstrocylindersMultiRunLM_Fitter
fitters.
TensorCylinderAstrosticksLM_Fitter
fitters.
TensorCylinderAstrosticksMultiRunLM_Fitter
fitters.
TensorCylinderDotLM_Fitter
fitters.
TensorCylinderDotMultiRunLM_Fitter
fitters.
TensorCylinderLM_Fitter
fitters.
TensorCylinderMultiRunLM_Fitter
fitters.
TensorCylinderSphereLM_Fitter
fitters.
TensorCylinderSphereMultiRunLM_Fitter
fitters.
TensorGDRCylindersAstrocylindersLM_Fitter
fitters.
TensorGDRCylindersAstrocylindersMultiRunLM_Fitter
fitters.
TensorGDRCylindersAstrosticksLM_Fitter
fitters.
TensorGDRCylindersAstrosticksMultiRunLM_Fitter
fitters.
TensorGDRCylindersDotLM_Fitter
fitters.
TensorGDRCylindersDotMultiRunLM_Fitter
fitters.
TensorGDRCylindersLM_Fitter
fitters.
TensorGDRCylindersMultiRunLM_Fitter
fitters.
TensorGDRCylindersSphereLM_Fitter
fitters.
TensorGDRCylindersSphereMultiRunLM_Fitter
fitters.
TensorStickAstrocylindersLM_Fitter
fitters.
TensorStickAstrocylindersMultiRunLM_Fitter
fitters.
TensorStickAstrosticksLM_Fitter
fitters.
TensorStickAstrosticksMultiRunLM_Fitter
fitters.
TensorStickDotLM_Fitter
fitters.
TensorStickDotMultiRunLM_Fitter
fitters.
TensorStickLM_Fitter
fitters.
TensorStickMultiRunLM_Fitter
fitters.
TensorStickSphereLM_Fitter
fitters.
TensorStickSphereMultiRunLM_Fitter
fitters.
ZeppelinCylinderAstrocylindersLM_Fitter
fitters.
ZeppelinCylinderAstrocylindersMultiRunLM_Fitter
fitters.
ZeppelinCylinderAstrosticksLM_Fitter
fitters.
ZeppelinCylinderAstrosticksMultiRunLM_Fitter
fitters.
ZeppelinCylinderDotCSF_LM_DirectFitter
fitters.
ZeppelinCylinderDotCSF_MultiRunLM_DirectFitter
fitters.
ZeppelinCylinderDotLM_DirectFitter
fitters.
ZeppelinCylinderDotMultiRunLM_DirectFitter
fitters.
ZeppelinCylinderDotLM_Fitter
fitters.
ZeppelinCylinderDotMultiRunLM_Fitter
fitters.
ZeppelinCylinderDotLM_GaussianFitter
fitters.
ZeppelinCylinderDotMultiRunLM_GaussianFitter
fitters.
ZeppelinCylinderLM_DirectFitter
fitters.
ZeppelinCylinderMultiRunLM_DirectFitter
fitters.
ZeppelinCylinderLM_Fitter
fitters.
ZeppelinCylinderMultiRunLM_Fitter
fitters.
ZeppelinCylinderLM_GaussianFitter
fitters.
ZeppelinCylinderMultiRunLM_GaussianFitter
fitters.
ZeppelinCylinderSphereLM_Fitter
fitters.
ZeppelinCylinderSphereMultiRunLM_Fitter
fitters.
ZeppelinCylinderSphereMultiRunLM_GaussianFitter
fitters.
ZeppelinCylinderTortLM_Fitter
fitters.
ZeppelinCylinderTortMultiRunLM_Fitter
fitters.
ZeppelinGDRCylindersAstrocylindersLM_Fitter
fitters.
ZeppelinGDRCylindersAstrocylindersMultiRunLM_Fitter
fitters.
ZeppelinGDRCylindersAstrosticksLM_Fitter
fitters.
ZeppelinGDRCylindersAstrosticksMultiRunLM_Fitter
fitters.
