NAMIC Wiki - User contributions [en]

2007 December Slicer IGT Programming

2007-12-14T17:49:55Z

Jstoll: /* 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
*Learning IGSK-Slicer
*Interface to scanners

=Agenda=
==Wednesday, December 12 ==
'''Theme: Where are we?'''
*12noon: lunch
*12:55pm: Welcome (Ron Kikinis)
*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]
***IGSTK has time stamping for tracker and event.
***Monitors to ensure the minimal latency between display and data acquisition (possible take away from IGSTK to Slicer).
***works on FLTK, Qt

*215-330pm: Setting goals for meeting: Each IGT group present what they want to achieve at this meeting.
**2:30-3:00pm - [[Media:2007_Slicer_programming_meeting-CIMIT.ppt|NCIGT CIGL Stoll]] and Demo
***Issues for Slicer
#Move toward multi-process model, keep idea of GPU capability in mind for future
#online/unsupervised segmentation, online/fast registration (almost like tracking); can trade some accuracy for speed
#flexibility in registration techniques - data collection is not perfectly constrained (patient positions vary, image quality varies, fiducials sometimes/not) - tools for anatomy-based registration
**3:00-3:15 - NA-MIC Collaborator Georgetown Cleary/Yaniv
**3:15-3:30 - NA-MIC DBP Queens/JHU Gobbi/Csoma/Kazanzides
*3:30pm-3:45pm: Review of today's progress
** Did you find what the others are doing with Slicer?

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

===9-10:00am Demos:===
*Hata (Tracking at BWH)
*Freudling (Pieper) (Volume rendering)

===1000-10:30am Demonstrations===
**[[Media:Neuro-Dec07.pdf‎|Robot-assisted neurosurgery with Slicer ]] (Kazanzides)
**Robot connected to Slicer via Robot control unit (with Real time OS)
**Slicer CT coords != Stealthstation CT coords
**Needs rasToIjk matrix from xml file
**Inter-computer communication

*Slicer 3 IGT update

===10:30am: Identifying the unmet needs===
(At this point, representatives from each site should start thinking which part of the unment needs they can take primary responsibility, and take home as homework.)

#Queens: NA-MIC DBP
#JHU: BRP
#BWH: NCIGT etc.
#Georgetown: Liver RF
#Kitware-BWH

*Identify the unique needs in IGT
*Identify commonality among the projects
*which one is to be covered by actively funded project?

*Identity and prioritize unmet needs
*Find commonality among the needs, consolidate if necessary
*Identify 2x three focus groups for afternoon

=====Plug-in mechanism=====
[[Slicer/Features/Modules | Plug-in mechanism / Modules]]
*Currently we use CMake + Slicer3
*Compile vs. Run-time -> run-time is current choice for Steve
*Slicer Base version 3.0
*Binary distributed againg Base version
*Firefox extension
*'''How do you balance testing and flexibility.'''
*Version control necessary
*which is module

*'''effort underway in NA-MIC/NAC'''
*Be ready by XXXXXX.

*Module/function dependency

*Tracker I/O (BWH Hata)
**Tracker On/Off
*Real-Image I/O (BWH Hata)
**'''Video capturing'''
**Simple loading image
**Imager control for each modality
***MRI (NCIGT Tokuda)

*Image re-slicing based on tracker (BWH Hata Liu)

*GUI configuration control (XXX)

*Human interface control
**Foot pedal (BWH Liu)

*Stereo
*Output to outside display

*Logging replay and saving
**IGSTK has fast version
**MRML scene recorder (Georgetown)

*Module/function dependency
{| border="1" cellpadding="5" cellspacing="0" align="center"
|-
| align="left" | Features
| align="left" | Base
| align="left" | Module
|-
| align="left" | Visualization
| align="left" | MRML, Arbitary ViewPoint (Pre-defined)
| align="left" | Liver RF
|-
| align="left" | Filtering
| align="left" | None
| align="left" | Command Line Module
|-
| align="left" | IGT
| align="left" | Intra-op Image I/O
| align="left" | Liver RF
|-
| align="left" | Registration
| align="left" | Transform Display, Edit and Save/Resotre
| align="left" | Calculae Transforms, Resample Data
|-
| align="left" | Segmentation
| align="left" | Label Maps, Parcellated Surface
| align="left" | Segmentation Algorighms
|-
| align="left" | Quantification
| align="left" | Label, Image, Volume Statistics; Numpy access to MRML
| align="left" | Applications in Python or MATLAB
|-
| align="left" | Real-time Integration
| align="left" | VTK Rendering, KWWidgets framework, Tracker Support (as Transforms)
| align="left" | Direct Manipulation of the MRL Scene; 2D/3D Widgets; Device Interface
|-
| align="left" | Diffusion Imaging
| align="left" | DWI, DTI, Fiber Bundles
| align="left" | Tractography, Clustering, Atlases
|-
| align="left" | Application
| align="left" | Bundles of Modules in Distribution: Registration Editor, some Filters
| align="left" | Customized Extensions, Domain specific code, optimized Interface
|-
|}

