Difference between revisions of "Modules:Volumes:Diffusion Editor-Documentation"

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===Diffusion Editor===
+
=Diffusion Editor=
  
 
{|
 
{|
−
|[[Image:DiffusionEditor helix.jpg|thumb|280px|Diffusion Editor, showing tracts and glyphs on helix example]]
+
|[[Image:DiffusionEditor helix.jpg|thumb|250px|Diffusion Editor, showing tracts and glyphs on helix example]]
−
|[[Image:Tracts_glyphs.jpg|thumb|280px|tracts and glyphs view]]
+
|[[Image:Tracts_glyphs.jpg|thumb|250px|tracts and glyphs view]]
−
|[[Image:Tracts_glyphs_90degrees.jpg|thumb|280px|tracts and glyphs view - +90° rotation of measurement frame]]
+
|[[Image:Tracts_glyphs_90degrees.jpg|thumb|250px|tracts and glyphs view - +90° rotation of measurement frame]]
 
|}
 
|}
  
−
== General Information ==
+
= General Information =
−
===Module Type & Category===
+
==Module Type & Category==
  
 
Type: Interactive
 
Type: Interactive
Line 17: Line 17:
 
Category: Diffusion Imaging
 
Category: Diffusion Imaging
  
−
===Authors, Collaborators & Contact===
+
==Authors, Collaborators & Contact==
 
* Author: Kerstin Kessel
 
* Author: Kerstin Kessel
 
* Supervisor: Steve Pieper, Ron Kikinis
 
* Supervisor: Steve Pieper, Ron Kikinis
  
−
===Module Description===
+
==Module Description==
−
<font color="Red"> TODO: Overview of what the module does goes here.</font>
+
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 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.
+
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.  
  
−
*1.Step: Generate a Nrrd-header of your DWI data. Use the "Dicom to Nrrd" module in Slicer3 (Modules->Converters->Dicom to Nrrd).
+
=== Measurement Frame ===
−
**-> A .nhdr file will be created.
+
The measurement frame of all DWI is always displayed in the RAS space. That's because Slicer stores all internal coordinates in RAS.  
−
*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.
 
  
 +
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 [[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.
  
−
== Usage ==
+
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.
  
−
===Examples, Use Cases & Tutorials===
+
=== Used Tractography Fiducial Seeding ===  
−
<font color="Red"> TODO:
+
The Diffusion Editor uses the Tractography Fiducial Seeding module of Slicer to compute tracts.
−
* Note use cases for which this module is especially appropriate, and/or link to examples.
+
* 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.
−
* Link to examples of the module's use </font>
+
* 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.
  
−
Tutorials
+
=== 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#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"
 
{| border="1"
 
|- bgcolor="#abcdef"
 
|- bgcolor="#abcdef"
−
! Title !! short description
+
! title !!short description
 
|-
 
|-
−
| Load || Load a dicom data set in Slicer
+
| [[Tutorials:DiffusionEditor-Load DWI-Dicom| Load DICOM]]  ||Load a DWI dicom data set in Slicer.
 
|-
 
|-
−
| Measurement frame || Change the measurement frame by rotating, swaping, negating or changing to idendity
+
| [[Tutorials:DiffusionEditor-Edit Gradients | Edit gradients ]]||Change gradients manually and load them from a file. Save your changes afterwards.
 
|-
 
|-
−
| Gradients || Change gradients manually or loading from a file
+
| [[Tutorials:DiffusionEditor-Edit Measurement frame| 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
+
| [[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===
+
==Quick Tour of Features and Use==
  
−
[[Image:Diffusion Editor v1.jpg|right|overview]]
+
[[Image:DiffusionEditor_v8.jpg|right|overview]]
  
−
<font color="Red"> TODO:
+
* '''Measurement frame:'''
−
List all the panels in your interface, their features, what they mean, and how to use them. For instance:
 
  
−
* '''Measurement Frame panel:'''
+
# The determinant of the measurement frame has to be 1. This is checked by the editor.
−
* '''Gradients panel:'''
+
# '''Invert''': Select the columns you want to invert.
−
* '''Testing panel:'''</font>
+
# '''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.
  
−
==== What you can do with the Gradient Editor====
+
* '''Gradients frame:'''
−
''TODO: more details.''
+
# 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 ]]).
  
−
#'''Choose measurement frame'''.
+
* '''Undo/Redo/Restore:'''
−
## '''Negative''': Select the columns you want to negative.
 
−
## '''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.
 
−
#'''Define gradients'''.
 
−
## If the .nhdr file has the information about the gradients, the editor will put them in the text field.
 
−
## You can copy/paste your own gradients in the text field.
 
−
## You can load gradients from a plain text file or .nhdr file.
 
 
#'''Undo''': Undo the last change of measurement/gradient values.
 
#'''Undo''': Undo the last change of measurement/gradient values.
 
#'''Redo''': Redo the last change of measurement/gradient values.
 
#'''Redo''': Redo the last change of measurement/gradient values.
 
#'''Restore''': All parameters are restored to original.
 
