NAMIC Wiki - User contributions [en]

2010 Summer Project Week Breakout Session:OpenIGTLink

2010-05-28T00:24:36Z

PatrickCheng: /* Agenda */

Back to [[2010_Summer_Project_Week]]

Organizer: Junichi Tokuda 
Date: Thursday, June 24, 2010 
OpenIGTLink Home Page: [[OpenIGTLink]]

=Agenda=

Please note that this agenda is currently under construction and will be finalized by May 28th.

*9-10am:
**Case Experience
**Summary of OpenIGTLink
**Discussion on protocol version 2.
*10a-12pm: Hands-on session. Specifics of this session will be decided after the May 27th tcon.
*12-1pm: Break for lunch
*1-2pm: Demos of working OpenIGTLink based systems
**AIST demos (TBD)
*2-3pm: OpenIGTLink Library, 3D Slicer and other tools
*3-4pm: Simulator Discussion

Suggestions for agenda from TCON:
*Tracker simulator (Haiying)
*General session on simulators (maybe there should be a general discussion on this)
*Suggestions for hands-on session
**hello world type demo application
**5-10 minutes from each of the vendors on how they can use it?
**compare OpenIGTLink with Steathlink protocol
**hands-on help in WPI system up and running (Greg will confirm)
**planning to interface aurora tracker with Slicer using OpenIGTLink (Tamas)
**discussion about the implementation -- message queueing idea/transport layer (Patrick Georgetown, Steve to followup)
*** Comments from Patrick
**** For latest update on this, please refer to the CTK wiki: http://www.commontk.org/index.php/Documentation/Messaging
**** '''Suggestion:''' use [http://msdn.microsoft.com/en-us/library/ff647328.aspx Message Bus] and [http://msdn.microsoft.com/en-us/library/ff649664(v=pandp.10).aspx Publisher/Subscriber] design pattern for system integration
**** OpenIGTLink can be used to define the common message schema, and ZeroMQ can be used to handle the transportation layer abstraction
**** [http://www.zeromq.org/ ZeroMQ] is a small and fast implementation of the [http://en.wikipedia.org/wiki/Advanced_Message_Queuing_Protocol Advanced Message Queuing Protocol] under the LGPL license
**** It supports both synchronous and asynchronous messaging mode
**** It supportsTCP, Multicast/PGM, Inter-process, and inter-thread transportation
**** CMake version of library can be found here http://github.com/PatrickCheng/zeromq2
**** API can be found here http://api.zeromq.org/zmq.html
--------------

=Notes=
==Discussion on OpenIGTLink Protocol version 2==
*Finalize version 2 protocol
**[[OpenIGTLink/ProtocolV2/Summary| Summary of version 2 protocol]]
**New support for image-guided systems
***Discussion on new commands is [[OpenIGTLink/Discussion/NewCommands|in progress]].
**Matlab integration
***There have been several requests for Matlab OpenIGTLink interface.
***[[OpenIGTLink/Matlab|Prototype Matlab/Octave interface]] is available.
***New message type to support "remote procedure call"??
**(Please put your agenda here)
==Dissemination, collaboration etc.)==
The following item is part of NCIGT. We need inputs from Ron and Tina.
*Tutorial (how we do now, and how it should be)
*web presence (how we are, and how it should be)
*Ctest (how we do)
*Use Slicer ML or dedicated ML?
==Hands-on session (11am-12pm)==
*Opportunity for IGT developers to consult with OpenIGTLink experts and find solutions for their project.
==OpenIGTLink Library, 3D Slicer and other tools==
*Features
*Message classes
*Example programs
*Timeline

<hr/>

=Demo Session=
==AIST demos==
*(TBD)

=Collaborators=
*list of potential collaborator

=Participants=
*Junichi Tokuda
*Nobuhiko Hata
*Haiying Liu

<hr/>

=Teleconference on May 27 (Thu) 3pm-=
==Objectives==
*Topics to discuss during the event
*Finalize the schedule
*Action items

==Participants==
*Please feel free to put your name here
*Junichi Tokuda (BWH)
*Tina Kapur, BWH

==Agenda==
* Agenda in the project week
**Summary of OpenIGTLink
***Short presentation about overview and updates of OpenIGTLink for those who are not in the presentation on Tuesday.
**Discussion on protocol version 2.
***New features for 3D Slicer
***Matlab
***Messages for sensor data (proposed by AIST project)
***Endoscope/camera control
**Hands-on session. Specifics of this session will be decided after the May 27th tcon.
**Demos of working OpenIGTLink based systems
**OpenIGTLink Library, 3D Slicer and other tools
***Matlab interfaces
***3D Slicer user interface
***Tutorials

* Demos (please feel free to add)
**IGSTK demo from Haiying
**AIST demo (may be video)
**New 3D Slicer OpenIGTLink IF

* Breakout session schedule
**Make sure that all participants can sessions they need
**Order of sessions

* Action items by Project Week
** List all potential applications
** List all problems, issues regrading the current protocol
** Feedbacks

2010 Summer Project Week Breakout Session:OpenIGTLink

2010-05-27T23:31:48Z

PatrickCheng: /* Agenda */

Back to [[2010_Summer_Project_Week]]

Organizer: Junichi Tokuda 
Date: Thursday, June 24, 2010 
OpenIGTLink Home Page: [[OpenIGTLink]]

=Agenda=

Please note that this agenda is currently under construction and will be finalized by May 28th.

*9-10am:
**Case Experience
**Summary of OpenIGTLink
**Discussion on protocol version 2.
*10a-12pm: Hands-on session. Specifics of this session will be decided after the May 27th tcon.
*12-1pm: Break for lunch
*1-2pm: Demos of working OpenIGTLink based systems
**AIST demos (TBD)
*2-3pm: OpenIGTLink Library, 3D Slicer and other tools
*3-4pm: Simulator Discussion

Suggestions for agenda from TCON:
*Tracker simulator (Haiying)
*General session on simulators (maybe there should be a general discussion on this)
*Suggestions for hands-on session
**hello world type demo application
**5-10 minutes from each of the vendors on how they can use it?
**compare OpenIGTLink with Steathlink protocol
**hands-on help in WPI system up and running (Greg will confirm)
**planning to interface aurora tracker with Slicer using OpenIGTLink (Tamas)
**discussion about the implementation -- message queueing idea/transport layer (Patrick Georgetown, Steve to followup)
*** Comments from Patrick
**** '''Suggestion:''' use [http://msdn.microsoft.com/en-us/library/ff647328.aspx Message Bus] and [http://msdn.microsoft.com/en-us/library/ff649664(v=pandp.10).aspx Publisher/Subscriber] design pattern for system integration
**** OpenIGTLink can be used to define the common message schema, and ZeroMQ can be used to handle the transportation layer abstraction
**** [http://www.zeromq.org/ ZeroMQ] is a small and fast implementation of the [http://en.wikipedia.org/wiki/Advanced_Message_Queuing_Protocol Advanced Message Queuing Protocol] under the LGPL license
**** It supports both synchronous and asynchronous messaging mode
**** It supportsTCP, Multicast/PGM, Inter-process, and inter-thread transportation
**** CMake version of library can be found here http://github.com/PatrickCheng/zeromq2
**** API can be found here http://api.zeromq.org/zmq.html
--------------

=Notes=
==Discussion on OpenIGTLink Protocol version 2==
*Finalize version 2 protocol
**[[OpenIGTLink/ProtocolV2/Summary| Summary of version 2 protocol]]
**New support for image-guided systems
***Discussion on new commands is [[OpenIGTLink/Discussion/NewCommands|in progress]].
**Matlab integration
***There have been several requests for Matlab OpenIGTLink interface.
***[[OpenIGTLink/Matlab|Prototype Matlab/Octave interface]] is available.
***New message type to support "remote procedure call"??
**(Please put your agenda here)
==Dissemination, collaboration etc.)==
The following item is part of NCIGT. We need inputs from Ron and Tina.
*Tutorial (how we do now, and how it should be)
*web presence (how we are, and how it should be)
*Ctest (how we do)
*Use Slicer ML or dedicated ML?
==Hands-on session (11am-12pm)==
*Opportunity for IGT developers to consult with OpenIGTLink experts and find solutions for their project.
==OpenIGTLink Library, 3D Slicer and other tools==
*Features
*Message classes
*Example programs
*Timeline

<hr/>

=Demo Session=
==AIST demos==
*(TBD)

=Collaborators=
*list of potential collaborator

=Participants=
*Junichi Tokuda
*Nobuhiko Hata
*Haiying Liu

<hr/>

=Teleconference on May 27 (Thu) 3pm-=
==Objectives==
*Topics to discuss during the event
*Finalize the schedule
*Action items

==Participants==
*Please feel free to put your name here
*Junichi Tokuda (BWH)
*Tina Kapur, BWH

==Agenda==
* Agenda in the project week
**Summary of OpenIGTLink
***Short presentation about overview and updates of OpenIGTLink for those who are not in the presentation on Tuesday.
**Discussion on protocol version 2.
***New features for 3D Slicer
***Matlab
***Messages for sensor data (proposed by AIST project)
***Endoscope/camera control
**Hands-on session. Specifics of this session will be decided after the May 27th tcon.
**Demos of working OpenIGTLink based systems
**OpenIGTLink Library, 3D Slicer and other tools
***Matlab interfaces
***3D Slicer user interface
***Tutorials

* Demos (please feel free to add)
**IGSTK demo from Haiying
**AIST demo (may be video)
**New 3D Slicer OpenIGTLink IF

* Breakout session schedule
**Make sure that all participants can sessions they need
**Order of sessions

* Action items by Project Week
** List all potential applications
** List all problems, issues regrading the current protocol
** Feedbacks

2010 Summer Project Week Breakout Session:OpenIGTLink

2010-05-27T22:23:18Z

PatrickCheng: /* Agenda */

Back to [[2010_Summer_Project_Week]]

Organizer: Junichi Tokuda 
Date: Thursday, June 24, 2010 
OpenIGTLink Home Page: [[OpenIGTLink]]

=Agenda=

Please note that this agenda is currently under construction and will be finalized by May 28th.

