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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, Contributor1: Raúl San José-Estepar Contributor2: Lauren O'Donnel

Surgical Planning Laboratory   NAC

Module Description

Seed tracts on a Diffusion Tensor Image (DT) from 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 DTI Volume: Input DTI volume
  • Input Label Map: Label map with seeding ROIs
  • Output Fiber bundle: Tractography result
  • Write Fibers To Disk: Write fibers to disk or create in the scene?
  • Output Directory: Directory in which to save fiber(s)
  • File Prefix Name: Name to use for fiber files
• Seed Placement Options
  • Use Index Space: Seed at IJK voxel grid
  • Seed Spacing: Spacing (in mm) between seed points, only matters if use Use Index Space is off
  • Random Grid: Enable random placing of seeds
  • Linear Measure Start Threshold: Minimum Linear Measure for the seeding to start.
• Tractography Seeding Parameters
  • Minimum Length: Minimum length of the fibers (in mm)
  • Maximum Length: Maximum length of fibers (in mm)
  • Stopping Mode: Tensor measurement used to stop the tractography
  • Stopping Value: Tractography will stop when the stopping measurement drops below this value
  • Stopping Track Curvature: Tractography will stop if radius of curvature becomes smaller than this number units are degrees per mm
  • Integration Step Length(mm): Distance between points on the same fiber in mm
• Label definition
  • Seeding label: Label value that defines seeding region.

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

Information for Developers

Section under construction.