1) Inputs and Outputs
The input is tractography from the whole brain. The supported file format is vtkPolyData and the filenames should end in either .vtk or .vtp. (These are the older and newer vtk file formats and either will work.)
For the whitematteranalysis scripts, the input is either one vtkPolyData file or a directory that contains vtkPolyData files from all subjects to be analyzed. Each command can be run with --help to learn what is the expected input.
The output data, depending on the script that is run, will be clustered or registered vtkPolyData files. For atlas creation and application of the atlas to segment individual subjects, a MRML (Slicer 4 scene) file will also be produced for visualization of the output.
The MRML file, when opened in Slicer, should display something like this, where the spectral embedding has been used to give color to each cluster.