*9-10am:
**Case Experience
**Summary of OpenIGTLink
**Discussion on protocol version 2.
*10a-12pm: Hands-on session. Specifics of this session will be decided after the May 27th tcon.
*12-1pm: Break for lunch
*1-2pm: Demos of working OpenIGTLink based systems
**AIST demos (TBD)
*2-3pm: OpenIGTLink Library, 3D Slicer and other tools
*3-4pm: Simulator Discussion

Suggestions for agenda from TCON:
*Tracker simulator (Haiying)
*General session on simulators (maybe there should be a general discussion on this)
*Suggestions for hands-on session
**hello world type demo application
**5-10 minutes from each of the vendors on how they can use it?
**compare OpenIGTLink with Steathlink protocol
**hands-on help in WPI system up and running (Greg will confirm)
**planning to interface aurora tracker with Slicer using OpenIGTLink (Tamas)
**discussion about the implementation -- message queueing idea/transport layer (Patrick Georgetown, Steve to followup)
*** Comments from Patrick
**** '''Suggestion:''' Using [http://msdn.microsoft.com/en-us/library/ff647328.aspx Message Bus] and [http://msdn.microsoft.com/en-us/library/ff649664(v=pandp.10).aspx Publisher/Subscriber] design pattern for system integration
**** OpenIGTLink can be used to define the common message schema, and ZeroMQ can be used to handle the transportation layer abstraction
**** [http://www.zeromq.org/ ZeroMQ] is a small and fast implementation of the [http://en.wikipedia.org/wiki/Advanced_Message_Queuing_Protocol Advanced Message Queuing Protocol] under the LGPL license
**** It supports both synchronous and asynchronous messaging mode
**** It supportsTCP, Multicast/PGM, Inter-process, and inter-thread transportation
**** CMake version of library can be found here http://github.com/PatrickCheng/zeromq2
**** API can be found here http://api.zeromq.org/zmq.html
--------------

=Notes=
==Discussion on OpenIGTLink Protocol version 2==
*Finalize version 2 protocol
**[[OpenIGTLink/ProtocolV2/Summary| Summary of version 2 protocol]]
**New support for image-guided systems
***Discussion on new commands is [[OpenIGTLink/Discussion/NewCommands|in progress]].
**Matlab integration
***There have been several requests for Matlab OpenIGTLink interface.
***[[OpenIGTLink/Matlab|Prototype Matlab/Octave interface]] is available.
***New message type to support "remote procedure call"??
**(Please put your agenda here)
==Dissemination, collaboration etc.)==
The following item is part of NCIGT. We need inputs from Ron and Tina.
*Tutorial (how we do now, and how it should be)
*web presence (how we are, and how it should be)
*Ctest (how we do)
*Use Slicer ML or dedicated ML?
==Hands-on session (11am-12pm)==
*Opportunity for IGT developers to consult with OpenIGTLink experts and find solutions for their project.
==OpenIGTLink Library, 3D Slicer and other tools==
*Features
*Message classes
*Example programs
*Timeline

<hr/>

=Demo Session=
==AIST demos==
*(TBD)

=Collaborators=
*list of potential collaborator

=Participants=
*Junichi Tokuda
*Nobuhiko Hata
*Haiying Liu

<hr/>

=Teleconference on May 27 (Thu) 3pm-=
==Objectives==
*Topics to discuss during the event
*Finalize the schedule
*Action items

==Participants==
*Please feel free to put your name here
*Junichi Tokuda (BWH)
*Tina Kapur, BWH

==Agenda==
* Agenda in the project week
**Summary of OpenIGTLink
***Short presentation about overview and updates of OpenIGTLink for those who are not in the presentation on Tuesday.
**Discussion on protocol version 2.
***New features for 3D Slicer
***Matlab
***Messages for sensor data (proposed by AIST project)
***Endoscope/camera control
**Hands-on session. Specifics of this session will be decided after the May 27th tcon.
**Demos of working OpenIGTLink based systems
**OpenIGTLink Library, 3D Slicer and other tools
***Matlab interfaces
***3D Slicer user interface
***Tutorials

* Demos (please feel free to add)
**IGSTK demo from Haiying
**AIST demo (may be video)
**New 3D Slicer OpenIGTLink IF

* Breakout session schedule
**Make sure that all participants can sessions they need
**Order of sessions

* Action items by Project Week
** List all potential applications
** List all problems, issues regrading the current protocol
** Feedbacks

2010 Summer Project Week Breakout Session:OpenIGTLink

2010-05-27T22:08:37Z

PatrickCheng: /* Agenda */

Back to [[2010_Summer_Project_Week]]

Organizer: Junichi Tokuda 
Date: Thursday, June 24, 2010 
OpenIGTLink Home Page: [[OpenIGTLink]]

=Agenda=

Please note that this agenda is currently under construction and will be finalized by May 28th.

*9-10am:
**Case Experience
**Summary of OpenIGTLink
**Discussion on protocol version 2.
*10a-12pm: Hands-on session. Specifics of this session will be decided after the May 27th tcon.
*12-1pm: Break for lunch
*1-2pm: Demos of working OpenIGTLink based systems
**AIST demos (TBD)
*2-3pm: OpenIGTLink Library, 3D Slicer and other tools
*3-4pm: Simulator Discussion

Suggestions for agenda from TCON:
*Tracker simulator (Haiying)
*General session on simulators (maybe there should be a general discussion on this)
*Suggestions for hands-on session
**hello world type demo application
**5-10 minutes from each of the vendors on how they can use it?
**compare OpenIGTLink with Steathlink protocol
**hands-on help in WPI system up and running (Greg will confirm)
**planning to interface aurora tracker with Slicer using OpenIGTLink (Tamas)
**discussion about the implementation -- message queueing idea/transport layer (Patrick Georgetown, Steve to followup)
*** Comments from Patrick
**** '''Suggestion:''' Using [http://msdn.microsoft.com/en-us/library/ff647328.aspx Message Bus] and [http://msdn.microsoft.com/en-us/library/ff649664(v=pandp.10).aspx Publisher/Subscriber] design pattern for system integration
**** OpenIGTLink can be used to define the common message schema, and ZeroMQ can be used to handle the transportation layer abstraction
**** [http://www.zeromq.org/ ZeroMQ] is a small and fast implementation of the [http://en.wikipedia.org/wiki/Advanced_Message_Queuing_Protocol Advanced Message Queuing Protocol] under the LGPL license
**** It supports both synchronous and asynchronous messaging mode
**** It supportsTCP, Multicast/PGM, Inter-process, and inter-thread transportation
**** CMake version of library can be found here [http://github.com/PatrickCheng/zeromq2 ZeroMQ]
**** API can be found here http://api.zeromq.org/zmq.html
--------------

=Notes=
==Discussion on OpenIGTLink Protocol version 2==
*Finalize version 2 protocol
**[[OpenIGTLink/ProtocolV2/Summary| Summary of version 2 protocol]]
**New support for image-guided systems
***Discussion on new commands is [[OpenIGTLink/Discussion/NewCommands|in progress]].
**Matlab integration
***There have been several requests for Matlab OpenIGTLink interface.
***[[OpenIGTLink/Matlab|Prototype Matlab/Octave interface]] is available.
***New message type to support "remote procedure call"??
**(Please put your agenda here)
==Dissemination, collaboration etc.)==
The following item is part of NCIGT. We need inputs from Ron and Tina.
*Tutorial (how we do now, and how it should be)
*web presence (how we are, and how it should be)
*Ctest (how we do)
*Use Slicer ML or dedicated ML?
==Hands-on session (11am-12pm)==
*Opportunity for IGT developers to consult with OpenIGTLink experts and find solutions for their project.
==OpenIGTLink Library, 3D Slicer and other tools==
*Features
*Message classes
*Example programs
*Timeline

<hr/>

=Demo Session=
==AIST demos==
*(TBD)

=Collaborators=
*list of potential collaborator

=Participants=
*Junichi Tokuda
*Nobuhiko Hata
*Haiying Liu

<hr/>

=Teleconference on May 27 (Thu) 3pm-=
==Objectives==
*Topics to discuss during the event
*Finalize the schedule
*Action items

==Participants==
*Please feel free to put your name here
*Junichi Tokuda (BWH)
*Tina Kapur, BWH

