Documentation/Nightly/Modules/TractographyLabelMapSeeding

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Introduction and Acknowledgements

This work is part of 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. Information on NA-MIC can be obtained from the NA-MIC website. Author: Demian Wassermann, SPL, LMI, PNL, Brigham and Women's Hospital, Harvard Medical School Contact: Demian Wassermann, <email>demian@bwh.harvard.edu</email> Contributor1: Raúl San José-Estepar Contributor2: Lauren O'Donnel

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

• Slicer4 Diffusion Tensor Imaging Tutorial: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial

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

Tractography Fiducial Seeding

References

Publications related to this module go here. Links to pdfs would be useful. For extensions: link to the source code repository and additional documentation