===12:00-1pm First round of break out session===
(topics to be decided in the morning session)

Report template

http://wiki.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming:report-template

Reports

*[[2007_December_Slicer_IGT_Programming_IGSTK_Slicer_Integration|December 12-14, 2007, Slicer IGT Programming - IGSTK Slicer Integration]]

===1pm: lunch===

===Afternoon===

*1:30-2:30pm Discussion continues

[[Slicer/Features/Events_and_communication | Events / Data transfer]]
** Data/communication/event...
*** Data Workflow I/O
*** ticking and latency management
*** Threads to read-in tracker info
*** Special DICOM and PACS
*** Priority control of events? -> Event Manager
*** Realtime needs
*** Inter-communication mechanism to/from Slicer

*** '''Socket mechanism in SlicerDaemon'''
*** Steve's presentation of small programming sending coords to SlicerDaemon and updating MRML
*** Scenesnapshot can be used as logging. Replay. Crash recovery.

*** State machines may be useful mechanism in Slicer
***

***Connection with commercial navigation system
****MR/T BWH
****Brainlab
****Neuromate
****Medtronics

*3-4pm: List 2
** [[Slicer/Features/Middleware | Inter-communication mechanism to/from Slicer]]
*** Tracker Image
*** Publish subscribe ORB/ACE [Peter]
*** Socket IGSTK [Junichi Patrick]

** Volume rendering
*** Performance and speed continue to be upgraded
*** GPU, fastere volume rendering
*** 4D IGT
*** Real I/O
*** New MRML? Time-series MRML volume?

** (Regulartory approval) (Legal issue/ form / guideline)

=====4:00 Discussion=====

** [[Slicer/Features/GUI | GUI]]
*** GUI-Workflow (David)
*** David's opening statement from Queens' perspective
*** How can we add additional windows?
*** KWWidgets has workflow mechanism
*** Compacting GUI - necessary
*** Single screen? Two screen setup? Two screen setup to be tried by David
*** [http://www.kwwidgets.org/Wiki/KWWidgets/Wizard_Workflow KWWidgets Wizard Workflow] [http://www.kwwidgets.org/Wiki/images/5/53/KWWidgets_-_Wizard_Workflow_-_IGT_-_07%2C_Dec.ppt Powerpoint presentation].

*** Observing events (convenience)

*** Status window is nice
*** short cut
**** pre-defined view point
**** lower left (two complicated)
*** GUI Layout to be stored in MRML (as log)
*** Turning off lower left
*** Status (window) part

*** human interface--
**** Voice
**** configurable GUI using current XML mechanism
***** What's the mechanism for Slicer-IGT

*** Overlay of tools in 2D view of Slicer

*5pm: Review day and plan for Friday (Hata)

*5:30pm: adjourn

[[Image:2007_December_Slicer_IGT_Programming_photo.jpg]]

==Friday, December 14==
----
*9:00am: breakfast, work
*9:30-11:00am

*Review of the meeting
*Discuss how we can continue this effort in what way
**Hands on IGT Week
***Outreaching to animal research community
***Training and simulation
***

*Action Items
**[[2007_Slier_IGTWS_homework_NCIGT| NCIGT]]
**[[2007_Slier_IGTWS_homework_GT| Georgetown]]
**[[2007_Slier_IGTWS_homework_Kitware | Kitware ]]
**[[2007_Slicer_IGTWS_homework_Queens| Queens ]]
**[[2007_Slicer_IGTWS_homework_JHU| JHU ]]
*11:00am-noon: Wrapup/Suggestion to NAC, NCIGT, NAC, and ultimately NIH(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)

2007 December Slicer IGT Programming

2007-12-14T17:48:00Z

Jstoll: /* 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
*Learning IGSK-Slicer
*Interface to scanners

=Agenda=
==Wednesday, December 12 ==
'''Theme: Where are we?'''
*12noon: lunch
*12:55pm: Welcome (Ron Kikinis)
*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]
***IGSTK has time stamping for tracker and event.
***Monitors to ensure the minimal latency between display and data acquisition (possible take away from IGSTK to Slicer).
***works on FLTK, Qt

*215-330pm: Setting goals for meeting: Each IGT group present what they want to achieve at this meeting.
**2:30-3:00pm - [[Media:2007_Slicer_programming_meeting-CIMIT.ppt|NCIGT CIGL Stoll]] and Demo
***Issues for Slicer
#Move toward multi-process model, keep idea of GPU capability in mind for future
#online/unsupervised segmentation, online/fast registration (almost like tracking)
#flexibility in registration techniques - data collection is not perfectly constrained (patient positions vary, imaging qualities vary, fiducials sometimes/not)
**3:00-3:15 - NA-MIC Collaborator Georgetown Cleary/Yaniv
**3:15-3:30 - NA-MIC DBP Queens/JHU Gobbi/Csoma/Kazanzides
*3:30pm-3:45pm: Review of today's progress
** Did you find what the others are doing with Slicer?