==Agenda==
* Agenda in the project week
**Summary of OpenIGTLink
***Short presentation about overview and updates of OpenIGTLink for those who are not in the presentation on Tuesday.
**Discussion on protocol version 2.
***New features for 3D Slicer
***Matlab
***Messages for sensor data (proposed by AIST project)
***Endoscope/camera control
**Hands-on session. Specifics of this session will be decided after the May 27th tcon.
**Demos of working OpenIGTLink based systems
**OpenIGTLink Library, 3D Slicer and other tools
***Matlab interfaces
***3D Slicer user interface
***Tutorials

* Demos (please feel free to add)
**IGSTK demo from Haiying
**AIST demo (may be video)
**New 3D Slicer OpenIGTLink IF

* Breakout session schedule
**Make sure that all participants can sessions they need
**Order of sessions

* Action items by Project Week
** List all potential applications
** List all problems, issues regrading the current protocol
** Feedbacks

Events:CTK-Pre-Hackfest-2010

2010-03-13T16:53:40Z

PatrickCheng: /* The Common Toolkit Hackfest at the DKFZ in Heidelberg, Germany hosted by the MBI. */

=The Common Toolkit Hackfest at the [http://www.dkfz.de/index.html DKFZ] in Heidelberg, Germany hosted by the [http://www.dkfz-heidelberg.de/en/mbi/index.html MBI].=

{|
|align="left"|This is a working meeting - the goal is to start writing code!
|[[image:Heidelberg corr.jpg|thumb|300px|<big>Heidelberg</big> Source: http://upload.wikimedia.org/wikipedia/commons/b/b4/Heidelberg_corr.jpg]]
|[[File:IMG 0941.JPG|thumb|300px|<big>Group picture at a local restaurant</big>]]
|}

=Links=
*[http://www.CommonTk.org http://www.CommonTk.org] (under development)

----

=Topics=

== (1) Memory Management ==
* Large Image Handling
** streaming
** out of core data management (memory mapped files, etc)
** level of detail
** Google Earth 3D
** caching
* Decide on smartpointers e.g. C++0x/Boost
** Afternoon: check Qt vs C++0x/Boost smartpointers
** Rule: Use Smartpointers of the super-class; if there is no super-class, use the one decided upon in the afternoon...

== (2) Migrate some code to the repository (e.g. Qt widgets) and use it in our respective toolkits ==
Steve: goal to make some progress on consolidating some Qt widgets from our various projects into a repository that we can all contribute to.
[http://www.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer Slicer Qt Project]

See also [http://www.commontk.org/cgi-bin/trac.cgi/wiki/WidgetPlans CTK Widget Wish List]
Make use of [http://www.libqxt.org/ Qxt]? [http://qwt.sourceforge.net/ Qwt]?

[[Projects:ARRA:SlicerAM| Slicer Annotation and Markup project for reporting]]

== (3) DICOM IO layer on top of DCMTK: interpretation of DICOM data ==

* [http://www.atamai.com/cgi-bin/viewvc.cgi/AtamaiVTK/vtkAtamaiIO/?root=cvspriv David Gobbi's CMake/VTK wrappers for DCMTK]
* [http://graphics.tudelft.nl/Projects/DeVIDE Delft project includes DCMTK]

== (4) Interoperability of plugins ==
Steve: Summarize what would it take to make a standard that could handle at least the three following systems:
* [http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation Slicer Command Line Execution Model]
* [https://collab01a.scr.siemens.com/xipwiki/index.php/Main_Page XIP / DICOM WG23 Application Hosting]
* [https://collab01a.scr.siemens.com/xipwiki/index.php/Main_Page XIP-Builder / Visual Programming Interface integration]
* [http://www.nitrc.org/projects/jist/ MIPAV/JIST plugins]
*[http://www.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink]
If we can handle those, then that's probably broad enough to cover many common scenarios.

Jc: [[Events:CTK-Hackfest-2010/SlicerPythonQt | PythonQt]] and the [[Events:CTK-Hackfest-2010/SlicerQtPluginArchitecture | Qt based plugin architecture used in SlicerQt]]

Sascha, Olivier: Generic service oriented approach to expose modules for multiple platforms.

== (5) Generic event mechanism (e.g. event bus, translate events into signals) ==
* Sascha

----

=Proposed Agenda=
==Sunday==
*19:00 Welcome Dinner at Hotel Ritter
==Monday - Thursday==
*9:00 Transfer by bus from Ritter to DKFZ (''Note: every day'')
==Monday at DKFZ==
*9:30 Short presentation of agenda
*9:45 – 12:00 Presentation of topic leaders 20 min each including discussion: requirements, existing libraries, … Coffee breaks on demand
*12:00 – 13:00 Lunch
*13:00 – 13:30 General discussion Goal: select three topics to start with in smaller teams
*13:30 – 16:00 More detailed exploration of topics
*16:00 Presentation of first results, planning of further agenda
==Tuesday==

Hacking...

* [http://github.com/pieper/CTK CTK Git repository]
** Initial layout supports cross-toolkit code in the Libs directory (i.e. qCTKDCMTK that combines Qt with DCMTK)
** We may refactor the directory layout later
** We can consider making an automated [http://blog.fallingsnow.net/2007/08/17/maintaining-an-svn-mirror-directly-from-git/|svn mirror of git]
** [http://www.cmake.org/Wiki/CMake/Git CMake wiki page with git hints]

* Distributing CTK:
** Provide an initial CmakeLists.txt file that exposes a series of options
** Use [[2010_Winter_Project_Week_CMAKE_Build_process| CMake external project (SuperBuild)]]

* DICOM Database schema example
** [http://www.slicer.org/slicerWiki/index.php/DICOM:Database Discussion here].

* Volume rendering [http://dl.dropbox.com/u/1686930/polyp1.nrrd test data]

==Wednesday==

* DICOM interface discussion
** [http://www.slicer.org/slicerWiki/index.php/DICOM:Interface Slicer notes on dicom interface and other server/database interfaces].

* Effort to plug some XIP code into MITK

* Drafting a first generic plugin framework (based on Qt)

* CTK Repository Naming Conventions:
** CTK
*** Libs
**** Core (depends on QtCore, filenames start with ctk)
***** ctkBundleActivator.h
***** ctkBundleContext.h
**** DICOM
**** Scripting
***** PythonQt
**** Visualization
***** VTK
***** OpenInventor
**** Widgets
*** Utilities
**** DCMTK
**** KWStyle
**** ZMQ
*** Testing
*** Examples
*** Documentation

* CTK File Naming Conventions
** ''Considerations:''
*** allow KWStyle regular expressions to identify coding style (style is based on parent class - vtkObjects use vtk style, QObjects use Qt style).
*** name should indicate dependencies - using ctk prefix implies QtCore dependency

* [http://www.zeromq.org/ Zero Message Queue] ported to CMake and added to repository

* [http://my.cdash.org/index.php?project=CTK CTK Dashboard hosted by my.cdash.org]

==Thursday==

* TODO items for the day and beyond ''updates in italics''
** Add xip as external project to CTK superbuild ''requires small change to handle svn repository with a password (Jc)''
*** widget needs to be added to ctk git ''done (Ivo/Oliver) - widget is plugged into MITK - need to plan follow up meeting to work out use cases for NA-MIC integration of XIP - could be done in Boston or in Princeton (Steve and Oliver)''
** Setup PythonQt as external project and add related widgets to CTK repository ''requires small rework - Jc will do''
** Setup nightly builds for windows, mac, linux ''linux set up, more to follow''
** Messaging - ctk class event manager and dispatcher as a demo (e.g. send IGSTK messages to MITK) - zmq supports both in-process and cross-process messaging. ''Patrick hecked in example multi-process messaging app (client/server)''
** Slicer CLI in MITK ''delayed a bit - Jc is refactoring the slicerqt CLI code into more generic widget and xml parser)''
** OpenIGTLink as superbuild external project ''(done - Patrick)''
** Qt Mobility running in linux - example service for discovering CLI ''in-process (Sascha)''
** Launcher in Qt ''todo (Steve/JC/J2)''
*** Fast splash screen
*** setting paths
*** launching debuggers with paths resolved
*** monitor main application behavior (auto bug report?)
** DICOM
*** Indexer working with CTK-built DCMTK - CLI existing - ''done (Marco)''
*** Example application to tie sql database to qt widgets - ''mockup query/retrieve front end (Steve), database tree display widget (Julien)''
** Transfer function widget (next week or two) ''todo (Marco to help AlexY port to CTK to support integration with slicer)''

----

=Attendees=
* Steve Pieper, Boston
* Oliver Kutter, Siemens (SCR)
* Patrick Cheng, Georgetown University
* Julien Finet, Kitware Inc.
* Jean-Christophe Fillion-Robin, Kitware Inc.
* Julien Jomier, Kitware Inc.
* Marco Nolden, DKFZ
* Ivo Wolf, DKFZ
* Sascha Zelzer, DKFZ

