Difference between revisions of "Modules:Volumes:Diffusion Editor-Documentation"
|Line 81:||Line 81:|
* '''Testing frame:'''
* '''Testing frame:'''
# . the .
# Select a DTI volume from the current mrml scene and
Revision as of 20:29, 24 April 2008Home < Modules:Volumes:Diffusion Editor-Documentation
- 1 Diffusion Editor
- 2 General Information
- 3 Usage
- 4 Development
- 5 More Information
Module Type & Category
Category: Diffusion Imaging
Authors, Collaborators & Contact
- Author: Kerstin Kessel
- Supervisor: Steve Pieper, Ron Kikinis
TODO: Overview of what the module does goes here.
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.
- 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.
Examples & Tutorials
- Download example data: _________
|Load||Load a DWI dicom data set in Slicer.|
|Measurement frame||Change the measurement frame by rotating, swaping, negating or changing to idendity.|
|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
TODO: List all the panels in your interface, their features, what they mean, and how to use them.
- Measurement frame:
- Negate: Select the columns you want to negate.
- Swap: Select two columns you want to swap.
- Rotate: Select one column you want to rotate by an angle you can choose from a given set of values or set yourself.
- Idendity: Set the measurement frame to the idendity matrix.
- Set your own values.
- Gradients frame:
- If the active volume is a DWI the editor will put the gradients in the text field; otherwise this frame is disabled.
- You can copy/paste your own gradients in the text field or change them manually.
- You can load gradients from a text file or .nhdr file. For the .txt file the format is easy, it can contain only values (see example data).
- Undo: Undo the last change of measurement/gradient values.
- Redo: Redo the last change of measurement/gradient values.
- Restore: All parameters are restored to original.
NOTE: You lose all previous changes when a new active volume is loaded or selected.
- Testing frame:
- Run tensor estimation. The new tensor node shows up in the DTI selector.
- Select a DTI volume from the current mrml scene and
- view glyphs. Select the planes on which you want to see the glyphs.
- view tracts with Tractography Fiducial Seeding. Add some fiducials and choose the fiducial list in the selector.
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: 75%
- tensor estimation with existing clm: 100%
- glyphs view in all32 planes with the possibility to change resolution: 100%
- alternative tensor estimation with new filter: 0%
- filter for tensor rotation: 0%
- tractography fiducial seeding: 100%
- testing: 0%
- documentation, tutorials (videos): 40%
- writing master thesis: 5% :-)
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:
Source code & documentation
Source code is available here:
Links to documentation generated by doxygen:
Include funding and other support here.
Publications related to this module go here. Links to pdfs would be useful.
DICOM for DWI and DTI : http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI