Command List¶
Table of Contents
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. |
| SHCoefficientsFit | Spherical Harmonics fit from spherical function samples. |
| SHCoefficientsPower | Power of a spherical function represented by SH basis. |
| SHCoefficientsRotate | Spherical Harmonics Rotation. |
| 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 | Spherical Polar Fourier Imaging (SPFI): estimate SPF coefficients from DWI signals. |
| TensorFormatConverter | Convert different tensor storage formats. |
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 |
|---|---|
| 4DImageMath | Perform math operators on 4D image (4D itk::Image or 3D itk::VectorImage). |
| 4DToVectorImageConverter | Convert a 4D image to a vector image. |
| ImageInfo | Display image information. |
| PrintImage | print image (4D image, tensors, SH coefficients). |
| 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. |
| MeshFromDiscreteFiberODF | Create a mesh (a spherical profile of DWI/EAP/ODF) from discrete fiber ODF for visualization. |
| MeshFromPeaks | Create a mesh from peaks for visualization. |
| MeshFromSHCoefficients | Create a mesh from spherical harmonics coefficients for visualization. |
| MeshFromSphericalFunctionTessellatedSamples | Create a mesh from spherical samples using tessellation. |
| MeshFromTensors | Create a mesh from tensors for visualization. |
| MeshFromTracts | Create a mesh from fiber tracts for visualization. |
| OrientationsViewer | Single and multi-shell orientations viewer. |
| RGBImageToVTKXMLImageConverter | Convert an ITK image to a VTK XML image. |
| 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. |
| VTKXMLImageToVectorImageConverter | Convert a VTK XML image to an ITK image. |
| VectorImageToVTKXMLImageConverter | Convert an ITK image to a VTK XML image. |
| vtkviewer | visualize vtk files. |