File:IMG 0941.JPG

2010-03-13T16:50:34Z

PatrickCheng: CTK pre-hackfest, March 8 ~ March 11, Heidelberg

CTK pre-hackfest, March 8 ~ March 11, Heidelberg

Events:CTK-Pre-Hackfest-2010

2010-03-08T09:30:21Z

PatrickCheng: /* (4) Interoperability of plugins */

Events:CTK-Workshop-September-2009

2009-10-01T16:25:19Z

PatrickCheng: /* Slides */

__NOTOC__
=The Common Toolkit Workshop at [http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=Siemens+Molecular+Imaging,+23-38+Hythe+Bridge+St.,+Oxfordshire,+OX1+2EP,+Oxford,+United+Kingdom&sll=37.0625,-95.677068&sspn=78.056642,54.580078&ie=UTF8&ll=51.753244,-1.266561&spn=0.007731,0.009023&z=17&iwloc=A Siemens Molecular Imaging] in Oxford, UK =
'''September 25 2009'''
{|
|align="left"|The purpose of this meeting is to convene a number of groups who are working on FOSS Medical Image Computing platform development using '''BSD''' style licenses and to explore meaningful ways of coordination and integration. This follows a two-day [[Events:CTK-Workshop-June-2009|initial meeting in June]].
CTK is a pro-tempore group of like minded technically oriented softare tool builders. We expect to release a first version of CTK within a year. If you are interested to learn more, please contact Hans Peter Meinzer or Ron Kikinis.
|[[image:CTK Oxford.JPG|thumb|250px|<big>Oxford</big>]]
|}

=Links=
*[http://www.CommonTk.org http://www.CommonTk.org] (under development - reserved as future home page)
*[http://my-trac.assembla.com/protoctk http://my-trac.assembla.com/protoctk] Prototype trac installation for CTK hosted by assembla.com.
=Schedule=
'''THURSDAY, SEPT. 24th'''
*Guests arrive at the [http://www.barcelo-hotels.co.uk/hotels/central-england/barcelo-oxford-hotel/ Barcelo Hotel]. CTK attendees are offered a discounted rate of £88.00 per night including breakfast.
*20.00-21.30: Private Dining at Barcelo Hotel

'''FRIDAY, SEPT. 25th'''
*Relocation from Hotel: 09.00AM
*09.30-10.00 Introductions
*10.00-11.00: Architecture
*11.00-12.00: Dicom: DCMTK
*12.00-13.00: Lunch at Siemens
*13.00-14.00: Data Structures
*14.00-15.00: Scene Graphs
*15.00-15.15: Break
*15.15-17.00: Widgets
*17.00-18.00: Action Items
*18.00-19.30: Brief tour of Oxford landmarks, followed by drinks at the [http://www.theturftavern.co.uk/ Turf Tavern]
*19.30-21.30: Dinner at The Living Room restaurant
*Relocation to hotel

=Detailed Agenda=
[[media:CTK_Agenda_2009-09-25.pdf|Agenda (.pdf format)]]
<gallery widths="250px" heights="200px" perrow="2">
image:CTKWS2S2.png
image:CTKWS2S3.png
image:CTKWS2S4.png
image:CTKWS2S5.png
</gallery>

=Minutes=
==Introduction==
*GP introduces the meeting agenda and briefly summarizes the main conclusions reached in Heidelrberg meeting
*Board appoint RK as meeting Chair and MV as minuting secretary.
*GP we should look at FNIH for sustain to the CTK initiative
**Seminal money can create a collective identity for the CTK consortium
**MV we need to design this as a non unique initiative so that if similar opportunities arise in Europe or elsewhere we can catch them
**SA we should copy Insight consortium by limiting the possibility for this ID to go for funding.
*When do we open up? Balance between the need to build a vision and the grass nature
*Web page up and running SA take lead on it
*MV add a public statement on how the CTK initiative has formed and how it is evolving
*RK and MV are requested to draft a statement that recognise the pro tempore nature of group, set to 12 months its horizon, and post-pone any newcomer to then
*GP will follow-up FNIH idea
*RK proposes to have next meeting in RSNA 2009 29-11 through 4-12 Chicago. LT will check with the organization for the logistics.
*Another meeting could be done in SPIE medical imaging 13 - 18 February 2010 San Diego, California, USA. CK will explore this possibility and report to the group.

==Architecture brainstorm==
*LT discuss the DICOM support with CTK (DCMTK vs DCM4CHE) and in general the problem if using non C++ libraries and services to deal with ancillary functions.
*Discussion moves to the issue of DCMTK and its plans with respect to the vision of a full DICOM/PACS implementations
*MO gives and OFFIS presentation.
*GP request that image data read by DCMTK can be stored into an existing buffer defined by the calling application
*LT request that image processing module is designed to create the look-up table that can be applied on the raw data into the caller application.
*CTK group could become an advisory / specification body for the various teams developing the various frameworks. This includes the possibility to create a repository of benchmarking datasets for I/O compliance and algorithmic testing.
*MV asks for extension of DCM Standards toward image processing and image-based modelling data types with respect to DCMTK development plans. MO recognise the importance of this aspect, but express concern that the OFFIS group can tackle this alone, suggesting that this aspect is taken as CTK goal.
*SA inform of a NLM meeting on the next round for ITK v4, where its has been discussed the possibility to support the further development of DCMTK as dicom library for ITK.

==Data Structures and Scene Graphs==
*Data object model emerge from the discussion on how ITK can be used as part of the CTK effort. The problem is clearly open and so far not unique solution appears to establish. Further discussion is required.
*WS suggest that a discussion point is on software processing (make, dashboard) and wrappers.
*LT explain how WG23 is working to define a mechanism called “abstract multidimensional image model” for coping with different data representations.
*SA proposes the possibility of developing as part of CTK database services that provide a unified presentation to some basic properties of each dataset.
*Discussion follows on data objects models: there is a conflict between the need for extensibility and the generality
*JW points the group to Aim@shape.net EU project developed a taxonomy.
*INRIA group suggest that what CTK needs is not a concrete implementation of the DOM, but only a taxonomy of abstract data types, and the functions / methods that we associate to them. The idea is discussed extensively.
*SP summarise: a common data model with services and methods that are toolkit independent, with façade classes that expose the abstract types according to the need to specific toolkit (VTK, ITK, etc.).
*ACTION: JW will post on the wiki the table of abstract classes and associated methods they developed in INRIA, so that we can all see if there are gaps for other tooolkits
*GP describes the role of Open Inventor inside XIP.
*Discussion starts on versioning. LT points the DirectX mechanism that ensures that the current version can be request to expose the API of any previous version. In general we should ensure that different versions can coexist on the same machine.
*SP asks the wrapping mechanism for data nodes.
*MO points out the risk of “private nodes” that you cannot load because you do not have the specific library was used to create them. MV suggests that the DOM discussion could bring some solutions in this respect.
*Discussion continues on how specific libraries can be wrapped so to be exposed in XIP.
*SP asks what is the open source availability of XIP Builder; GP confirm that the visual programming environment is not open source, but the binary is free, whereas all object libraries are open source.
==Widgets==
*[http://en.wikipedia.org/wiki/Qt_%28toolkit%29 We have agreed on Qt for widgets]
*LT reports about new IHE profile regarding "Basic Image Review" which can serve as a basis for CTK widgets, which then can be expanded. Must be checked whether it is appropriate. The profile that can be downloaded [http://www.ihe.net/Technical_Framework/upload/IHE-RAD_TF_Suppl_Basic_Image_Review_2009-06-21.pdf here].
** Intended audience is referring physicians who have requested a radiological study
** Covers icons, mouse movements/buttons, etc
** XIP is developing a reference implementation
* Slicer has design guidelines on its [http://www.slicer.org/slicerWiki/index.php/Slicer3:Human_Interface_and_Style_Guide_for_Developers wiki])
* DTK (Dream Toolkit) is the foundation of MedINRIA's toolkits. It is discussed on the web [http://www-sop.inria.fr/dream/blog/category/dream-toolkit/ here]
* XIP will be releasing Qt widgets used in XIP Builder as open-source
*Review of [http://my-trac.assembla.com/protoctk/wiki/WidgetPlans wiki list of desirable widgets for ctkGUI].
*SP reported on contacts with Qt group at Nokia. The group agreed to extend an invitation that someone from Nokia attend the next CTK meeting in Chicago.
*WS, SP, SA, RK report on new widgets being developed for slicer in Qt. Group agrees these new developments can be branded as ctkGUI. RW agrees to offer MedInria/DTK Qt widgets to ctkGUI. IW and MN to review MITK for unique widgets for contribution as well.
* Goals
** CTK should provide a recommended icon set, widgets, and behaviors
*** …should be extensions to BIR
* Implementation
** Subclasses of Qt object
** Follow Qt documentation standards
** Uses qtCore data structs
*** QtAbstractModel and QtTreeModel will be used to store hierarchies
** Demo applications of widgets should depent only on Qt when possible
*** E.g., QTransformWidget should take a QMatrix
**** Derived version takes vtkTransform
**** Another derived version takes itkRigidTransform

=Participants=
*Hans-Peter Meinzer, German Cancer Research Center, Heidelberg
*Marco Nolden, German Cancer Research Center, Heidelberg
*Ivo Wolf, Hochschule Mannheim, Institut für Medizinische Informatik, Mannheim
*Steve Pieper, Isomics, Cambridge
*Ron Kikinis, Harvard Medical School, Boston
*Kevin Cleary, Georgetown University, ISIS, Washington DC
*Lawrence Tarbox, Mallinckrodt Institute of Radiology, St.Louis
*Stephen Aylward, Kitware Inc., Carborro, NC, USA
*Marco Viceconti, Laboratorio di Tecnologia Medica, Bologna
*Michael Onken, OFFIS DICOM Team, Oldenburg
*Olivier Clatz, Sofia Antipolis, INRIA, Nice
*Julien Wintz, Sofia Antipolis, INRIA, Nice
*Pierre Fillard, Sofia Antipolis, INRIA, Nice
*Gianluca Paladini, Program Manager, Siemens Corporate Research, Princeton
*Will Schroeder, President Kitware, Inc., Clifton Park, NY, USA

