Command List

DWIProcessing

Command Description
CorrectBValues group similar b values into several shells.
DWIMultipleShellSplit Split mutiple shell DWI data into several single shell data.
DWINoiseGenerator Add noise to a set of DWI data.
DWIPreprocess Read DWI images, gradients, b values, and output the formal normalized formalt in a configuration file.
DWISimulator Simulate DWI data.
DWISingleVoxelSimulator Simulate DWI data with fixed single voxel configuration.

DiffusionModels

Command Description
ComputeSHCoefficientsOfDWIFromSymmetricTensor Compute SH coefficients of DWI signal in DTI with symmetric tensor (along z-axis).
MeanDiffusivityEstimator Estimate Mean Diffusivity in each voxel.
ODFNormalization Normalize ODF (VectorImage) represented by SH basis or uniform spherical samples.
SHCoefficientsToGFA calculate GFA from SH coefficients.
SHCoefficientsToSphericalFunctionSamples conversion from SH coefficients to spherical function samples.
SPFToODF Convert SPF coefficients to ODFs (represented by SH basis or discrete samples).
SPFToProfile Convert SPF coefficients to DWI/EAP profile (represented by SH basis or discrete samples).
SPFToScalarMap Estimate scalar maps using SPFI.
SphereTessellator Tessellation of a sphere via subdivision of basic polyhedrons.
SphericalPolarFourierImaging SPFI: estimate SPF coefficients from DWI signals.

SamplingScheme

Command Description
OrientationStatistics Get statistics information from a given orientation file. Show the (min, max, mean, std) of the minimal angles of all samples. Show electrostatic energy, spherical code cost function.
SamplingSchemeDistance Calculate the distance (maximum of the minimal angles) between two single shell sampling schemes.
SamplingSchemeQSpace1OptEstimation 1-Opt estimation for single and multiple shell sampling scheme
SamplingSchemeQSpaceIMOCEstimation Single and multi-shell sampling scheme estimation using Iterative Maximum Overlap Construction (IMOC).
SamplingSchemeQSpaceIncrementalEstimation Incrementatl estimation for single and multiple shell sampling scheme.
SamplingSchemeQSpaceRandomEstimation Random generator for multi-shell schemes.

Scripts

Command Description
CombineVTKPolyData.py Combine several vtk files into one vtk file.
ConvertGurobiSolToIndex.py Covert .sol file (by gurobi) to index file for subsampling gradients. It is used for subsampling gradients by Mixed Integer Linear Programming (MILP)
VTKPolyData.py Render a list of VTK data and (or) a nifti image, then view or save PNG or save WebGL. The code is modified from ITKExamples.
VTKPolyData_gui.py GUI for VTKPolyData.py.

Utilities

Command Description
4DToVectorImageConverter Convert a 4D image to a vector image.
ImageInfo Display image information.
ImageMultiplication Scale each voxel in a 3D vector image or 4D image.
TextFileOperator Operations for text files.
VectorImageNormalization Normalize each voxel in a VectorImage or SparseVectorImage.
VectorTo4DImageConverter Convert a vector image to a 4D image.

Visualization

Command Description
CombineVTKPolyData.py Combine several vtk files into one vtk file.
MeshFromSHCoefficients Create a mesh from spherical harmonics coefficients for visualization.
MeshFromSphericalFunctionTessellatedSamples Create a mesh from spherical samples using tessellation.
OrientationsViewer Single and multi-shell orientations viewer.
VTKPolyData.py Render a list of VTK data and (or) a nifti image, then view or save PNG or save WebGL. The code is modified from ITKExamples.
VTKPolyData_gui.py GUI for VTKPolyData.py.
vtkviewer visualize vtk files.