Difference between revisions of "Documentation/Nightly/Modules/FiberTractMeasurements"

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|Image:Logo-splnew.jpg|Surgical Planning Laboratory
 
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Most frequently used for these scenarios:
 
Most frequently used for these scenarios:
  
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* Use Case 1: Create a brain mask from diffusion-weighted images (DWI). Use the brain mask to restrict tensor computation to the inside of the brain (remove noisy data outside the head). This makes a more attractive FA image.
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* Use Case 1: Compute measurements from all tractography files in a directory (from command-line interface or Slicer).
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* Use Case 2: Create a brain mask from diffusion-weighted images (DWI). Use the brain mask for seeding tractography.
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* 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
 
Links to tutorials that use this module
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* Slicer4 Diffusion Tensor Imaging Tutorial: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial
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* 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
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* Usage from CLI with whitematteranalysis: https://github.com/SlicerDMRI/whitematteranalysis/wiki/Visualization-and-Analysis-of-Clustered-Tracts
  
 
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Latest revision as of 13:59, 27 November 2019

Home < Documentation < Nightly < Modules < FiberTractMeasurements


For the latest Slicer documentation, visit the read-the-docs.


Introduction and Acknowledgements


Title: Tractography Measurements
Author(s)/Contributor(s): Alex Yarmarkovich, Fan Zhang, Lauren O'Donnell (SPL, LMI, BWH, SlicerDMRI)
License: 3D Slicer Contribution and Software License Agreement
Acknowledgements: The SlicerDMRI developers gratefully acknowledge funding for this project provided by NIH NCI ITCR U01CA199459 (Open Source Diffusion MRI Technology For Brain Cancer Research), NIH P41EB015898 (National Center for Image-Guided Therapy) and NIH P41EB015902 (Neuroimaging Analysis Center), as well as the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

Contact: <email>slicer-users@bwh.harvard.edu</email>
Website: http://slicerdmri.github.io/

SlicerDMRI  
Surgical Planning Laboratory  
NAC  
Multiple tracts from Corpus callosum (CC)  
Tensor measurements of the CC tracts  

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

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

References

Information for Developers

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