=Slides=
September 25 2009

<gallery widths="150px" heights="150px" perrow="3">
image:KitwareLogo2.jpg|[[media:CTK-KitwareOverview-Aylward.ppt|ITK, VTK, IGSTK, InfoVis, FARSIGHT, Maverick]] (Stephen Aylward)
image:3DSlicerLogo-H-Color-424x236.png|[[media:3D-Slicer-presentation-June-29-2009.ppt|Slicer3]] (Ron Kikinis, Steve Pieper)
image:INRIAlogo.png|[[media:MedINRIA-presentation-June-29-2009.ppt|MedINRIA]] (Olivier Clatz, Julien Wintz, Pierre Fillard)
image:Siemens-logo.jpg|[[media:SCR_CTK_XIP.pdf|OpenXIP Extensible Imaging Platform]] (Gianluca Paladini)
image:B3C.png|[[media:Pres_maf3_Heidelberg2009.pdf‎|MAF3]] (Paolo Quadrani)
image:Mitk-logo.png|[[media:MITK-CTK-Workshop-June2009.ppt‎|MITK]] (Ivo Wolf, Marco Nolden)
image:WashU logo.jpg|[[media:DicomApplicationHosting.ppt|Working Group 23]] (Lawrence Tarbox)
image:Igstk.jpg|[[media:IGSTK Overview - Cleary.ppt|IGSTK]] (Kevin Cleary)
image:Offis logo.gif|[[media:ToBeProvidedbyMichael|DCMTK (OFFIS)]] (Michael Onken)
</gallery>

File:IGSTK Overview - Cleary.ppt

2009-10-01T16:23:02Z

PatrickCheng: IGSTK slides for CMT meeting in London 2009

IGSTK slides for CMT meeting in London 2009

Liver RFA project mtg 7 30 2008

2008-07-31T15:01:53Z

PatrickCheng: /* Action Items */

Georgetown University, ISIS Center, July 30 ~ August 1st, 2008 
Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng

=== Day 1 ===
* Update project status.
*# Demonstrating Slicer 3.0 semi-auto segmentation and navigation capability
*# Showing the existing IGSTK RFA system
* Experiment in DynaCT room (C-arm CT flouro room) to show the work flow of Georgetown system
* Disccusion the integration effort
*# In the near term, working on the semi-automatic segmentation of tumor in liver using slicer modules
*# Setting up DICOM receiver on the Slicer workstation so it can receive data from DynaCT scanner [Finished by Haiying using DCMTK and tested]
*# Ziv will work on a Tracker server application during this meeting (A standard alone application that can talk to different tracking device and send out transform using OpenIGTLink)
*# In the long term, implement registration and navigation interface in Slicer
*# Integrate the optimization algorithm

<graphviz>
digraph G {
DICOM->Segmentation->Optimization->Registration->Navigation;
[rankdir="LR"]
}
</graphviz>

=== Day 2 ===
* Discussion of project road map
*# Goals in two years and obstacles
*## Fully integrated system. Using Slicer 3.0 as front end, implement segmentation and navigation in Slicer, integrate optimization, and talk to IGSTK tracker client using OpenIGTLink
*## Major components in place. Slicer 3.0 need improvement in performance
*# Action item for the 1 year
*## Animal study in summer 09
*## Provide IGSTK-OpenIGTLink application
*## Provide a thorogh documentation page on how to setup the Slicer-RFA, detialed step-by-step guide for user
*## Publications
*# Segmentation
*## Using traditional CT image first instead of cone-beam CT (Georgetown has liver data base and segmented the liver, need to segment ribs and vascular tree)
*## Sota working on the segmentation using slicer, indentify the problem and tacle those problems in the NCIGT workshop next January

=== Action Items ===
Georgetown:
# IGSTK-OpenIGTLink client and tutorial [Finish before next meeting in Boston, Dec 2008]
# Process all liver image in the data base.
# Run the segmented data through optimization and study the outcomes. Publish 1 paper out of this study
# Publish results on animal study: validation of the RFA study is big problem
# Compare the planning results between different doctors and optimization

Slicer-IGT:
# Sota will segment 3~5 cases using Slicer and pass the results through optimization. Identify the limitation in Slicer segmentation method
# Implement IGSTK navigation interface in Slicer

Liver RFA project mtg 7 30 2008

2008-07-31T14:48:40Z

PatrickCheng: /* Day 1 */

Georgetown University, ISIS Center, July 30 ~ August 1st, 2008 
Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng

=== Day 1 ===
* Update project status.
*# Demonstrating Slicer 3.0 semi-auto segmentation and navigation capability
*# Showing the existing IGSTK RFA system
* Experiment in DynaCT room (C-arm CT flouro room) to show the work flow of Georgetown system
* Disccusion the integration effort
*# In the near term, working on the semi-automatic segmentation of tumor in liver using slicer modules
*# Setting up DICOM receiver on the Slicer workstation so it can receive data from DynaCT scanner [Finished by Haiying using DCMTK and tested]
*# Ziv will work on a Tracker server application during this meeting (A standard alone application that can talk to different tracking device and send out transform using OpenIGTLink)
*# In the long term, implement registration and navigation interface in Slicer
*# Integrate the optimization algorithm

<graphviz>
digraph G {
DICOM->Segmentation->Optimization->Registration->Navigation;
[rankdir="LR"]
}
</graphviz>

=== Day 2 ===
* Discussion of project road map
*# Goals in two years and obstacles
*## Fully integrated system. Using Slicer 3.0 as front end, implement segmentation and navigation in Slicer, integrate optimization, and talk to IGSTK tracker client using OpenIGTLink
*## Major components in place. Slicer 3.0 need improvement in performance
*# Action item for the 1 year
*## Animal study in summer 09
*## Provide IGSTK-OpenIGTLink application
*## Provide a thorogh documentation page on how to setup the Slicer-RFA, detialed step-by-step guide for user
*## Publications
*# Segmentation
*## Using traditional CT image first instead of cone-beam CT (Georgetown has liver data base and segmented the liver, need to segment ribs and vascular tree)
*## Sota working on the segmentation using slicer, indentify the problem and tacle those problems in the NCIGT workshop next January

=== Action Items ===
Georgetown:
# IGSTK-OpenIGTLink client and tutorial
# Process all liver image in the data base.
# Run the segmented data through optimization and study the outcomes. Publish 1 paper out of this study
# Publish results on animal study: validation of the RFA study is big problem

Slicer-IGT:
#
#

Liver RFA project mtg 7 30 2008

2008-07-31T14:47:10Z

PatrickCheng: /* Day 2 */

Georgetown University, ISIS Center, July 30 ~ August 1st, 2008 
Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng

=== Day 1 ===
* Update project status.
*# Demonstrating Slicer 3.0's segmentation and navigation capability
*# Showing the existing IGSTK RFA system
* Experiment in DynaCT room (C-arm CT flouro room) to show the work flow of Georgetown's system
* Disccusion the integration effort
*# In the near term, working on the semi-automatic segmentation of tumor in liver using slicer modules
*# Setting up DICOM receiver on the Slicer workstation so it can receive data from DynaCT scanner [Finished by Haiying using DCMTK and tested]
*# Ziv will work on a Tracker server application during this meeting (A standard alone application that can talk to different tracking device and send out transform using OpenIGTLink)
*# In the long term, implement registration and navigation interface in Slicer
*# Integrate the optimization algorithm

<graphviz>
digraph G {
DICOM->Segmentation->Optimization->Registration->Navigation;
[rankdir="LR"]
}
</graphviz>

=== Day 2 ===
* Discussion of project road map
*# Goals in two years and obstacles
*## Fully integrated system. Using Slicer 3.0 as front end, implement segmentation and navigation in Slicer, integrate optimization, and talk to IGSTK tracker client using OpenIGTLink
*## Major components in place. Slicer 3.0 need improvement in performance
*# Action item for the 1 year
*## Animal study in summer 09
*## Provide IGSTK-OpenIGTLink application
*## Provide a thorogh documentation page on how to setup the Slicer-RFA, detialed step-by-step guide for user
*## Publications
*# Segmentation
*## Using traditional CT image first instead of cone-beam CT (Georgetown has liver data base and segmented the liver, need to segment ribs and vascular tree)
*## Sota working on the segmentation using slicer, indentify the problem and tacle those problems in the NCIGT workshop next January

=== Action Items ===
Georgetown:
# IGSTK-OpenIGTLink client and tutorial
# Process all liver image in the data base.
# Run the segmented data through optimization and study the outcomes. Publish 1 paper out of this study
# Publish results on animal study: validation of the RFA study is big problem

Slicer-IGT:
#
#

Liver RFA project mtg 7 30 2008

2008-07-31T14:44:42Z

PatrickCheng: /* Action Items */

Georgetown University, ISIS Center, July 30 ~ August 1st, 2008 
Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng

