Modules:Volumes:Diffusion Editor-Documentation-3.6

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Gallery of New Features

Module Name

Diffusion Editor

Diffusion Editor, showing tracts and glyphs on helix example
tracts and glyphs view
tracts and glyphs view - +90° rotation of measurement frame

General Information

Module Type & Category

Type: Interactive

Category: Diffusion Imaging

Authors, Collaborators & Contact

  • Author1: Kerstin Kessel
  • Contact:

Module Description

Overview of what the module does goes here.


Use Cases, Examples

This module is especially appropriate for these use cases:


  • Use Case 1: Edit gradients manually or load existing gradients from file (.txt or .nhdr).
  • Use Case 2: Edit the measurement frame manually or simply rotate/swap/invert columns by selecting them.
  • Use Case 3: Test the parameters by estimating a tensor and displaying glyphs and tracts.


  • Use Case 2: Edit the measurement frame as described above.
  • Use Case 3: Test by displaying glyphs and tracts.

Examples of the module in use:

  • Measurement frame:
  1. The determinant of the measurement frame has to be 1. This is checked by the editor.
  2. Invert: Select the columns you want to invert.
  3. Swap: Select two columns you want to swap.
  4. Rotate: Select one column you want to rotate by an angle you can choose from a given set of values or set yourself.
  5. Identity: Set the measurement frame to the identity matrix.
  6. Set your own values.
  • Gradients frame:
  1. If the active volume is a DWI the editor will put the gradients in the text field; otherwise this frame is disabled.
  2. You can copy/paste your own gradients in the text field or change them manually.
  3. You can load gradients from a text file or .nhdr file. For the .txt file the format of gradients is easy, it can contain only values ( see example data ).
  • Undo/Redo/Restore:
  1. Undo: Undo the last change of measurement/gradient values.
  2. Redo: Redo the last change of measurement/gradient values.
  3. Restore: All parameters are restored to original.

NOTE: You lose all previous changes when a new active volume is loaded or selected.

  • Testing frame:
  1. Run tensor estimation. The new tensor node shows up in the DTI selector.
  2. Select a DTI node from the current mrml scene and for
    1. Glyph visibility: Select the planes on which you want to see glyphs and adjust the glyph spacing.
    2. Tract visibility: Add some fiducials and choose the fiducial list in the selector. Show tracts with Tractography Fiducial Seeding.


Links to tutorials explaining how to use this module:

  • Tutorial 1
    • Data Set 1

Quick Tour of Features and Use

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

  • Input panel:
    • First input
    • Second input
  • Parameters panel:
    • First parameter
    • Second parameter
  • Output panel:
    • First output
    • Second output
  • Viewing panel:
User Interface


Notes from the Developer(s)

Algorithms used, library classes depended upon, use cases, etc.


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


On the Dashboard, these tests verify that the module is working on various platforms:

Known bugs

Links to known bugs in the Slicer3 bug tracker

Usability issues

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

Source code & documentation

Links to the module's source code:

Source code:

Doxygen documentation:

More Information


Include funding and other support here.


Publications related to this module go here. Links to pdfs would be useful.