Slicer3:Diffusion Editor

Overview

The goal of this project is to add a Gradient Editor for DWI data in the Volumes modul 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.

Interface

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

• Interface
• 

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

• 
• 

  integrated in Slicer3 branch

• 

  1st Version (tcl)

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 now

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
      1. choose from a given set of values.
      2. set yourself.
   4. 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. Run test.
   1. Add a Feducial Mask. To see if the chosen parameters are reasonable, you can run a test that automatically
      1. computes the Tensor
      2. visualizes them by Tractography Seeding. (both with standard values)
4. Cancel: All parameters are restored to original.

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): 90%
• gradients (gui/load/change/save): 50%
• test (gui/...): 5%
• writing master thesis: 0%

Additional information

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