=== Day 1 ===
* Update project status.
*# Demonstrating Slicer 3.0's segmentation and navigation capability
*# Showing the existing IGSTK RFA system
* Experiment in DynaCT room (C-arm CT flouro room) to show the work flow of Georgetown's system
* Disccusion the integration effort
*# In the near term, working on the semi-automatic segmentation of tumor in liver using slicer modules
*# Setting up DICOM receiver on the Slicer workstation so it can receive data from DynaCT scanner [Finished by Haiying using DCMTK and tested]
*# Ziv will work on a Tracker server application during this meeting (A standard alone application that can talk to different tracking device and send out transform using OpenIGTLink)
*# In the long term, implement registration and navigation interface in Slicer
*# Integrate the optimization algorithm

<graphviz>
digraph G {
DICOM->Segmentation->Optimization->Registration->Navigation;
[rankdir="LR"]
}
</graphviz>

=== Day 2 ===
* Discussion of project road map
*# Goals in two years and obstacles
*## Major components in place. Slicer 3.0 need improvement in performance
*# Action item for the 1 year
*## Animal study in summer 09
*## Provide IGSTK-OpenIGTLink application
*## Provide a thorogh documentation page on how to setup the Slicer-RFA, detialed step-by-step guide for user
*## Publications
*# Segmentation
*## Using traditional CT image first instead of cone-beam CT (Georgetown has liver data base and segmented the liver, need to segment ribs and vascular tree)
*## Sota working on the segmentation using slicer, indentify the problem and tacle those problems in the NCIGT workshop next January

=== Action Items ===
Georgetown:
# IGSTK-OpenIGTLink client and tutorial
# Process all liver image in the data base.
# Run the segmented data through optimization and study the outcomes. Publish 1 paper out of this study
# Publish results on animal study: validation of the RFA study is big problem

Slicer-IGT:
#
#

Liver RFA project mtg 7 30 2008

2008-07-31T14:43:29Z

PatrickCheng: /* Action Items */

Georgetown University, ISIS Center, July 30 ~ August 1st, 2008 
Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng

=== Day 1 ===
* Update project status.
*# Demonstrating Slicer 3.0's segmentation and navigation capability
*# Showing the existing IGSTK RFA system
* Experiment in DynaCT room (C-arm CT flouro room) to show the work flow of Georgetown's system
* Disccusion the integration effort
*# In the near term, working on the semi-automatic segmentation of tumor in liver using slicer modules
*# Setting up DICOM receiver on the Slicer workstation so it can receive data from DynaCT scanner [Finished by Haiying using DCMTK and tested]
*# Ziv will work on a Tracker server application during this meeting (A standard alone application that can talk to different tracking device and send out transform using OpenIGTLink)
*# In the long term, implement registration and navigation interface in Slicer
*# Integrate the optimization algorithm

<graphviz>
digraph G {
DICOM->Segmentation->Optimization->Registration->Navigation;
[rankdir="LR"]
}
</graphviz>

=== Day 2 ===
* Discussion of project road map
*# Goals in two years and obstacles
*## Major components in place. Slicer 3.0 need improvement in performance
*# Action item for the 1 year
*## Animal study in summer 09
*## Provide IGSTK-OpenIGTLink application
*## Provide a thorogh documentation page on how to setup the Slicer-RFA, detialed step-by-step guide for user
*## Publications
*# Segmentation
*## Using traditional CT image first instead of cone-beam CT (Georgetown has liver data base and segmented the liver, need to segment ribs and vascular tree)
*## Sota working on the segmentation using slicer, indentify the problem and tacle those problems in the NCIGT workshop next January

=== Action Items ===
Georgetown:
# IGSTK-OpenIGTLink client and tutorial
# Process all liver image in the data base.
# Run the segmented data through optimization and study the outcomes. Publish 1 paper out of this study
# Publish results on animal

Slicer-IGT:
#
#

Liver RFA project mtg 7 30 2008

2008-07-31T14:41:52Z

PatrickCheng:

Georgetown University, ISIS Center, July 30 ~ August 1st, 2008 
Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng

=== Day 1 ===
* Update project status.
*# Demonstrating Slicer 3.0's segmentation and navigation capability
*# Showing the existing IGSTK RFA system
* Experiment in DynaCT room (C-arm CT flouro room) to show the work flow of Georgetown's system
* Disccusion the integration effort
*# In the near term, working on the semi-automatic segmentation of tumor in liver using slicer modules
*# Setting up DICOM receiver on the Slicer workstation so it can receive data from DynaCT scanner [Finished by Haiying using DCMTK and tested]
*# Ziv will work on a Tracker server application during this meeting (A standard alone application that can talk to different tracking device and send out transform using OpenIGTLink)
*# In the long term, implement registration and navigation interface in Slicer
*# Integrate the optimization algorithm

<graphviz>
digraph G {
DICOM->Segmentation->Optimization->Registration->Navigation;
[rankdir="LR"]
}
</graphviz>

=== Day 2 ===
* Discussion of project road map
*# Goals in two years and obstacles
*## Major components in place. Slicer 3.0 need improvement in performance
*# Action item for the 1 year
*## Animal study in summer 09
*## Provide IGSTK-OpenIGTLink application
*## Provide a thorogh documentation page on how to setup the Slicer-RFA, detialed step-by-step guide for user
*## Publications
*# Segmentation
*## Using traditional CT image first instead of cone-beam CT (Georgetown has liver data base and segmented the liver, need to segment ribs and vascular tree)
*## Sota working on the segmentation using slicer, indentify the problem and tacle those problems in the NCIGT workshop next January

=== Action Items ===
Georgetown:
# IGSTK-OpenIGTLink client and tutorial
# Process all liver image in the data base.
# Run the segmented data through optimization and study the outcomes. Publish 1 paper out of this study

Slicer-IGT:
#
#

Liver RFA project mtg 7 30 2008

2008-07-31T14:39:41Z

PatrickCheng: /* Action Items */

Georgetown University, ISIS Center, July 30 ~ August 1st, 2008
Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng

=== Day 1 ===
* Update project status.
*# Demonstrating Slicer 3.0's segmentation and navigation capability
*# Showing the existing IGSTK RFA system
* Experiment in DynaCT room (C-arm CT flouro room) to show the work flow of Georgetown's system
* Disccusion the integration effort
*# In the near term, working on the semi-automatic segmentation of tumor in liver using slicer modules
*# Setting up DICOM receiver on the Slicer workstation so it can receive data from DynaCT scanner [Finished by Haiying using DCMTK and tested]
*# Ziv will work on a Tracker server application during this meeting (A standard alone application that can talk to different tracking device and send out transform using OpenIGTLink)
*# In the long term, implement registration and navigation interface in Slicer
*# Integrate the optimization algorithm

<graphviz>
digraph G {
DICOM->Segmentation->Optimization->Registration->Navigation;
[rankdir="LR"]
}
</graphviz>

=== Day 2 ===
* Discussion of project road map
*# Goals in two years and obstacles
*## Major components in place. Slicer 3.0 need improvement in performance
*# Action item for the 1 year
*## Animal study in summer 09
*## Provide IGSTK-OpenIGTLink application
*## Provide a thorogh documentation page on how to setup the Slicer-RFA, detialed step-by-step guide for user
*## Publications
*# Segmentation
*## Using traditional CT image first instead of cone-beam CT (Georgetown has liver data base and segmented the liver, need to segment ribs and vascular tree)
*## Sota working on the segmentation using slicer, indentify the problem and tacle those problems in the NCIGT workshop next January

=== Action Items ===
Georgetown:
# IGSTK-OpenIGTLink client and tutorial
# Process all liver image in the data base.
# Run the segmented data through optimization and study the outcomes. Publish 1 paper out of this study

Slicer-IGT:
#
#

Liver RFA project mtg 7 30 2008

2008-07-31T14:37:44Z

PatrickCheng: /* Day 2 */

Georgetown University, ISIS Center, July 30 ~ August 1st, 2008
Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng

=== Day 1 ===
* Update project status.
*# Demonstrating Slicer 3.0's segmentation and navigation capability
*# Showing the existing IGSTK RFA system
* Experiment in DynaCT room (C-arm CT flouro room) to show the work flow of Georgetown's system
* Disccusion the integration effort
*# In the near term, working on the semi-automatic segmentation of tumor in liver using slicer modules
*# Setting up DICOM receiver on the Slicer workstation so it can receive data from DynaCT scanner [Finished by Haiying using DCMTK and tested]
*# Ziv will work on a Tracker server application during this meeting (A standard alone application that can talk to different tracking device and send out transform using OpenIGTLink)
*# In the long term, implement registration and navigation interface in Slicer
*# Integrate the optimization algorithm

<graphviz>
digraph G {
DICOM->Segmentation->Optimization->Registration->Navigation;
[rankdir="LR"]
}
</graphviz>

=== Day 2 ===
* Discussion of project road map
*# Goals in two years and obstacles
*## Major components in place. Slicer 3.0 need improvement in performance
*# Action item for the 1 year
*## Animal study in summer 09
*## Provide IGSTK-OpenIGTLink application
*## Provide a thorogh documentation page on how to setup the Slicer-RFA, detialed step-by-step guide for user
*## Publications
*# Segmentation
*## Using traditional CT image first instead of cone-beam CT (Georgetown has liver data base and segmented the liver, need to segment ribs and vascular tree)
*## Sota working on the segmentation using slicer, indentify the problem and tacle those problems in the NCIGT workshop next January

