Documentation/Nightly/Modules/TractographyLabelMapSeeding

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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: <email>slicer-users@bwh.harvard.edu</email> 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

• Slicer4 Diffusion Tensor Imaging Tutorial: https://www.slicer.org/wiki/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

• TractographyInteractiveSeeding: https://www.slicer.org/wiki/Documentation/Nightly/Modules/TractographyInteractiveSeeding

References

• http://slicerdmri.github.io/

Information for Developers

• https://github.com/SlicerDMRI