ZeppelinGDRCylindersAstrosticksLM_GaussianFitter
fitters.
ZeppelinGDRCylindersAstrosticksMultiRunLM_GaussianFitter
fitters.
ZeppelinGDRCylindersDotLM_Fitter
fitters.
ZeppelinGDRCylindersDotMultiRunLM_Fitter
fitters.
ZeppelinGDRCylindersDotLM_GaussianFitter
fitters.
ZeppelinGDRCylindersDotMultiRunLM_GaussianFitter
fitters.
ZeppelinGDRCylindersLM_Fitter
fitters.
ZeppelinGDRCylindersMultiRunLM_Fitter
fitters.
ZeppelinGDRCylindersLM_GaussianFitter
fitters.
ZeppelinGDRCylindersMultiRunLM_GaussianFitter
fitters.
ZeppelinGDRCylindersSphereLM_Fitter
fitters.
ZeppelinGDRCylindersSphereMultiRunLM_Fitter
fitters.
ZeppelinGDRCylindersSphereLM_GaussianFitter
fitters.
ZeppelinGDRCylindersSphereMultiRunLM_GaussianFitter
fitters.
ZeppelinStickAstrocylindersLM_Fitter
fitters.
ZeppelinStickAstrocylindersMultiRunLM_Fitter
fitters.
ZeppelinStickAstrocylindersLM_GaussianFitter
fitters.
ZeppelinStickAstrocylindersMultiRunLM_GaussianFitter
fitters.
ZeppelinStickAstrosticksLM_Fitter
fitters.
ZeppelinStickAstrosticksMultiRunLM_Fitter
fitters.
ZeppelinStickAstrosticksLM_GaussianFitter
fitters.
ZeppelinStickAstrosticksMultiRunLM_GaussianFitter
fitters.
ZeppelinStickDotLM_Fitter
fitters.
ZeppelinStickDotMultiRunLM_Fitter
fitters.
ZeppelinStickDotLM_GaussianFitter
fitters.
ZeppelinStickDotMultiRunLM_GaussianFitter
fitters.
ZeppelinStickLM_DirectFitter
fitters.
ZeppelinStickMultiRunLM_DirectFitter
fitters.
ZeppelinStickLM_Fitter
fitters.
ZeppelinStickMultiRunLM_Fitter
fitters.
ZeppelinStickLM_GaussianFitter
fitters.
ZeppelinStickMultiRunLM_GaussianFitter
fitters.
ZeppelinStickSphereLM_Fitter
fitters.
ZeppelinStickSphereMultiRunLM_Fitter
fitters.
ZeppelinStickSphereLM_GaussianFitter
fitters.
ZeppelinStickSphereMultiRunLM_GaussianFitter
fitters.
ZeppelinStickTortLM_Fitter
fitters.
ZeppelinStickTortMultiRunLM_Fitter
simulation.dynamics.
FixedLengthStepGenerator
(implements simulation.dynamics.
StepGenerator
)
tractography.
FreeFormROI
(implements tractography.
RegionOfInterest
)
numerics.
GammaFunctions
numerics.
GammaRandom
apps.
GatherStats
data.
GaussianMixture
(implements data.
ModelPDF
)
apps.
GenerateMFR_LUT
tractography.
Graph
tractography.
HistBin
tractography.
Histogram
imaging.
ImageHeader
imaging.
AnalyzeHeader
imaging.
MetaImageHeader
imaging.
Nifti1Dataset
apps.
ImportSH_Coeffs
numerics.
IncompleteBeta
java.io.InputStream (implements java.io.Closeable)
java.io.FilterInputStream
tools.
BufferedInflaterInputStream
java.io.DataInputStream (implements java.io.DataInput)
imaging.
EndianCorrectInputStream
tools.
LEFilterInputStream
(implements java.io.DataInput)
sphfunc.
ISCodes
tools.
KeyboardInput
simulation.geometry.elements.
