NAMIC Wiki - User contributions [en]

Slicer3:Diffusion Editor

2008-05-05T00:41:04Z

Kerstin:

see new wiki on slicer.org: [http://www.slicer.org/slicerWiki/index.php/Modules:Volumes:Diffusion_Editor-Documentation http://www.slicer.org/slicerWiki/index.php/Modules:Volumes:Diffusion_Editor-Documentation]

Slicer3:Diffusion Editor

2008-05-05T00:40:07Z

Kerstin: Removing all content from page

Slicer3:Developers

2008-04-24T21:45:10Z

Kerstin: /* Slicer 3 Projects */

{| class="toccolours" style="margin-right: 25px" align="right"
! bgcolor="#ccccff" align="center" | Slicer3
|-
|
[[Slicer3|Home]]
|-
|
[[Slicer3:About|About]]
|-
|
[[Slicer3:FAQ|FAQ]]
|-
|
[[Slicer3:Status|Status]]
|-
|
[[Slicer3:Downloads|Downloads]]
|-
|
[[Slicer3:Documentation|Documentation]]
|-
|
[[Slicer3:Community_Support|Community Support]]
|-
| '''Developers'''
|-
|
[[Slicer3:Acknowledgements|Acknowledgements]]
|-
|
[[Slicer3:Links|Links]]
|}

== Slicer 3 Overview ==
[[Image:Slicer3LogoHorizontalBeta.png]]

* For more details on the slicer architecture see: [[media:Slicer 3-beta-2007-04-16.ppt | Architecture Slides]] (updated April, 2007).
* Highlights of the new architecture

{|
|[[Image:Slicer3-Architecture.jpg|thumb|200px]]
|[[Image:Slicer3-Architecture-MRML.jpg|thumb|200px]]
|[[Image:Slicer3-Architecture-Layers.jpg|200px|thumb]]
|[[Image:ExecutionModelPlugins.png|200px|thumb]]
|}

== Information for Developers ==
This section centrally locates many existing (and developing) wiki pages useful to Slicer3 developers. The content developed for the January 2007 AHM.

=== Introduction to Slicer3 ===
* [[Media:SlicerHistoricalTimeline.ppt | Slicer3 Historical Timeline]]
* [[Slicer3:Status_Summary | Status overview]] and [http://slicerl.bwh.harvard.edu/tmp/slicer3-PreAHMBeta%20Demo/slicer3-PreAHMBeta.htm Demo]
* [[Media:GUIMap.png|Schematic of application interface & functionality]]
* [[Media:SliceGUI.png|Schematic of slice GUI]]
* [[Slicer3:Build_Instructions | Getting the software and troubleshooting]]
* [[media:Slicer 3-beta-2007-01-10.ppt | Overall Architecture]] and [[Slicer3:Style|Slicer 3 Coding Style]]
* [[Slicer3:Contributing_codes_to_Slicer3| Contributing codes to Slicer3]]

=== Two module types (Command line and Interactive) ===
* [[Slicer3:Execution_Model_Documentation | Command line modules and how to implement one]] (Jim and Bill) [[media:Slicer3-ExecutionModelJune2006.ppt| Intro]]
*[[Slicer3:How_to_implement_an_Interactive_Module_GUI | How to implement an interactive module]] (wjp)

=== MRML [http://www.na-mic.org/Wiki/images/e/e3/Slicer3_MRML.ppt MRML Slides](Alex) ===
Medical Reality Modeling Language (MRML) is a language implemented as a type of XML document, with new tags defined to handle medical image data types such as volumes, models or coordinate transforms.

* [[Slicer3:Data_Model#Creating_Custom_MRML_Node_Classes | Creating and using new MRML node types]] (Alex)
* [[Slicer3:Data_Model#References_to_MRML_Nodes | Keeping references to MRML nodes ]] (Alex)
* [[Slicer3:Data_Model#Undo/Redo_Mechanism | How undo/redo works, and how to enable it in your code]] (Alex)

=== GUI ===
* [[Slicer3:StatelessGUI | Keeping the GUI stateless]] (wjp)
* [[Slicer3:EventBindings | Adding keyboard shortcuts]] (wjp)
* [[Slicer3:Human_Interface_and_Style_Guide_for_Developers | GUI style guidelines]] (wjp)
* [[Slicer3:Usability#User-centered_design_practice_for_3DSlicer | User-centered design practice]] (wjp)
* [[Slicer3:Slicer3Brand | 3DSlicer's logo and visual communication guidelines]] (wjp)
* [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3 | Incorporating your group's logo and attributions]] (Jim)
* [[Slicer3:GUI_Experiments | Some experiments/advanced techniques for developing slicer3 interfaces]] (Steve)

=== Engineering ===
* Tips for avoiding memory leaks
** Current Practice (Steve)
** [[Slicer3:Memory Management | Suggested change to SmartPointers]] (Jim)
* Generating tests (Bill)
* [[Slicer3:Testing | Setting up Testing]]
* [[Slicer3:Launcher| The Launcher]]

=== Documenting your module ===
* As soon as the wiki page template is finalized, and the infrastructure is added to link to this wiki page from the "Help & Acknowledgment" panel in your module's GUI, we will ask developers to fill out a brief document describing your module and its use. Stay tuned for developments...
* [[Slicer3:DocumentationWink|Documenting a module with wink]]

=== Integrate Slicer3 into a development environment ===
* [[Slicer3::Eclipse | Eclipse]] (keilhack)
* [[Slicer3::MSVS200X | Microsoft Visual Studio 200x]]

== Slicer 3 Projects ==

Projects should correspond to the outstanding issues listed on the '''[[Slicer3:Status_Summary|Status Summary]]'''. Please refer to the '''[[Slicer3:FeatureRequests|Feature Requests]]''' from users when planning your implementations.

''If your name is in bold, you are responsible for that aspect of the project''

* '''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata)
* '''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve)
* '''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
* '''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan)
* '''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
** [[Slicer3:DTMRI|DTMRI]]<nowiki>: </nowiki>'''Alex''' with help from Diffusion Images: '''Raul''', Tractography: '''Lauren''' [http://lmi.bwh.harvard.edu LMI]
** [[Slicer3:Editor|Editor]]<nowiki>: </nowiki>'''Steve'''
** [[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''
** [[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]<nowiki>: </nowiki>'''Haiying'''
** [[Slicer3:EM|EMSegment Interface]]<nowiki>: </nowiki>'''Brad Davis'''
** [[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]<nowiki>: </nowiki>'''Steve Pieper'''
* '''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)
* '''[[Slicer3:Pipeline_Integration|Loni Pipeline Integration]]''' ('''Jags''')
* '''[[Slicer3:Batchmake_Integration|Batchmake/GRID Integration]]''' ('''Julien Jomier''')
* '''[[Slicer3:Registration|Registration Modules]]''' ('''Jim Miller''', Steve Pieper)
* '''[http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization Improvements to the registration framework]''' ('''Stephen Aylward''')
* '''[[Slicer3:Python|Python Integration]]''' ('''Dan Blezek''')
* '''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Jeff Grethe''', Neil)
* '''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')
* '''[[Slicer3:ThreadingToolKit|Threading ToolKit]]''' ('''Dan Blezek, James Miller, Stephen Aylward''')
* '''[[Slicer3:Volume Rendering |Volume Rendering]]''' ('''Andy''')
* '''[[Slicer3:Volume Rendering With Cuda|Volume Rendering With CUDA]]''' ('''Ben''')
* '''[[Slicer3:XNAT |XNAT Interface]]''' ('''Steve''', Wendy, Dan Marcus, Tim Olsen)
* '''[[Slicer3:LDDMM |LDDMM Interface]]''' ('''Steve''', Anthony Kolasny)
* '''[[Slicer3:Web Presence |Web Presence]]''' ('''Nicole Aucoin'''), Zack Galbreath
* '''[[Slicer3:Loadable Modules |Loadable Modules]]''' ('''Alex Yarmarkovich'''), Steve Pieper
* '''[http://www.slicer.org/slicerWiki/index.php/Modules:Volumes:Diffusion_Editor-Documentation Diffusion Editor]''' ('''Kerstin''')
* '''[[Slicer3:TimeSeries and Multi-Volume Data | TimeSeries and Multi-Volume Data]]''' (Steve Pieper, Daniel Blezek, Dominik Meier, Wendy Plesniak)
* '''[[Slicer3:Remote Data Handling | Remote Data Handling]]''' (Steve Pieper, Nicole Aucoin, Wendy Plesniak)
* '''[[Slicer3:Module:QueryAtlas |Query Atlas]]''' ('''Wendy Plesniak''')

== Slicer 3 Quick links to the Source code ==

The Slicer3 svn repository:

svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3

Use [http://www.na-mic.org/ViewVC/index.cgi/ ViewVC to browse the repository]

[[Engineering:SandBox|Instructions for NA-MIC svn]]

[[Slicer3:Build_Instructions|Slicer3 build instructions]]

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Doxygen documentation for Slicer3].

The [[Slicer3:VisualBlog|Slicer3 VisualBlog]] shows screenshots of slicer developments.

Developers should follow the [[Slicer3:Style|Slicer 3 Coding Style]].

[http://www.na-mic.org/Slicer3/Dashboard Slicer3 Dashboard]

[http://na-mic.org/Mantis/main_page.php Slicer Bug Tracker]

Discussion of slicer3 takes place on the slicer-devel@massmail.spl.harvard.edu list. To join developer's mailing list, send a request to: [mailto:slicer-devel-request@massmail.spl.harvard.edu slicer-devel-request@massmail.spl.harvard.edu] with the keyword ''subscribe'' as the subject. Or access the [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel slicer-devel archives and web administration interface].

== Design Information ==

May 23, 2006: [[Algorithms:Core1Visit_May06|Algorithm Core workshop.]]

<br /> April 3, 2006: [[Media:Slicer_3-alpha-2006-04-03.ppt| Slicer 3 alpha]] technical powerpoint presentation.

<br />

= Events =

== Upcoming ==

=== Slicer3.0 ===

* the first product release of Slicer3 is scheduled for the AHM in January of 2008
* there will be a code freeze on Nov. 15 2007
** if you want your module to be part of Slicer3.0 submit it by then
** After that date, we will only accept bug fixes. It means that there will be no features added after the freeze in the main trunk.

** Any people working on new features can do so in their own branch and they will be responsible for merging these back into the trunk after the freeze is lifted (at which point the release will be in a maintenance branch).

== Retrospective ==

=== Slicer 3 Snapshot Builds ===

* Initial releases began end of March 2007
** Base code functional and usable
** Several usable modules include (auto segmentaiton, editor, registration...)
** Image Guided Therapy example modules
* Updated versions summer 2007
** With DTI and other application modules
** Bug fixes and performance enhancements

=== Migration Tutorials (from Slicer 2.x to 3.0) ===

The first set of user tutorials will be released in Fall 2007.
Slicer3 programming courses will be released in January 2008.

== Past ==

=== Slicer3.0 Beta ===

* Official release at [[AHM_2007 | AHM January 2007]]

=== April 3, 2006 ===

There was a [[Slicer3:_Alpha1_Meeting|Slicer3 Alpha1 Design Review]] meeting.

'''[[Slicer3:Alpha|Definition of Alpha Milestone]]'''

=== Slicer3 Alpha2/Beta1 by End of July 2006 ===

* Initial Testing with Core 3 participation
* Base functionality in place, but still subject to API changes and other improvements.
* Packaged versions not yet available, but testers are able to easily build their own versions.

=== Implementation of Slicer3 Alpha1 by end of March 2006 ===

Slicer3:Developers

2008-04-24T15:44:56Z

Kerstin: /* Slicer 3 Projects */

{| class="toccolours" style="margin-right: 25px" align="right"
! bgcolor="#ccccff" align="center" | Slicer3
|-
|
[[Slicer3|Home]]
|-
|
[[Slicer3:About|About]]
|-
|
[[Slicer3:FAQ|FAQ]]
|-
|
[[Slicer3:Status|Status]]
|-
|
[[Slicer3:Downloads|Downloads]]
|-
|
[[Slicer3:Documentation|Documentation]]
|-
|
[[Slicer3:Community_Support|Community Support]]
|-
| '''Developers'''
|-
|
[[Slicer3:Acknowledgements|Acknowledgements]]
|-
|
[[Slicer3:Links|Links]]
|}

== Slicer 3 Overview ==
[[Image:Slicer3LogoHorizontalBeta.png]]

* For more details on the slicer architecture see: [[media:Slicer 3-beta-2007-04-16.ppt | Architecture Slides]] (updated April, 2007).
* Highlights of the new architecture

{|
|[[Image:Slicer3-Architecture.jpg|thumb|200px]]
|[[Image:Slicer3-Architecture-MRML.jpg|thumb|200px]]
|[[Image:Slicer3-Architecture-Layers.jpg|200px|thumb]]
|[[Image:ExecutionModelPlugins.png|200px|thumb]]
|}

== Information for Developers ==
This section centrally locates many existing (and developing) wiki pages useful to Slicer3 developers. The content developed for the January 2007 AHM.

=== Introduction to Slicer3 ===
* [[Media:SlicerHistoricalTimeline.ppt | Slicer3 Historical Timeline]]
* [[Slicer3:Status_Summary | Status overview]] and [http://slicerl.bwh.harvard.edu/tmp/slicer3-PreAHMBeta%20Demo/slicer3-PreAHMBeta.htm Demo]
* [[Media:GUIMap.png|Schematic of application interface & functionality]]
* [[Media:SliceGUI.png|Schematic of slice GUI]]
* [[Slicer3:Build_Instructions | Getting the software and troubleshooting]]
* [[media:Slicer 3-beta-2007-01-10.ppt | Overall Architecture]] and [[Slicer3:Style|Slicer 3 Coding Style]]
* [[Slicer3:Contributing_codes_to_Slicer3| Contributing codes to Slicer3]]

=== Two module types (Command line and Interactive) ===
* [[Slicer3:Execution_Model_Documentation | Command line modules and how to implement one]] (Jim and Bill) [[media:Slicer3-ExecutionModelJune2006.ppt| Intro]]
*[[Slicer3:How_to_implement_an_Interactive_Module_GUI | How to implement an interactive module]] (wjp)

=== MRML [http://www.na-mic.org/Wiki/images/e/e3/Slicer3_MRML.ppt MRML Slides](Alex) ===
Medical Reality Modeling Language (MRML) is a language implemented as a type of XML document, with new tags defined to handle medical image data types such as volumes, models or coordinate transforms.

* [[Slicer3:Data_Model#Creating_Custom_MRML_Node_Classes | Creating and using new MRML node types]] (Alex)
* [[Slicer3:Data_Model#References_to_MRML_Nodes | Keeping references to MRML nodes ]] (Alex)
* [[Slicer3:Data_Model#Undo/Redo_Mechanism | How undo/redo works, and how to enable it in your code]] (Alex)

=== GUI ===
* [[Slicer3:StatelessGUI | Keeping the GUI stateless]] (wjp)
* [[Slicer3:EventBindings | Adding keyboard shortcuts]] (wjp)
* [[Slicer3:Human_Interface_and_Style_Guide_for_Developers | GUI style guidelines]] (wjp)
* [[Slicer3:Usability#User-centered_design_practice_for_3DSlicer | User-centered design practice]] (wjp)
* [[Slicer3:Slicer3Brand | 3DSlicer's logo and visual communication guidelines]] (wjp)
* [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3 | Incorporating your group's logo and attributions]] (Jim)
* [[Slicer3:GUI_Experiments | Some experiments/advanced techniques for developing slicer3 interfaces]] (Steve)

=== Engineering ===
* Tips for avoiding memory leaks
** Current Practice (Steve)
** [[Slicer3:Memory Management | Suggested change to SmartPointers]] (Jim)
* Generating tests (Bill)
* [[Slicer3:Testing | Setting up Testing]]
* [[Slicer3:Launcher| The Launcher]]

=== Documenting your module ===
* As soon as the wiki page template is finalized, and the infrastructure is added to link to this wiki page from the "Help & Acknowledgment" panel in your module's GUI, we will ask developers to fill out a brief document describing your module and its use. Stay tuned for developments...
* [[Slicer3:DocumentationWink|Documenting a module with wink]]

=== Integrate Slicer3 into a development environment ===
* [[Slicer3::Eclipse | Eclipse]] (keilhack)
* [[Slicer3::MSVS200X | Microsoft Visual Studio 200x]]

== Slicer 3 Projects ==

Projects should correspond to the outstanding issues listed on the '''[[Slicer3:Status_Summary|Status Summary]]'''. Please refer to the '''[[Slicer3:FeatureRequests|Feature Requests]]''' from users when planning your implementations.

''If your name is in bold, you are responsible for that aspect of the project''

