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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: kerstin@bwh.harvard.edu

Module Description

As the documentation of acquisition parameters in dicom data is not standardized, MRI scanners (Siemens, GE) handle gradients/bValues/measurement frame 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, which 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.

Measurement Frame

The measurement frame of all DWI is always displayed in the RAS space. That's because Slicer stores all internal coordinates in RAS. If you save changes in a new .nhdr file the measurement frame will always be in RAS.

Used Tensor Estimation

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

The module provides the linear-least-squares, non-linear-least squares and weighted-least-square method for the estimation. But the DiffusionEditor uses the linear-least-squares method by default, as it is the fastest and most robust.
See [1], [2] 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 and adjust parameters.

Used Tractography Fiducial Seeding

The Diffusion Editor uses the Tractography Fiducial Seeding module of Slicer to compute tracts.

The Diffusion Editor uses the default parameters. To change tractography parameters select the modul: Tractography/Seeding/Fiducial Seeding [3]. Changes there have an immediate impact for the tracts in the Diffusion Editor.
For more detailed exploring of tracts use the Fiducial Seeding module or for display options select the module Tractography/DisplayLoadSave [4].
See here for more information on the Tractography modules.

Usage

Use Cases, Examples

This module is especially appropriate for these use cases:

For DWI

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.

For DTI

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

Tutorials

Preparation

Download Slicer. The most recent stable Slicer version can be found here. Or load Slicer's latest snapshot.
You can also use SVN to checkout the trunk of the current version of Slicer. See here for more instructions on how to build Slicer.
Download example data: DiffusionEditor_ExampleData.zip and unzip it.

To start a tutorial video simply click on the link in the table.

title	short description
Load DICOM	Load a DWI dicom data set in Slicer.
Edit gradients	Change gradients manually and load them from a file. Save your changes afterwards.
Edit measurement frame	Change the measurement frame by swapping and inverting. Save your changes afterwards.
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

[[|right||thumb|280px|overview]]

Measurement frame:

The determinant of the measurement frame has to be 1. This is checked by the editor.
Invert: Select the columns you want to invert.
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.
Identity: Set the measurement frame to the identity 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 of gradients is easy, it can contain only values ( see example data ).

Undo/Redo/Restore:

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 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.

User Interface

Development

Notes from the Developer(s)

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

Dependencies

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

Tests

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

MyModuleTest1 MyModuleTest1.cxx
MyModuleTest2 MyModuleTest2.cxx

Known bugs

Links to known bugs in the Slicer3 bug tracker

Bug 000: description

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:

class1

More Information

Acknowledgment

Include funding and other support here.

References

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

@@ Line 25: / Line 25: @@
 ===Module Description===
-Overview of what the module does goes here.
+As the documentation of acquisition parameters in dicom data is not standardized, MRI scanners (Siemens, GE) handle gradients/bValues/measurement frame 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, which 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.
+==== Measurement Frame ====
+The measurement frame of all DWI is always displayed in the RAS space. That's because Slicer stores all internal coordinates in RAS.
+If you save changes in a new .nhdr file the measurement frame will always be in RAS.
+==== Used Tensor Estimation ====
+The Diffusion Editor uses the Tensor Estimation CLM (Command Line Module) of Slicer to compute tensors.
+* The module provides the linear-least-squares, non-linear-least squares and weighted-least-square method for the estimation. But the DiffusionEditor uses the linear-least-squares method by default, as it is the fastest and most robust.
+* See [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tensor_Estimation_from_DWI_Module], [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:TeemExamples#tend_estim:_tensor_estimation] 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 and adjust parameters.
+==== Used Tractography Fiducial Seeding ====
+The Diffusion Editor uses the Tractography Fiducial Seeding module of Slicer to compute tracts.
+* The Diffusion Editor uses the default parameters. To change tractography parameters select the modul: Tractography/Seeding/Fiducial Seeding [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Fiducial_Seeding_Module]. Changes there have an immediate impact for the tracts in the Diffusion Editor.
+* For more detailed exploring of tracts use the Fiducial Seeding module or for display options select the module Tractography/DisplayLoadSave [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Module].
+* See [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Module here] for more information on the Tractography modules.
 == Usage ==
@@ Line 39: / Line 61: @@
 For DTI
 * Use Case 2: Edit the measurement frame as described above.
-* Use Case 3: Test by displaying glyphs and tracts.
+* Use Case 3: Test the parameters by displaying glyphs and tracts.
+===Tutorials===
+==== Preparation ====
+* Download Slicer. The most recent stable Slicer version can be found [http://www.slicer.org/pages/Downloads here]. Or load Slicer's latest snapshot.
+* You can also use SVN to checkout the trunk of the current version of Slicer. See [[Slicer3:Build_Instructions| here]] for more instructions on how to build Slicer.
+* Download example data: [[ media:DiffusionEditor_ExampleData.zip | DiffusionEditor_ExampleData.zip ]] and unzip it.
+To start a tutorial video simply click on the link in the table.
+{| border="1"
+|- bgcolor="#abcdef"
+! title !!short description
+|-
+| [[Tutorials:DiffusionEditor-Load DWI-Dicom| Load DICOM]]  ||Load a DWI dicom data set in Slicer.
+|-
+| [[Tutorials:DiffusionEditor-Edit Gradients | Edit gradients ]]||Change gradients manually and load them from a file. Save your changes afterwards.
+|-
+| [[Tutorials:DiffusionEditor-Edit Measurement frame| Edit measurement frame]] ||Change the measurement frame by swapping and inverting. Save your changes afterwards.
+|-
+| [[Tutorials:DiffusionEditor-Testing | 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.
+|}
-[[Image:DiffusionEditor_v8.jpg|right|overview]]
+===Quick Tour of Features and Use===
+[[|right||thumb|280px|overview]]
-Examples of the module in use:
+{|
+|
 * '''Measurement frame:'''
 # The determinant of the measurement frame has to be 1. This is checked by the editor.
@@ Line 71: / Line 120: @@
 ## Tract visibility: Add some fiducials and choose the fiducial list in the selector. Show tracts with Tractography Fiducial Seeding.
+|[[Image:DiffusionEditor_v8.jpg|thumb|280px|User Interface]]
-===Tutorials===
-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:'''
-|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
 |}