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References

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[[Documentation|Return to Slicer Documentation]]

=Diffusion Editor=

{|
|[[Image:DiffusionEditor helix.jpg|thumb|250px|Diffusion Editor, showing tracts and glyphs on helix example]]
|[[Image:Tracts_glyphs.jpg|thumb|250px|tracts and glyphs view]]
|[[Image:Tracts_glyphs_90degrees.jpg|thumb|250px|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/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.

=== Current features of the Diffusion Editor===
For DWI
* Edit gradients manually or load existing gradients from file (.txt or .nhdr).
* Edit the [[Modules:Volumes:Diffusion_Editor-Documentation-3.2#Measurement_Frame| measurement frame]] manually or simply rotate/swap/invert 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 [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.

=== Tutorials ===
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.
|}

==Quick Tour of Features and Use==

[[Image:DiffusionEditor_v8.jpg|right|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 ([[ media:DiffusionEditor_ExampleData.zip | 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.
<font color="Red">NOTE:</font> 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
## Glyph visibility: Select the planes on which you want to see glyphs and adjust the glyph spacing.
## 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 for DWI with existing clm: 100%
** glyphs view in all three planes with the possibility to change spacing: 100%
** tractography fiducial seeding: 100%
*ctest: 100%
*documentation, tutorials (videos): 100%
*writing master thesis: 60% :-)

== 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 [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format#Describing_DWIs_with_differen_b-values 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 [http://www.slicer.org/slicerWiki/index.php/Slicer3:EventBroker Eventbroker] for performance analysis and if necessary turn off events.

== Source code & documentation ==

Source code is available here:

http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorWidget.cxx
http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorWidget.h

http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorLogic.cxx
http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorLogic.h

http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerMeasurementFrameWidget.cxx
http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerMeasurementFrameWidget.h

http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerGradientsWidget.cxx
http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerGradientsWidget.h

http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionTestingWidget.cxx
http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionTestingWidget.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==
Thesis: [http://www.slicer.org/slicerWiki/index.php/Image:Thesis_letter.pdf http://www.slicer.org/slicerWiki/index.php/Media:Thesis_letter.pdf]

DTMRI: [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI]

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

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

@@ Line 43: / Line 43: @@
 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 [[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]].
+* For more detailed exploring of tracts use the Fiducial Seeding module or for display options select the module Tractography/DisplayLoadSave [https://www.slicer.org/wiki/Slicer3:DTMRI#Tractography_Module]].* See [[Slicer3:DTMRI#Tractography_Module|here]] for more information on the Tractography modules.
 === Current features of the Diffusion Editor===

@@ Line 171: / Line 171: @@
 ==References==
-Thesis: [[Image:Thesis_letter.pdf|http://www.slicer.org/slicerWiki/index.php/Media:Thesis_letter.pdf]]
+Thesis: [[Image:Thesis_letter.pdf|https://www.slicer.org/wiki/Media:Thesis_letter.pdf]] DTMRI: [[Slicer3:DTMRI|https://www.slicer.org/wiki/Slicer3:DTMRI]] Nrrd format: [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format]
 DICOM for DWI and DTI : [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI]

@@ Line 34: / Line 34: @@
 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.
+* See [[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
@@ Line 42: / Line 42: @@
 === 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.
+* The Diffusion Editor uses the default parameters. To change tractography parameters select the modul: Tractography/Seeding/Fiducial Seeding [[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].
+* 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.
+* See [[Slicer3:DTMRI#Tractography_Module|here]] for more information on the Tractography modules.
 === Current features of the Diffusion Editor===
@@ Line 140: / Line 140: @@
 ** 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 [http://www.slicer.org/slicerWiki/index.php/Slicer3:EventBroker Eventbroker] for performance analysis and if necessary turn off events.
+** Future work: Use [[Slicer3:EventBroker|Eventbroker]] for performance analysis and if necessary turn off events.
 == Source code & documentation ==
@@ Line 171: / Line 171: @@
 ==References==
-Thesis: [http://www.slicer.org/slicerWiki/index.php/Image:Thesis_letter.pdf http://www.slicer.org/slicerWiki/index.php/Media:Thesis_letter.pdf]
+Thesis: [[Image:Thesis_letter.pdf|http://www.slicer.org/slicerWiki/index.php/Media:Thesis_letter.pdf]]
-DTMRI: [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI]
+DTMRI: [[Slicer3:DTMRI|http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI]]
 Nrrd format: [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format]
 DICOM for DWI and DTI : [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI]

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