* '''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata)
* '''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve)
* '''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
* '''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan)
* '''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
** [[Slicer3:DTMRI|DTMRI]]<nowiki>: </nowiki>'''Alex''' with help from Diffusion Images: '''Raul''', Tractography: '''Lauren''' [http://lmi.bwh.harvard.edu LMI]
** [[Slicer3:Editor|Editor]]<nowiki>: </nowiki>'''Steve'''
** [[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''
** [[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]<nowiki>: </nowiki>'''Haiying'''
** [[Slicer3:EM|EMSegment Interface]]<nowiki>: </nowiki>'''Brad Davis'''
** [[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]<nowiki>: </nowiki>'''Steve Pieper'''
* '''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)
* '''[[Slicer3:Pipeline_Integration|Loni Pipeline Integration]]''' ('''Jags''')
* '''[[Slicer3:Batchmake_Integration|Batchmake/GRID Integration]]''' ('''Julien Jomier''')
* '''[[Slicer3:Registration|Registration Modules]]''' ('''Jim Miller''', Steve Pieper)
* '''[http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization Improvements to the registration framework]''' ('''Stephen Aylward''')
* '''[[Slicer3:Python|Python Integration]]''' ('''Dan Blezek''')
* '''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Jeff Grethe''', Neil)
* '''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')
* '''[[Slicer3:ThreadingToolKit|Threading ToolKit]]''' ('''Dan Blezek, James Miller, Stephen Aylward''')
* '''[[Slicer3:Volume Rendering |Volume Rendering]]''' ('''Andy''')
* '''[[Slicer3:Volume Rendering With Cuda|Volume Rendering With CUDA]]''' ('''Ben''')
* '''[[Slicer3:XNAT |XNAT Interface]]''' ('''Steve''', Wendy, Dan Marcus, Tim Olsen)
* '''[[Slicer3:LDDMM |LDDMM Interface]]''' ('''Steve''', Anthony Kolasny)
* '''[[Slicer3:Web Presence |Web Presence]]''' ('''Nicole Aucoin'''), Zack Galbreath
* '''[[Slicer3:Loadable Modules |Loadable Modules]]''' ('''Alex Yarmarkovich'''), Steve Pieper
* '''[[Slicer3:Diffusion Editor |Diffusion Editor]]''' ('''Kerstin''')
* '''[[Slicer3:TimeSeries and Multi-Volume Data | TimeSeries and Multi-Volume Data]]''' (Steve Pieper, Daniel Blezek, Dominik Meier, Wendy Plesniak)
* '''[[Slicer3:Remote Data Handling | Remote Data Handling]]''' (Steve Pieper, Nicole Aucoin, Wendy Plesniak)
* '''[[Slicer3:Module:QueryAtlas |Query Atlas]]''' ('''Wendy Plesniak''')

== Slicer 3 Quick links to the Source code ==

The Slicer3 svn repository:

svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3

Use [http://www.na-mic.org/ViewVC/index.cgi/ ViewVC to browse the repository]

[[Engineering:SandBox|Instructions for NA-MIC svn]]

[[Slicer3:Build_Instructions|Slicer3 build instructions]]

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Doxygen documentation for Slicer3].

The [[Slicer3:VisualBlog|Slicer3 VisualBlog]] shows screenshots of slicer developments.

Developers should follow the [[Slicer3:Style|Slicer 3 Coding Style]].

[http://www.na-mic.org/Slicer3/Dashboard Slicer3 Dashboard]

[http://na-mic.org/Mantis/main_page.php Slicer Bug Tracker]

Discussion of slicer3 takes place on the slicer-devel@massmail.spl.harvard.edu list. To join developer's mailing list, send a request to: [mailto:slicer-devel-request@massmail.spl.harvard.edu slicer-devel-request@massmail.spl.harvard.edu] with the keyword ''subscribe'' as the subject. Or access the [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel slicer-devel archives and web administration interface].

== Design Information ==

May 23, 2006: [[Algorithms:Core1Visit_May06|Algorithm Core workshop.]]

<br /> April 3, 2006: [[Media:Slicer_3-alpha-2006-04-03.ppt| Slicer 3 alpha]] technical powerpoint presentation.

<br />

= Events =

== Upcoming ==

=== Slicer3.0 ===

* the first product release of Slicer3 is scheduled for the AHM in January of 2008
* there will be a code freeze on Nov. 15 2007
** if you want your module to be part of Slicer3.0 submit it by then
** After that date, we will only accept bug fixes. It means that there will be no features added after the freeze in the main trunk.

** Any people working on new features can do so in their own branch and they will be responsible for merging these back into the trunk after the freeze is lifted (at which point the release will be in a maintenance branch).

== Retrospective ==

=== Slicer 3 Snapshot Builds ===

* Initial releases began end of March 2007
** Base code functional and usable
** Several usable modules include (auto segmentaiton, editor, registration...)
** Image Guided Therapy example modules
* Updated versions summer 2007
** With DTI and other application modules
** Bug fixes and performance enhancements

=== Migration Tutorials (from Slicer 2.x to 3.0) ===

The first set of user tutorials will be released in Fall 2007.
Slicer3 programming courses will be released in January 2008.

