Modules:DTIDisplay-Documentation-3.6

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Module Name

FiberBundles

DTI fiber tracks displayed as Lines
DTI fiber tracks displayed as Tubes
DTI fiber tracks displayed as Glyphs

General Information

Module Type & Category

Type: Interactive

Category: Tractography

Authors, Collaborators & Contact

  • Alex Yarmarkovich, Isomics, SPL
  • Contact: Alex Yarmarkovich, alexy@bwh.harvard.edu

Module Description

This module is used for loading, saving, and changing the appearance of DTI fiber tracts.

Usage

Load

  • Load Tractography allows the user to load a single track file. The file should be a VTK polydata file (.vtk or .vtp) containing polylines with Tensor point data.
  • Load Tractography directory will load all the VTK models (*.vtk) that are located in in the selected directory

Display

  • Fiber Bundle Select: Select the bundle that you want to modify from a list
  • Display for Lines/Tubes/Glyphs: select which representation to edit. Note that you can have more than one representation visible at the same time, for example Lines and Glyphs.
  • Visibility: Turn a fiber bundle on or off in the 3D window
  • Color By Scalar: Select from the list of derived tensor scalar properties such as Fractional Anisotropy, etc.
  • Scalar Color Map: Select the color mapping used to map from the scalar values to colors.
  • Scalar Color Visibility: Toggle the coloring by the scalar values.
  • Clipping: Set clipping on or off for this bundle. Once it is on, go to the Models->Clipping pane to set the options.
  • Opacity: Set how transparent this track is.
  • Set Color: Set the base color for this bundle.
  • Glyph Display Properties: Only applicable to glyphs.
    • Glyph Type: Lines, Tubes, or Ellipsoids.
    • Scale factor: Controls glyph size.
    • Spacing: Controls the number of glyphs along the tract.

Save

  • Fiber Bundle To Save: Select a bundle from the list.
  • Save Tractography: Opens a file browser to let you select the location to which to save the file. The valid extensions and file types that can be used are:
    • .vtk poly data
    • .vtp xml poly data


Examples, Use Cases & Tutorials

loading and viewing data].

Quick Tour of Features and Use

  • Load: Load fiber tracts into Slicer3
  • Display: Adjust track display parameters
  • Save: Saves models onto disk

Development

Dependencies

Other modules or packages that are required for this module's use.

Known bugs

Follow this link to the Slicer3 bug tracker.

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Follow this link to the source code in ViewVC.

Documentation generated by doxygen.

More Information

Acknowledgment

References