Line
tractography.
LookupTable
Jama.
LUDecomposition
(implements java.io.Serializable)
Jama.examples.
MagicSquareExample
optimizers.
MarkovChainMonteCarlo
optimizers.
MCMC_Minimizer
(implements optimizers.
Minimizer
)
optimizers.
MCMC_GaussianMinimizer
optimizers.
MCMC_OffGaussMinimizer
optimizers.
MCMC_RicianMinimizer
optimizers.
MCMCMinimiserTest
optimizers.
MarquardtMinimiser
optimizers.
LM_Minimizer
(implements optimizers.
Minimizer
)
optimizers.
LM_GaussianMinimizer
optimizers.
LM_OffGaussMinimizer
optimizers.
LM_RicianMinimizer
optimizers.
MarquardtChiSqFitter
inverters.
BallStickFitter
inverters.
DiffDataFitter
inverters.
TensorModelFitter
inverters.
DiffTensorFitter
inverters.
DiffTensorUnConFitter
inverters.
ThreeTensorFitter
inverters.
ThreeTensorCholFitter
inverters.
ThreeTensorCholFixMP_Fitter
inverters.
ThreeTensorOneAxiSymFitter
inverters.
ThreeTensorOneAxiSymFixMP_Fitter
inverters.
ThreeTensorTwoAxiSymFitter
inverters.
ThreeTensorAxiSymFitter
inverters.
ThreeTensorAxiSymFixMP_Fitter
inverters.
ThreeTensorTwoAxiSymFixMP_Fitter
inverters.
TwoTensorFitter
inverters.
TwoTensorCholFitter
inverters.
TwoTensorCholFixMP_Fitter
inverters.
TwoTensorOneAxiSymFitter
inverters.
TwoTensorAxiSymFitter
inverters.
TwoTensorAxiSymFixMP_Fitter
inverters.
TwoTensorOneAxiSymFixMP_Fitter
mesd.
MESD_Fitter
optimizers.
MarquardtMinimiserTest
numerics.
TwoFibreFixedPropWatsonFitter
numerics.
TwoFibreBipolarWatsonFitter
numerics.
TwoFibreWatsonFitter
Jama.util.
Maths
data.
MatlabArrayDataSource
(implements data.
DataSource
)
Jama.
Matrix
(implements java.lang.Cloneable, java.io.Serializable)
apps.
MESD
optimizers.
MultiRunMinimizer
(implements optimizers.
Minimizer
)
optimizers.
MultiRunLM_Minimizer
optimizers.
MultiRunLM_GaussianMinimizer
optimizers.
MultiRunLM_OffGaussMinimizer
optimizers.
MultiRunLM_RicianMinimizer
simulation.geometry.elements.
MyelinatedCylinder
(implements simulation.geometry.elements.
Cylinder
, simulation.geometry.elements.
SubstrateObject
)
numerics.
NewtonRaphsonSolver
numerics.
NumDeriv
numerics.
NumericalIntegration
data.
OutputManager
java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
java.io.FilterOutputStream
java.io.DataOutputStream (implements java.io.DataOutput)
imaging.
EndianCorrectOutputStream
tools.
LEFilterOutputStream
(implements java.io.DataOutput)
models.
ParametricModel
data.compartments.
Astrocylinders
models.compartments.
Astrocylinders
data.compartments.
Astrosticks
models.compartments.
Astrosticks
data.compartments.
Ball
models.compartments.
Ball
models.
BallAndStickModel
data.compartments.
CompartmentModel
(implements data.
DataSource
)
models.compartments.
CompartmentModel
(implements data.
DataSource
)
data.compartments.
CylinderGPD
models.compartments.
CylinderGPD
data.compartments.
Dot
models.compartments.
Dot
data.compartments.
ListDistributionCompartment
data.compartments.
GammaDistribRadiiCylinders
models.compartments.
ListDistributionCompartment
models.compartments.
GDRCylinders
data.compartments.
SphereGPD
models.compartments.
