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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

• Author: Kerstin Kessel
• Supervisor: Steve Pieper, Ron Kikinis

Module Description

As the documentation of acquisition parameters in dicom data is not standardized, MRI scanners (Siemens, GE) handle gradients/bValues differently in their dicom headers. Because of that there is a big need to add/modify them manually.

The Diffusion Editor is a 3D Slicer module that allows modifying parameters (gradients, bValues, measurement frame) of DWI data and provides a quick way to interpret them. For that it estimates a tensor and shows glyphs and tracts for visual exploration.

Used Tensor Estimation

The Diffusion Editor uses the Tensor Estimation CLM (Command Line Module) of Slicer to compute tensors.

• See here for more information on the Tensor Estimation CLM.

The testing frame provides just a small subset of DTI display options. For more detailed settings

• load the DTI as the active volume in the volumes modul
• go to the display frame

Used Tractography Fiducial Seeding

The Diffusion Editor uses the Tensor Estimation CLM (Command Line Module) of Slicer to compute tensors.

• To change tractography parameters go to the ____TODO______. Changes there have an immediate impact for the tracts in the Diffusion Editor.
• See here for more information on the Tractography Fiducial Seeding module.

Current features of the Diffusion Editor

• For DWI
  • Edit gradients manually or load existing gradients from file (.txt or .nhdr).
  • Edit the measurement frame manually or simply rotate/swap/negate columns by selecting them.
  • Test the parameters by estimating a tensor and displaying glyphs and tracts.
• For DTI
  • Edit the measurement frame as described above.
  • Test by displaying glyphs and tracts.

Usage

Examples & Tutorials

Preparation

• Download Slicer. The most recent stable Slicer version can be found here. To use the current version download the latest Slicer snapshot.
• You can also use SVN to checkout the trunk of the very latest version of Slicer. See here for more instructions on how to build Slicer.
• Download example data: DiffusionEditor_ExampleData.zip

Tutorials

TODO: Tutorials; add ExampleData

title	used data	short description
Load	___	Load a DWI dicom data set in Slicer.
Measurement frame	___	Change the measurement frame by rotating, swapping, inverting or changing to identity.
Gradients	___	Change gradients manually or load them from a file.
Testing	___	Run tensor estimation and show glyphs and tracts; Run second estimation with 90°rotation and switch between both tensors and see the impact of that change.

Quick Tour of Features and 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.

Development

Status / Implementation Progress

The editor is now successfully integrated in the Volumes module of the trunk version of Slicer3.

• measurement frame (gui/load/change/save): 100%
• gradients (gui/load/change/save): 100%
• undo/redo/restore mechanism: 100%
• testing frame: 100%
  • tensor estimation with existing clm: 100%
  • glyphs view in all three planes with the possibility to change spacing: 100%
  • tractography fiducial seeding: 100%
• ctest: 50%
• documentation, tutorials (videos): 50%
• writing master thesis: 5% :-)

Known issues / bugs

Follow this link to the Slicer3 bug tracker to see known bugs, or to report a new one. Please select the usability issue category when browsing or contributing:

http://na-mic.org/Mantis/main_page.php

Queries, feature requests and other feedback should be directed to slicer-devel |at| bwh.harvard.edu. You can also sign up for Slicers user and developer list to make sure you hear of new developments, releases and bug fixes.

Issues

• Changing the measurement frame of a DTI has no impact. The tensor is not estimated again.
  • Future work: Adding new rotation filter for tensors (contributed by Raul San Jose)
• Multiple bValues are not displayed. Currently to describe acquisitions with different b-values the magnitudes of the gradients are changed. See the nrrd format page about describing DWIs with different b-values.
  • Future work: Adding different views of gradients/bValues.
• Checking gradients when one types new values in the textbox is slowly. Reason: SetDiffusionGradients of the vtkMRMLDiffusionWeightedVolumeNode seems to trigger many events.
  • Future work: Use Eventbroker for performance analysis and if necessary turn off events.

Source code & documentation

Source code is available here:

http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorWidget.cxx http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorWidget.h

http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorLogic.cxx http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorLogic.h

http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerMeasurementFrameWidget.cxx http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerMeasurementFrameWidget.h

http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerGradientsWidget.cxx http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerGradientsWidget.h

http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerDWITestingWidget.cxx http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerDWITestingWidget.h

Links to documentation generated by doxygen:

http://www.na-mic.org/Slicer/Documentation/Slicer3/html/

More Information

Acknowledgement

This research project was part of a Master thesis (Diplomarbeit) in cooperation of the faculty of Medical Informatics, University of Heidelberg/Germany and the Surgical Planning Lab. It was supported by a grant of the Lions Club Heilbronn/Franken.

References

TODO: add link to thesis, papers...

Nrrd format: http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format

DTMRI: http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI

DICOM for DWI and DTI : http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI