Slicer3:Diffusion Editor

Overview

The goal of this project is to add a Gradient Editor for DWI data in the Volumes module of Slicer3. As the documentation of gradients in dicom data is not standardized, MRI scanners handle them differently. Because of that there is a big need to add/modify gradients manually.

Background (why specific editor features are needed)

TODO

Interface

This screenshots show the interface and its changes during the last months.

• Interface
• 

  1st Version (tcl)

• 

  integrated in Slicer3 branch

• 

  integrated in Slicer3 trunk, some GUI elements are no longer necessary

• 

  new features added

How to use the editor

• 1.Step: Generate a Nrrd-header of your DWI data. Use the "Dicom to Nrrd" module in Slicer3 (Modules->Converters->Dicom to Nrrd).
  • -> A .nhdr file will be created.
• 2.Step: Use the output (.nhdr file) as an input of the Volumes module.
  • -> The Gradient Editor will be enabled. If you load any other type of dataset the editor will be disabled.

What you can do with the Gradient Editor

TODO: more details.

1. Choose measurement frame.
   1. Negative: Select the columns you want to negative.
   2. Swap: Select two columns you want to swap.
   3. Rotate: Select one column you want to rotate by an angle you can choose from a given set of values or set yourself.
   4. Idendity: Set the measurement frame to the idendity matrix.
   5. Set your own values.
2. Define gradients.
   1. If the .nhdr file has the information about the gradients, the editor will put them in the text field.
   2. You can copy/paste your own gradients in the text field.
   3. You can load gradients from a plain text file or .nhdr file.
3. Undo: Undo the last change of measurement/gradient values.
4. Redo: Redo the last change of measurement/gradient values.
5. Restore: All parameters are restored to original.
6. Run test.
   1. Add a Fiducial List. To see if the chosen parameters are reasonable, you can run a test that automatically
      1. computes the Tensor and
      2. visualizes them by Tractography Seeding. (both with standard values)
7. Display DTI: Select a DTI volume from the current mrml scene and see its tracts.

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%
• test: 60%
  • tensor estimation with existing clm: 95%
  • alternative tensor estimation with new filter: 0%
    • filter for tensor rotation: 0%
  • tractography fiducial seeding: 100%
• testing: 0%
• documentation, demo video: 0%
• writing master thesis: 5% :-)

Additional Information

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