SphereGPD
data.compartments.
Stick
models.compartments.
Stick
data.compartments.
Tensor
models.compartments.
Tensor
data.compartments.
Zeppelin
models.compartments.
Zeppelin
sphfunc.
PD
sphfunc.
PDList
fitters.
Perturbation
fitters.
FixedSTD_GaussianPerturbation
tractography.
PICoBootstrapRandomizer
(implements tractography.
PICoRandomizer
)
simulation.geometry.
PLYreader
numerics.
Point3D
tractography.
PointListROI
(implements tractography.
RegionOfInterest
)
numerics.
PolynomialFunction
numerics.
PolynomialFunction1D
numerics.
PolynomialFunction2D
optimizers.
PowellMinimiser
fitters.
Prior
Jama.
QRDecomposition
(implements java.io.Serializable)
simulation.geometry.elements.
Quad
java.util.Random (implements java.io.Serializable)
numerics.
MTRandom
numerics.
RealMatrix
(implements java.lang.Cloneable, java.io.Serializable)
apps.
Reorient
apps.
RGB_ScalarImage
numerics.
Rotations
misc.
ScalarImage
simulation.measurement.
ScanFactory
apps.
SchemeToFSL
apps.
SequenceStats
tractography.
SimplePICoRandomizer
(implements tractography.
PICoRandomizer
)
tractography.
PICoACGRandomizer
tractography.
PICoBinghamRandomizer
tractography.
PICoWatsonRandomizer
optimizers.
SimulatedAnnealingOptimizer
misc.
OrderedAcqMinimizer
misc.
OrderedAcqSingleSubsetMinimizer
misc.
OrderedAcqSubsetMinimizer
misc.
OrderedAcqWeightedMinimizer
simulation.
SimulationParams
Jama.
SingularValueDecomposition
(implements java.io.Serializable)
misc.
SparseVectorImage
(implements misc.
VoxelwiseStatisticalImage
)
simulation.dynamics.
SpatiallyVaryingStepGenerator
(implements simulation.dynamics.
StepGenerator
)
mesd.
SphDeconvKernels
numerics.
SphericalDistributionFitter
numerics.
ACG_Fitter
numerics.
BinghamFitter
numerics.
WatsonFitter
sphfunc.
SphericalFunction
sphfunc.
LinearBasisFunction
sphfunc.
RealSH
sphfunc.
ImagSH
sphfunc.
TuchRBF
sphfunc.
LinearBasisSum
sphfunc.
EvenSHS
sphfunc.
RBF_Sum
sphfunc.
TuchRBF_Sum
sphfunc.
MaxEntProfile
numerics.
SphericalHarmonics
misc.
SphericalPoints
sphfunc.
SphericalPointSet
apps.
SphFuncPICoCalibrationData
simulation.geometry.elements.
SquashyCylinder.Chord
data.
StandardTestFunctions
simulation.measurement.
StatisticsModule
simulation.measurement.
MSdispStatsModule
simulation.measurement.
StickyStatsModule
simulation.measurement.
StatisticsModuleFactory
simulation.dynamics.
StepAmenderFactory
simulation.dynamics.
StepGeneratorFactory
tractography.
StreamlineROI_Filter
simulation.geometry.substrates.
Substrate
simulation.geometry.substrates.
CellularLattice
simulation.geometry.substrates.
PercCellularLattice
simulation.geometry.substrates.
StripedCellularLattice
simulation.geometry.substrates.
CylinderSubstrate
simulation.geometry.substrates.
CrossingCylinderSubstrate
simulation.geometry.substrates.
DistributedRadiusCylinderSubstrate
simulation.geometry.substrates.
ParallelCylinderSubstrate
simulation.geometry.substrates.
StickyCylinderSubstrate
simulation.geometry.substrates.
SquashyInflammationSubstrate
simulation.geometry.substrates.
PercolationSubstrate
simulation.geometry.substrates.
EmptySubstrate
simulation.geometry.substrates.
