Documentation/Nightly/Modules/FiberBundleLabelSelect

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Introduction and Acknowledgements

Title: Tractography ROI Selection Author(s)/Contributor(s): Demian Wassermann, Fan Zhang, 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   Whole brain tractography   Corpus callosum (CC) tract selection

Module Description

Fiber bundle label select allows a user to select tracts passing or not passing through single or multiple labels. (Selection region label maps may be created with the Editor module or other segmentation tools.)

Use Cases

Most frequently used for these scenarios:

• Use Case 1: Filter out a subset of DTI fiber tracts which are passing through selected region(s) defined in the label map volume.
• Use Case 2: Filter out a subset of DTI fiber tracts which are NOT passing through selected region(s) defined in the label map volume.
• Use Case 3: A combination of Case 1 and Case 2.

Tutorials

Links to tutorials that use this module

• Slicer4 Fiber Bundle Selection and Scalar Measurements Tutorial: https://www.slicer.org/wiki/Documentation/4.5/Training#Fiber_Bundle_Selection_and_Scalar_Measurements * Tractography selection and measurements in command line interface (CLI) mode: http://dmri.slicer.org/tutorials/tractography_measurement

Panels and their use

Parameters:

• IO: Input/output parameters
  • Selection Region Label Map (InputLabel_A): Label map volume defining selection region
  • Input Fiber Bundle (InputFibers): Input tractography for region-based selection.
  • Output Fiber Bundle (OutputFibers): Selected tractography result from region-based selection.
• Tract selection region labels:
  • Inclusion labels (comma-separated) (PassLabel): Comma-separated list of label values defining inclusion region. Fibers passing through these labels will be retained.
  • Inclusion label combination logic (PassOperation): AND: Fiber must pass through all specified labels.
    OR: Fiber must pass through any specified label (at least one).
  • Exclusion labels (comma-separated) (NotPassLabel): Comma-separated list of label values defining exclusion region. Fibers passing through these labels will be removed.
  • Exclusion label combination logic (NoPassOperation): AND: Any fiber passing through all specified labels is excluded.
    OR: Fibers passing through any specified label (at least one) are excluded.
• Advanced Settings: Advanced settings
  • Sampling distance (mm) (SamplingDistance): Sampling Distance

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 Label Map Seeding

References

• http://slicerdmri.github.io/

Information for Developers

• https://github.com/SlicerDMRI