=== Action Items ===
Georgetown:
# Process all liver image in the data base.
# Run the segmented data through optimization and study the outcomes. Publish 1 paper out of this study

Slicer-IGT:
#
#

Liver RFA project mtg 7 30 2008

2008-07-31T14:33:03Z

PatrickCheng: /* Day 2 */

Liver RFA project mtg 7 30 2008

2008-07-31T14:28:51Z

PatrickCheng: /* Day 2 */

Georgetown University, ISIS Center, July 30 ~ August 1st, 2008
Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng

=== Day 1 ===
* Update project status.
*# Demonstrating Slicer 3.0's segmentation and navigation capability
*# Showing the existing IGSTK RFA system
* Experiment in DynaCT room (C-arm CT flouro room) to show the work flow of Georgetown's system
* Disccusion the integration effort
*# In the near term, working on the semi-automatic segmentation of tumor in liver using slicer modules
*# Setting up DICOM receiver on the Slicer workstation so it can receive data from DynaCT scanner [Finished by Haiying using DCMTK and tested]
*# Ziv will work on a Tracker server application during this meeting (A standard alone application that can talk to different tracking device and send out transform using OpenIGTLink)
*# In the long term, implement registration and navigation interface in Slicer
*# Integrate the optimization algorithm

<graphviz>
digraph G {
DICOM->Segmentation->Optimization->Registration->Navigation;
[rankdir="LR"]
}
</graphviz>

=== Day 2 ===
* Discussion of project road map
*# Goals in two years and obstacles
*## Major components in place. Slicer 3.0 need improvement in performance
*# Action item for the 1 year
*## Animal study in summer 09
*## Provide IGSTK-OpenIGTLink application
*## Provide a thorogh documentation page on how to setup the Slicer-RFA, detialed step-by-step guide for user
*## Publications
*# Segmentation
*## Using traditional CT image first instead of cone-beam CT (Georgetown has liver data base and segmented the liver)
*## Sota working on the segmentation using slicer, indentify the problem and tacle those problems in the NCIGT workshop next January

Liver RFA project mtg 7 30 2008

2008-07-31T14:23:57Z

PatrickCheng: /* Day 1 */

Liver RFA project mtg 7 30 2008

2008-07-31T14:21:46Z

PatrickCheng:

Georgetown University, ISIS Center, July 30 ~ August 1st, 2008
Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng

=== Day 1 ===
* Update project status.
*# Demonstrating Slicer 3.0's segmentation and navigation capability
*# Showing the existing IGSTK RFA system
* Experiment in DynaCT room (C-arm CT flouro room) to show the work flow of Georgetown's system
* Disccusion the integration effort
*# In the near term, working on the semi-automatic segmentation of tumor in liver using slicer modules
*# Setting up DICOM receiver on the Slicer workstation so it can receive data from DynaCT scanner [Finished by Haiying using DCMTK and tested]
*# Ziv will work on a Tracker server application during this meeting (A standard alone application that can talk to different tracking device and send out transform using OpenIGTLink)
*# In the long term, implement registration and navigation interface in Slicer
*# Integrate the optimization algorithm

<graphviz>
digraph G {
DICOM->Segmentation->Optimization->Registration->Navigation;
}
</graphviz>

=== Day 2 ===
* Discussion of project road map
*# Goals in two years and obstacles
*## Major components in place. Slicer 3.0 need improvement in performance
*# Action item for the 1 year
*## Animal study in summer 09
*## Provide IGSTK-OpenIGTLink application
*## Provide a thorogh documentation page on how to setup the Slicer-RFA, detialed step-by-step guide for user
*## Publications

Liver RFA project mtg 7 30 2008

2008-07-31T14:20:30Z

PatrickCheng: /* Day 1 */

Georgetown University, ISIS Center, July 30 ~ August 1st, 2008
Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng

=== Day 1 ===
* Update project status.
*# Demonstrating Slicer 3.0's segmentation and navigation capability
*# Showing the existing IGSTK RFA system
* Experiment in DynaCT room (C-arm CT flouro room) to show the work flow of Georgetown's system
* Disccusion the integration effort
*# In the near term, working on the semi-automatic segmentation of tumor in liver using slicer modules
*# Setting up DICOM receiver on the Slicer workstation so it can receive data from DynaCT scanner [Finished by Haiying using DCMTK and tested]
*# Ziv will work on a Tracker server application during this meeting (A standard alone application that can talk to different tracking device and send out transform using OpenIGTLink)
*# In the long term, implement registration and navigation interface in Slicer
*# Integrate the optimization algorithm

<graphviz>
digraph G {
DICOM->Segmentation->Optimization->Registration->Navigation;
}
</graphviz>

=== Day 2 ===
* Discussion of project road map
*# Goals in two years and obstacles
*## Major components in place. Slicer 3.0 need improvement in performance
*# Action item for the 1 year
*## Animal study in summer 09
*## Provide IGSTK-OpenIGTLink application
*## Provide a thorogh documentation page on how to setup the Slicer-RFA, detialed step-by-step guide for user

Liver RFA project mtg 7 30 2008

2008-07-31T14:09:22Z

PatrickCheng:

Liver RFA project mtg 7 30 2008

2008-07-31T14:08:37Z

PatrickCheng: /* Day 2 */

Liver RFA project mtg 7 30 2008

2008-07-31T14:01:55Z

PatrickCheng: /* Day 2 */

Liver RFA project mtg 7 30 2008

2008-07-31T13:56:56Z

PatrickCheng: /* Day 2 */

Liver RFA project mtg 7 30 2008

2008-07-31T13:54:52Z

PatrickCheng:

Liver RFA project mtg 7 30 2008

2008-07-31T13:54:33Z

PatrickCheng: /* Day 1 */

Liver RFA project mtg 7 30 2008

2008-07-31T13:53:02Z

PatrickCheng: /* Day 1 */

Liver RFA project mtg 7 30 2008

2008-07-31T13:44:46Z

PatrickCheng:

Liver RFA project mtg 7 30 2008

2008-07-31T13:43:03Z

PatrickCheng: New page: Georgetown University, ISIS Center, July 30 ~ August 1st, 2008 Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng Day 1: * Update project status. *# Demonstrating Slicer 3.0's se...

Georgetown University, ISIS Center, July 30 ~ August 1st, 2008
Attendee: Noby Hata, Haiying Liu, Yaniv Ziv, Patrick Cheng

Day 1:
* Update project status.
*# Demonstrating Slicer 3.0's segmentation and navigation capability
*# Showing the existing IGSTK RFA system
* Experiment in DynaCT room (C-arm CT flouro room) to show the work flow of Georgetown's system

Day 2:
* Discussion of project road map
*# Goals in two years and obstacles
*# Major components in place. Slicer 3.0 need improvement in performance

NA-MIC NCBC Collaboration:An Integrated System for Image-Guided Radiofrequency Ablation of Liver Tumors

2008-07-31T13:33:45Z

PatrickCheng: /* Abstract */

Back to [[NA-MIC_External_Collaborations]]

==Abstract==
The overall goal of this proposal is to develop and validate an integrated system based on open source software for improved visualization and probe placement during radiofrequency ablation (RFA) of liver tumors. While radiofrequency ablation is becoming an increasingly important treatment option for unresectable hepatocellular carcinoma (HCC) and liver metastases, the procedure has several technical limitations. These limitations are mostly related to the difficulty of precisely placing the RFA needle to ablate the entire tumor and achieve adequate margins. In particular, larger tumors require multiple overlapping needle placements, which can be difficult to achieve. The specific aims of the project are to:
# Develop an open source software architecture for a liver RFA planning/treatment workstation that builds on existing open source projects at the two collaborating institutions
# Develop and evaluate semi-automatic segmentation techniques for the liver, liver vasculature, and liver tumors. These techniques will be integrated with a graphical user interface and the segmentation results will be evaluated by comparison with expert radiologists.
# Based on the segmented liver data set, develop a path planning module for evaluating alternative paths to the liver tumor and incorporating multiple overlapping placements as needed.
# Integrate the two capabilities developed above along with electromagnetic tracking of the RFA probe to provide a complete software environment for liver tumor planning, visualization, and execution. This software environment will merge ongoing work at Georgetown and Brigham and Women's Hospital in developing open source software for image-guided procedures.
# Validate the clinical feasibility of the system in a swine animal model. Agar nodules will be created in the swine liver and the ability of the system to segment and provide path planning for these nodules will be assessed. The accuracy of the system will also be evaluated. This research is important in advancing the technology for treatment of liver cancer that presently can not be treated well with current available therapies. This technology would also enable a modern, individualized therapy, which relies on integration of high power computers and innovations in medical science. It would have a contribution to public health by developing liver cancer treatments without the need for more invasive surgeries.

==Grant#==
1R01CA124377-01

==Key Personnel==
Enrique Campos-Nanez, Patrick (Peng) Cheng, Kevin Cleary, Nobuhiko Hata, Ziv Yaniv

==Projects==

The NAV-RFA workflow and requirements document can be found [[NAV-RFA workflow and requirements| here]].

=== Open source workstation ===
Develop a planning and navigation system based on Slicer and IGSTK (Georgetown/BWH).

=== Segmentation ===
Semi-automated segmentation framework for liver, vasculature and tumors (Georgetown).

=== Path planning ===
Trajectory and ablation planning system for RFA probe (GW).