MeshSubstrate
simulation.geometry.substrates.
SubstrateFactory
numerics.
SVAnalyticalFunction
numerics.
WatsonD
data.
SyntheticBootstrapper
(implements data.
DataSource
)
tractography.
TargetCP_Image
apps.
TargetProbsToASCII
tractography.
TendInterpolator
(implements tractography.
ImageInterpolator
)
Jama.test.
TestMatrix
apps.
ThresholdB0
java.lang.Throwable (implements java.io.Serializable)
java.lang.Exception
numerics.
ComplexNumberException
optimizers.
ConjGradMinimizerException
numerics.
ConvergenceException
numerics.
ErrorFunctionException
numerics.
IncompleteBetaException
sphfunc.
ISCodesException
optimizers.
MinimizerException
optimizers.
MarkovChainMonteCarloException
optimizers.
MarquardtMinimiserException
optimizers.
MarquardtMinimiserNonConvergenceException
tractography.
OutsideLUTRangeException
optimizers.
PowellMinimiserException
java.lang.RuntimeException
misc.
LoggedException
data.
DataSourceException
numerics.
SphericalHarmonicException
numerics.
SVD_Exception
tractography.
Tract
tractography.
TractCollection
apps.
TractCounter
tractography.
TractographyImage
tractography.
BayesDiracTractographyImage
tractography.
BootstrapTractographyImage
tractography.
BS_DT_TractographyImage
tractography.
RepBS_DT_TractographyImage
tractography.
WildBS_DT_TractographyImage
tractography.
PD_TractographyImage
tractography.
BallStickTractographyImage
tractography.
DT_TractographyImage
tractography.
PICoTractographyImage
apps.
TractShredder
tractography.
TractSource
tractography.
TractStatisticFilter
tractography.
TractStatisticImage
apps.
TractStatistics
simulation.geometry.elements.
Triangle
(implements simulation.geometry.elements.
SubstrateObject
)
numerics.
Vector3D
tractography.
Voxel
(implements java.lang.Comparable<T>)
tractography.
VoxelList
apps.
VoxelMean
apps.
VTK_Streamlines
simulation.dynamics.
Walker
simulation.dynamics.
StickyWalker
simulation.dynamics.
WalkerFactory
numerics.
WatsonDistribution
(implements numerics.
AxialDistribution
)
data.
WildBootstrapDataSynth
(implements data.
DataSource
)
data.
WildBS_DT_DataSynth
apps.
WriteZeros
Interface Hierarchy
numerics.
AxialDistribution
data.
DataSource
tractography.
ImageInterpolator
tractography.
ProbabilisticInterpolator
optimizers.
Minimizer
data.
ModelPDF
tractography.
PICoRandomizer
tractography.
RegionOfInterest
imaging.
SimulableScheme
simulation.dynamics.
StepAmender
simulation.dynamics.
StepGenerator
simulation.geometry.elements.
SubstrateObject
simulation.geometry.elements.
Cylinder
simulation.measurement.
SyntheticScan
misc.
VoxelwiseStatisticalImage
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
apps.
StreamlineTractography.ImageType
data.compartments.
CompartmentType
fitters.
NoiseModel
fitters.
FitModel
fitters.
FitAlgorithm
simulation.geometry.elements.
CylinderFactory.CylType
simulation.measurement.
StatisticsModuleFactory.StatsModuleType
simulation.measurement.
ScanFactory.ScanType
inverters.
ModelIndex
inverters.
InversionIndex
models.compartments.
CompartmentType
imaging.
MetaImageHeader.DataType
imaging.
MetaImageHeader.ObjectType
imaging.
MetaImageHeader.AnatomicalOrientation
tractography.
PICoPDF
tractography.
DataModel
simulation.dynamics.
StepGeneratorFactory.StepType
simulation.dynamics.
StepAmenderFactory.AmenderType
simulation.geometry.substrates.
SubstrateFactory.SubstrateType
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