Difference between revisions of "Documentation/Nightly/Modules/FiberTractMeasurements"
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| − | + | Contact: <email>slicer-users@bwh.harvard.edu</email><br> | |
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| + | |Image:SlicerDMRIScreenshot.jpg|SlicerDMRI | ||
|Image:Logo-splnew.jpg|Surgical Planning Laboratory | |Image:Logo-splnew.jpg|Surgical Planning Laboratory | ||
|Image:NAC-logo.png|NAC | |Image:NAC-logo.png|NAC | ||
| + | |Image:Multple tracts.png|Multiple tracts from Corpus callosum (CC) | ||
| + | |Image:Csv measurements.png|Tensor measurements of the CC tracts | ||
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| + | Most frequently used for these scenarios: | ||
| − | * Use Case 1: | + | * 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. | ||
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| − | + | 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 | ||
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| − | + | * DWIToDTIEstimation | |
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Latest revision as of 13:59, 27 November 2019
Home < Documentation < Nightly < Modules < FiberTractMeasurements
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For the latest Slicer documentation, visit the read-the-docs. |
Introduction and Acknowledgements
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Contact: <email>slicer-users@bwh.harvard.edu</email> | |||||||||||
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Module Description
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.
Use Cases
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.
Tutorials
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
Parameters:
- 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.
List of parameters generated transforming this XML file using this XSL file. To update the URL of the XML file, edit this page.
Similar Modules
- DWIToDTIEstimation