=== Validation ===
Validate the clinical feasibility of the system in an animal model (Georgetown).

==Publications==

==Meetings==
*[[Liver_RFA_project_mtg_7_30_2008| Semi-annual project meeting, July 30, 2008]]
*[[Liver_RFA_project_mtg_7_30_2008| Semi-annual project meeting, Dec 8, 2008]]

==Resource Links==
* [http://www.igstk.org/ IGSTK]
* [http://www.slicer.org/ Slicer]

2007 Slier IGTWS homework GT

2007-12-14T16:42:50Z

PatrickCheng: /* Georgetown Action Items */

== Georgetown Action Items ==
* Integrate IGSTK into Slicer3 (compiling and linking)
* Enable socket communication for TrackerTool to send transform to Slicer3
** Use VTKSocketCommunicator to package and send IGSTKTransform, need to have a receive end on Slicer3 side
* Possibly add KWWidget GUI suppport
* Video Capturing (w. Stoll, Hata, Frank, Patrick)
* Need to discuss how the module would look like for the RFA application
* Support JHU and Queens to use IGSTK?
** Sending transform and images over socket - solution exists
** Support OptoTrack

== Existing Slicer Features We Will Use ==
* Possible segmentation algorithm for liver tumor segmentation
* GUI workflow wizard

== Planned Features That We Will Use ==
* Arbitrary reslicing

2007 Slier IGTWS homework GT

2007-12-14T16:31:35Z

PatrickCheng:

== Georgetown Action Items ==
* Integrate IGSTK into Slicer3 (compiling and linking)
* Enable socket communication for TrackerTool to send transform to Slicer3
** Use VTKSocketCommunicator to package and send IGSTKTransform, need to have a receive end on Slicer3 side
* Possibly add KWWidget GUI suppport
* Video Capturing (w. Stoll, Hata, Frank, Patrick)
* Need to discuss how the module would look like for the RFA application

== Existing Slicer Features We Will Use ==
* Possible segmentation algorithm for liver tumor segmentation
* GUI workflow wizard

== Planned Features That We Will Use ==
* Arbitrary reslicing

2007 Slier IGTWS homework GT

2007-12-14T16:30:04Z

PatrickCheng: /* Georgetown Action Items */

== Georgetown Action Items ==
* Integrate IGSTK into Slicer3 (compiling and linking)
* Enable socket communication for TrackerTool to send transform to Slicer3
** Use VTKSocketCommunicator to package and send IGSTKTransform, need to have a receive end on Slicer3 side
* Possibly add KWWidget GUI suppport
* Video Capturing (w. Stoll, Hata, Frank, Patrick)

== Existing Slicer Features We Will Use ==
* Possible segmentation algorithm for liver tumor segmentation
* GUI workflow wizard

== Planned Features That We Will Use ==

* Arbitrary reslicing
*

2007 Slier IGTWS homework GT

2007-12-14T16:19:50Z

PatrickCheng: /* Georgetown Action Items */

2007 Slier IGTWS homework GT

2007-12-14T16:18:23Z

PatrickCheng: /* Georgetown Action Items */

2007 Slier IGTWS homework GT

2007-12-14T16:16:36Z

PatrickCheng: /* Georgetown Action Items */

== Georgetown Action Items ==
* Integrate IGSTK into Slicer3 (compiling and linking)
* Enable socket communication for TrackerTool to send transform to Slicer3

== Existing Slicer Features We Will Use ==
* Possible segmentation algorithm for liver tumor segmentation
* GUI workflow wizard

== Planned Features That We Will Use ==
* Video Capturing
* Arbitrary reslicing
*

2007 Slier IGTWS homework GT

2007-12-14T16:15:25Z

PatrickCheng: /* Existing Slicer Features We Will Use */

== Georgetown Action Items ==
* Integrate IGSTK into Slicer3
* Enable socket communication for TrackerTool to send transform to Slicer3

== Existing Slicer Features We Will Use ==
* Possible segmentation algorithm for liver tumor segmentation
* GUI workflow wizard

== Planned Features That We Will Use ==
* Video Capturing
* Arbitrary reslicing
*

2007 Slier IGTWS homework GT

2007-12-14T16:14:43Z

PatrickCheng: New page: == Georgetown Action Items == * Integrate IGSTK into Slicer3 * Enable socket communication for TrackerTool to send transform to Slicer3 == Existing Slicer Features We Will Use == * Possib...

== Georgetown Action Items ==
* Integrate IGSTK into Slicer3
* Enable socket communication for TrackerTool to send transform to Slicer3

== Existing Slicer Features We Will Use ==
* Possible segmentation algorithm for liver tumor segmentation
*

== Planned Features That We Will Use ==
* Video Capturing
* Arbitrary reslicing
*

2007 December Slicer IGT Programming

2007-12-12T17:36:56Z

PatrickCheng: /* Wednesday, December 12 */

__NOTOC__
==Dates.Location.Hotels==
December 12-14, 2007

SPL at 1249 Boylston Street, Boston MA. ([http://www.spl.harvard.edu/Directions#Getting_to_1249_Boylston_Street Directions])

Area hotels: [[Boston_Hotels]]

==Goal==
*Continued [[Leadership:SlicerIGT_2007|'''discussion''']] of Slicer IGT infrastructure, applications, and timelines
*Introduce each team's effort in Slicer in the context of IGT
*active funding&future submissions
*on-going technical development
*find unmet needs
*find how we can share the work

=Agenda=
==Wednesday, December 12 ==
'''Theme: Where are we?'''
*12noon: lunch
*12:55pm: Welcome (Ferenc Jolesz)
*1-2pm:
**Slicer: overview of architecture, current status, and future plans (Pieper, Hata)
***History
***Clinical applications
***transition from 2.6 to 3
***resource
***[[media:Pieper-IGT-retreat-2007-12-12.ppt | Slicer Core]] + [[Slicer3:Loadable_Modules | Loadable Modules]]
**IGSTK
*** [[Media:IGSTK-Architecture-IGT-Meeting-Dec-12-2007.ppt‎|Architecture Overview]] (Ibanez)
*** Current status, and future plans (Cheng) [http://public.kitware.com/IGSTKWIKI/index.php/Design_Discussion Refactoring Design Discussion]
*2-3pm: Setting goals for meeting: Each IGT group present what they want to achieve at this meeting.
**2-2:15 - NA-MIC DBP Queens/JHU Gobbi/Csoma/Kazanzides
**2:15-2:30 - NA-MIC Collaborator Georgetown Cleary/Yaniv
**2:30-2:45 - NCIGT BWH Hata
**2:45-3:00 - Kitware
**3:00-3:30pm - NCIGT CIGL Stoll and Demo
*3:30pm Adjourn
*4-6pm (optional) demonstration of Slicer for control and display of MRI scanner (prostate module) @Advanced MRI center, 221 Longwood
**See [[2007_December_Slicer_IGT_Programming_MRI_DEMO| slicer-MRI demo]]

==Thursday, December 13==
'''Morning Theme: Where are we?'''
*9:00am breakfast, start work

*9-1030am Discussion over Demos:
**Hata (Tracking at BWH)
**Yaniv (Tracking at Georgetown)
**Freudling (Pieper) (Volume rendering)

*10:30am: coffee break
*11am: Review of demos
**which function is cool?
**which functionality has to be shared
**what is the common needs?
**who has those missing functions outside of IGT?

*12:30: lunch

'''Afternoon Theme: Where are we going?'''
*1:30pm-3pm
**Proposal for robot-assisted neurosurgery (Kazanzides)
**Resource sharing
**priority tasks
**Hypothetical RO1

*3-4pm: Coffee break (and NA-MIC TCON)
*4:00pm: Plan for Hands on IGT Week
*5pm: Review day and plan for Friday (Hata)
*5:30pm: adjourn

==Friday, December 14==
----
*9:00am: breakfast, work
**Focus group discussion ('''What do we do now?''')
**Report to NCIGT
**Action items
*11:15am-noon: Wrapup/Suggestion to NCIGT PIs (Hata)
*noon: adjourn and head out to group lunch

----

==Confirmed Attendees==
#Noby Hata, BWH (NCIGT)
#Steve Pieper, Isomics - (All Days) (NAMIC, NAC)
#Patrick Cheng, Georgetown (NAMIC Collab)
#Ziv Yaniv, Georgetown (NAMIC Collab)
#Kevin Cleary, Georgetown (Wed only) (NAMIC Collab)
#Luis Ibanez, Kitware (NAMIC)
#Sebastien Barre, Kitware (NCIGT)
#Stephen Aylward, Kitware (NCIGT)
#Jeff Stoll (except Thursday), BWH/CIMIT (NCIGT)
#Haiying Liu, BWH (NCIGT)
#Katie Hayes, BWH (NAC)
#Peter Kazanzides (except Friday), JHU (NAMIC Collab)
#Csaba Csoma, JHU (NAMIC/NCIGT Collab)
#David Gobbi, Queens (NAMIC/NCIGT Collab)
#Tina Kapur,BWH (NAMIC/NCIGT)
#Ron Kikinis, BWH (NAMIC/NCIGT)
#Junichi Tokuda, BWH (NCIGT)
#Raul San Jose, BWH (NAC)
#Neculai Archip, BWH (Wed only) (NCIGT)
#Nicholas Ayache (NCIGT) (Wed only)