Documentation/4.3/Modules/FiberBundleLabelSelect

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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: Alex Yarmarkovich, Isomics, SPL Contributor1: Demian Wassermann, SPL Contact: Alex Yarmarkovich, <email>alexy@bwh.harvard.edu</email>

Surgical Planning Laboratory

Module Description

This module is used for selecting a subset of DTI fiber tracts including or excluding certain fibers passing through a selected set of labels in the label map volume.

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

Slicer 4 Diffusion Tensor Tutorial

Panels and their use

A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:

Parameters panel: Parameters: select an existing setting for the module or create a new one. IO panel: Input Label Map: select an existing label map volume. Input FiberBundle: Select the fibers that you want to filter. Output FiberBundle: Select the bundle that you want to create or modify from a list. Label Regions Definition panel : Labels to include: A comma separated list of label values to include in the output fiber bundles set. Fiducail Seeding Step Size: Step between the seeding samples in the box (mm). Seed Selected Fiducials: Flag indicating whether to use only selected fiducials for seeding or all of them. Maximum Number of Seeds: Used with models to specify the limit of the number of vertices to be used for seeding.

Fiducial Tractography Seeding

Label Map Options panel: Use Index Space: if selected seed at IJK voxel grid Seed Spacing: spacing in between seed points within in the labelmap (in mm), only matters if use Use Index Space is off. Random Grid: use random placement. Linear Measure Start Threshold: place seeds only if linear measure (cl) is above this threshold. ROI Labels: a comma separated list of label to start seeding Write Fibers to Disk: option to save the results to disk for further analysis. Output Directory: path where the results are saved. File Prefix Name: name that would be used for each output bundle.

Label Map Tractography Seeding

• Tractography Seeding Parameters panel:
  • Minimum Path Length: Select only tracts that are longer than this value (mm).
  • Maximum Path Length: Select only tracts that are shorter than this value (mm).
  • Stopping Criteria: Select Linear Measure or FA to be used as stopping criteria.
  • Stopping Value: Select Linear Measure or FA stopping value, tracking will stop when the value drops below this one.
  • Stopping Track Curvature: Select the curvature stopping value in degree per mm, tracking will stop when the radius of curvature is smaller than this one.

• Enabling Options panel:
  • Create Tracts Initially As: Select Tubes or Lines

Similar Modules

• Tractography Label Map 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