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Home < Documentation < Nightly < Modules < TractographyLabelMapSeeding

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.


Surgical Planning Laboratory  
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.


Links to tutorials that use this module

Panels and their use


  • 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
    • Linear Measure 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.
  • ':
    • 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.

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