== Past ==

=== Slicer3.0 Beta ===

* Official release at [[AHM_2007 | AHM January 2007]]

=== April 3, 2006 ===

There was a [[Slicer3:_Alpha1_Meeting|Slicer3 Alpha1 Design Review]] meeting.

'''[[Slicer3:Alpha|Definition of Alpha Milestone]]'''

=== Slicer3 Alpha2/Beta1 by End of July 2006 ===

* Initial Testing with Core 3 participation
* Base functionality in place, but still subject to API changes and other improvements.
* Packaged versions not yet available, but testers are able to easily build their own versions.

=== Implementation of Slicer3 Alpha1 by end of March 2006 ===

Slicer3:Diffusion Editor

2008-04-24T15:44:06Z

Kerstin: Slicer3:DWI Gradient Editor moved to Slicer3:Diffusion Editor

== Overview ==
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.
=== Background (why specific editor features are needed) ===
''TODO''

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

<gallery caption="Interface" widths="150px" heights="150px" perrow="4">
Image:DWI_Gradient_Editor.jpg|1st Version (tcl)
Image:DWI_Gradient_Editor_v2.jpg|integrated in Slicer3 branch
Image:DWI_Gradient_Editor_v4.jpg|integrated in Slicer3 trunk, some GUI elements are no longer necessary
Image:DWI_Gradient_Editor_v5.jpg|new features added
</gallery>

== 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 with the Gradient Editor===
''TODO: more details.''

#'''Choose measurement frame'''.
## '''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.
#'''Redo''': Redo the last change of measurement/gradient values.
#'''Restore''': All parameters are restored to original.
#'''Run test'''.
## 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.

== 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, demo video: 40%
*writing master thesis: 5% :-)

== Additional Information ==

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]

DTMRI: [http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI]

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]

Slicer3:DWI Gradient Editor

2008-04-24T15:44:06Z

Kerstin: Slicer3:DWI Gradient Editor moved to Slicer3:Diffusion Editor

#REDIRECT [[Slicer3:Diffusion Editor]]

Kerstin: /* Additional Information */

== 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.

<gallery caption="Interface" widths="150px" heights="150px" perrow="4">
Image:DWI_Gradient_Editor_v4.jpg|integrated in Slicer3 trunk, some GUI elements are no longer necessary
Image:DWI_Gradient_Editor_v3.jpg
Image:DWI_Gradient_Editor_v2.jpg|integrated in Slicer3 branch
Image:DWI_Gradient_Editor.jpg|1st Version (tcl)
</gallery>

== 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 with the Gradient Editor===

#'''Choose measurement frame'''.
## '''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.
## 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.
#'''Run test'''.
## Add a Feducial 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)
#'''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 http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format]

DTMRI: [http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI]

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]

Slicer3:Diffusion Editor

2008-01-24T22:16:25Z

Kerstin: /* Additional Information */

Slicer3:Diffusion Editor

2008-01-24T22:16:14Z

Kerstin: /* Additional Information */

== 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.

<gallery caption="Interface" widths="150px" heights="150px" perrow="4">
Image:DWI_Gradient_Editor_v4.jpg|integrated in Slicer3 trunk, some GUI elements are no longer necessary
Image:DWI_Gradient_Editor_v3.jpg
Image:DWI_Gradient_Editor_v2.jpg|integrated in Slicer3 branch
Image:DWI_Gradient_Editor.jpg|1st Version (tcl)
</gallery>

== 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 with the Gradient Editor===

#'''Choose measurement frame'''.
## '''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.
## 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.
#'''Run test'''.
## Add a Feducial 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)
#'''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 http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format]
DTMRI: [http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI http://wiki.na-mic.org/Wiki/index.php/Slicer3:DTMRI]

2008-01-24T22:05:11Z

Kerstin: /* What you can do with the Gradient 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.

<gallery caption="Interface" widths="150px" heights="150px" perrow="4">
Image:DWI_Gradient_Editor_v4.jpg|integrated in Slicer3 trunk, some GUI elements were no longer necessary
Image:DWI_Gradient_Editor_v3.jpg
Image:DWI_Gradient_Editor_v2.jpg|integrated in Slicer3 branch
Image:DWI_Gradient_Editor.jpg|1st Version (tcl)
</gallery>

== 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 with the Gradient Editor===

#''' Choose measurement frame'''.
## '''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.
## 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.
#'''Run test'''.
## Add a Feducial 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)
#'''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 http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format]