#'''Restore''': All parameters are restored to original.
−
#'''Run test'''.
+
<font color="Red">NOTE:</font> You lose all previous changes when a new active volume is loaded or selected.
−
## Add a Fiducial List. To see if the chosen parameters are reasonable, you can run a test that automatically
 
−
### computes the Tensor and
 
−
### visualizes them by Tractography Seeding. (both with standard values)
 
−
#'''Display DTI''': Select a DTI volume from the current mrml scene and see its tracts.
 
  
−
== Development ==
+
* '''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.
  
−
=== Status / Implementation Progress ===
+
= Development =
 +
 
 +
== Status / Implementation Progress ==
 
The editor is now successfully integrated in the Volumes module of the trunk version of Slicer3.
 
The editor is now successfully integrated in the Volumes module of the trunk version of Slicer3.
 
*measurement frame (gui/load/change/save): 100%
 
*measurement frame (gui/load/change/save): 100%
 
*gradients (gui/load/change/save): 100%
 
*gradients (gui/load/change/save): 100%
 
*undo/redo/restore mechanism: 100%
 
*undo/redo/restore mechanism: 100%
−
*test: 75%
+
*testing frame: 100%
−
** tensor estimation with existing clm: 100%
+
** tensor estimation for DWI with existing clm: 100%
−
** glyphs view in all32 planes with the possibility to change resolution: 100%
+
** glyphs view in all three planes with the possibility to change spacing: 100%
−
** alternative tensor estimation with new filter: 0%
 
−
*** filter for tensor rotation: 0%
 
 
** tractography fiducial seeding: 100%
 
** tractography fiducial seeding: 100%
−
*testing: 0%
+
*ctest: 100%
−
*documentation, tutorials (videos): 40%
+
*documentation, tutorials (videos): 100%
−
*writing master thesis: 5% :-)
+
*writing master thesis: 60% :-)
  
−
===Known bugs===
+
== 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:
 
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:
Line 110: Line 131:
 
http://na-mic.org/Mantis/main_page.php
 
http://na-mic.org/Mantis/main_page.php
  
−
===Source code & documentation===
+
Queries, feature requests and other feedback should be posted on [https://discourse.slicer.org/ Slicer discourse website]. You can also sign up at the website 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 [[Slicer3:EventBroker|Eventbroker]] for performance analysis and if necessary turn off events.
 +
 
 +
== Source code & documentation ==
  
 
Source code is available here:
 
Source code is available here:
  
−
http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerGradientEditorWidget.cxx
+
http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorWidget.cxx
−
http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerGradientEditorWidget.h
+
http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorWidget.h
  
−
http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerGradientEditorLogic.cxx
+
http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorLogic.cxx
−
http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerGradientEditorLogic.h
+
http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionEditorLogic.h
  
−
http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerMeasurementFrameWidget.cxx
+
http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerMeasurementFrameWidget.cxx
−
http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerMeasurementFrameWidget.h
+
http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerMeasurementFrameWidget.h
  
−
http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerGradientsWidget.cxx
+
http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerGradientsWidget.cxx
−
http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerGradientsWidget.h
+
http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerGradientsWidget.h
  
−
http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerDWITestingWidget.cxx
+
http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionTestingWidget.cxx
−
http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Volumes/vtkSlicerDWITestingWidget.h
+
http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/vtkSlicerDiffusionTestingWidget.h
  
 
Links to documentation generated by doxygen:
 
Links to documentation generated by doxygen:
Line 133: Line 164:
 
http://www.na-mic.org/Slicer/Documentation/Slicer3/html/
 
http://www.na-mic.org/Slicer/Documentation/Slicer3/html/
  
−
== More Information ==
+
= More Information =
−
<font color="Red">
 
−
===Acknowledgement===
 
−
Include funding and other support here.
 
−
 
 
−
===References===
 
−
Publications related to this module go here. Links to pdfs would be useful. </font>
 
  
−
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]
+
== 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.
  
−
DTMRI: [http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI]
+
==References==
 +
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]
 
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]

Latest revision as of 14:52, 27 November 2019

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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

  • 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 [[Slicer3:DTMRI#Tensor_Estimation_from_DWI_Module],|[1]] 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 [[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 [2]].* See 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 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 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.

Tutorials

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

overview
  • Measurement frame:
  1. The determinant of the measurement frame has to be 1. This is checked by the editor.
  2. Invert: Select the columns you want to invert.
  3. Swap: Select two columns you want to swap.
  4. Rotate: Select one column you want to rotate by an angle you can choose from a given set of values or set yourself.
  5. Identity: Set the measurement frame to the identity matrix.
  6. Set your own values.
  • Gradients frame:
  1. If the active volume is a DWI the editor will put the gradients in the text field; otherwise this frame is disabled.
  2. You can copy/paste your own gradients in the text field or change them manually.
  3. 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:
  1. Undo: Undo the last change of measurement/gradient values.
  2. Redo: Redo the last change of measurement/gradient values.
  3. Restore: All parameters are restored to original.

NOTE: You lose all previous changes when a new active volume is loaded or selected.

  • Testing frame:
  1. Run tensor estimation. The new tensor node shows up in the DTI selector.
  2. 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.

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 posted on Slicer discourse website. You can also sign up at the website 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 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 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: https://www.slicer.org/wiki/Media:Thesis_letter.pdf DTMRI: https://www.slicer.org/wiki/Slicer3:DTMRI 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

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