Introduction and Acknowledgements
Compute whole-fiber scalar measurements from a directory of VTK fiber bundle files. Files must have tensors stored in as cell data Slicer tensor convention.
Most frequently used for these scenarios:
- Use Case 1: Compute measurements from all tractography files in a directory (from command-line interface or Slicer).
- Use Case 2: Compute measurements using a fiber tract hierarchy to select and combine tractography files in a directory (for example to define corpus callosum subregions). Use this from command-line interface (CLI) only.
Links to tutorials that use this module
- Slicer4 Fiber Bundle Selection and Scalar Measurements Tutorial: https://www.slicer.org/wiki/Documentation/4.5/Training#Fiber_Bundle_Selection_and_Scalar_Measurements
- Tractography selection and measurements in command line interface (CLI) mode: http://slicerdmri.github.io/docs/tutorials/CLITutorial.pdf
- Usage from CLI with whitematteranalysis: https://github.com/SlicerDMRI/whitematteranalysis/wiki/Visualization-and-Analysis-of-Clustered-Tracts
Panels and their use
- IO: Input/output parameters
- Select Input Type (inputType): Type of input: MRML Hierarchy, or directory containing VTK polydata files.
- Fibers Hierarchy (FiberHierarchyNode): Fibers top hierarchy node
- Fibers File Folder (InputDirectory): Directory from which to read fibers
- Output Text File (outputFile): Output measurement file
- Select Output Format (outputFormat): Output format: print statistics along column vs. row.
- Output Field Separator (outputSeparator): Output file field separator (Comma, Space, or Tab).
- Print statistics for all clusters and children. (printAllStatistics): Print statistics for all clusters and children. In hierarchy mode, by default this module only prints statistics for specified cluster(s).
- Advanced Settings: Advanced settings
- Output more statistics (moreStatistics): Output additional statistics, including maximum, minimum, median, variance.