Documentation/Nightly/Modules/TractographyLabelMapSeeding

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For the stable Slicer documentation, visit the 4.6 page.


Introduction and Acknowledgements


Title: Tractography ROI Seeding
Author(s)/Contributor(s): Raul San Jose, Demian Wassermann, 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:
Website: http://slicerdmri.github.io/

SlicerDMRI  
Surgical Planning Laboratory  
NAC  
Seeding label map  
Output tractography  

Module Description

Seed tractography from a Diffusion Tensor Image (DTI) within a region defined by a label map.


Use Cases

Most frequently used for these scenarios:

  • Use Case 1: Using a label map, trace all the fibers emanating from it.
  • Use Case 2: Using a brain mask, perform a full brain tractography.

Tutorials

Links to tutorials that use this module

Panels and their use

Parameters:

  • IO: Input/output parameters
    • Input DTI Volume (InputVolume): DTI volume in which to seed (generate) tractography.
    • Input Label Map (InputROI): Label map defining region for seeding tractography.
    • Output Fiber Bundle (OutputFibers): Tractography result
  • Seeding Options: Options for seed placement
    • Start Threshold (ClTh): Minimum Linear Measure for the seeding to start.
  • Tractography Seeding Parameters: Parameters for the tractography method
    • Minimum Length (MinimumLength): Minimum length of the fibers (in mm)
    • Maximum Length (MaximumLength): Maximum length of fibers (in mm)
    • Stopping Criteria (ThresholdMode): Tensor measurement used to start and stop the tractography
    • Stopping Value (StoppingValue): Tractography will stop when the stopping measurement drops below this value
    • Stopping Track Curvature (StoppingCurvature): Tractography will stop if radius of curvature becomes smaller than this number units are degrees per mm
    • Integration Step Length(mm) (IntegrationStepLength): Distance between points on the same fiber in mm
  • Label definition: Selection of label(labels) for ROI definition
    • Seeding label (ROIlabel): Label value that defines seeding region.
  • Advanced:
    • Use Index Space (UseIndexSpace): Seed at IJK voxel grid
    • Seed Spacing (SeedSpacing): Spacing (in mm) between seed points, only matters if use Use Index Space is off
    • Random Grid (RandomGrid): Enable random placing of seeds


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

References

Information for Developers