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

===9-10:00am Demos:===
*Hata (Tracking at BWH)
*Freudling (Pieper) (Volume rendering)

===1000-10:30am Demonstrations===
**[[Media:Neuro-Dec07.pdf‎|Robot-assisted neurosurgery with Slicer ]] (Kazanzides)
**Robot connected to Slicer via Robot control unit (with Real time OS)
**Slicer CT coords != Stealthstation CT coords
**Needs rasToIjk matrix from xml file
**Inter-computer communication

*Slicer 3 IGT update

===10:30am: Identifying the unmet needs===
(At this point, representatives from each site should start thinking which part of the unment needs they can take primary responsibility, and take home as homework.)

#Queens: NA-MIC DBP
#JHU: BRP
#BWH: NCIGT etc.
#Georgetown: Liver RF
#Kitware-BWH

*Identify the unique needs in IGT
*Identify commonality among the projects
*which one is to be covered by actively funded project?

*Identity and prioritize unmet needs
*Find commonality among the needs, consolidate if necessary
*Identify 2x three focus groups for afternoon

=====Plug-in mechanism=====
[[Slicer/Features/Modules | Plug-in mechanism / Modules]]
*Currently we use CMake + Slicer3
*Compile vs. Run-time -> run-time is current choice for Steve
*Slicer Base version 3.0
*Binary distributed againg Base version
*Firefox extension
*'''How do you balance testing and flexibility.'''
*Version control necessary
*which is module

*'''effort underway in NA-MIC/NAC'''
*Be ready by XXXXXX.

*Module/function dependency

*Tracker I/O (BWH Hata)
**Tracker On/Off
*Real-Image I/O (BWH Hata)
**'''Video capturing'''
**Simple loading image
**Imager control for each modality
***MRI (NCIGT Tokuda)

*Image re-slicing based on tracker (BWH Hata Liu)

*GUI configuration control (XXX)

*Human interface control
**Foot pedal (BWH Liu)

*Stereo
*Output to outside display

*Logging replay and saving
**IGSTK has fast version
**MRML scene recorder (Georgetown)

*Module/function dependency
{| border="1" cellpadding="5" cellspacing="0" align="center"
|-
| align="left" | Features
| align="left" | Base
| align="left" | Module
|-
| align="left" | Visualization
| align="left" | MRML, Arbitary ViewPoint (Pre-defined)
| align="left" | Liver RF
|-
| align="left" | Filtering
| align="left" | None
| align="left" | Command Line Module
|-
| align="left" | IGT
| align="left" | Intra-op Image I/O
| align="left" | Liver RF
|-
| align="left" | Registration
| align="left" | Transform Display, Edit and Save/Resotre
| align="left" | Calculae Transforms, Resample Data
|-
| align="left" | Segmentation
| align="left" | Label Maps, Parcellated Surface
| align="left" | Segmentation Algorighms
|-
| align="left" | Quantification
| align="left" | Label, Image, Volume Statistics; Numpy access to MRML
| align="left" | Applications in Python or MATLAB
|-
| align="left" | Real-time Integration
| align="left" | VTK Rendering, KWWidgets framework, Tracker Support (as Transforms)
| align="left" | Direct Manipulation of the MRL Scene; 2D/3D Widgets; Device Interface
|-
| align="left" | Diffusion Imaging
| align="left" | DWI, DTI, Fiber Bundles
| align="left" | Tractography, Clustering, Atlases
|-
| align="left" | Application
| align="left" | Bundles of Modules in Distribution: Registration Editor, some Filters
| align="left" | Customized Extensions, Domain specific code, optimized Interface
|-
|}

===12:00-1pm First round of break out session===
(topics to be decided in the morning session)

Report template

http://wiki.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming:report-template

Reports

*[[2007_December_Slicer_IGT_Programming_IGSTK_Slicer_Integration|December 12-14, 2007, Slicer IGT Programming - IGSTK Slicer Integration]]

===1pm: lunch===

===Afternoon===

*1:30-2:30pm Discussion continues

[[Slicer/Features/Events_and_communication | Events / Data transfer]]
** Data/communication/event...
*** Data Workflow I/O
*** ticking and latency management
*** Threads to read-in tracker info
*** Special DICOM and PACS
*** Priority control of events? -> Event Manager
*** Realtime needs
*** Inter-communication mechanism to/from Slicer

*** '''Socket mechanism in SlicerDaemon'''
*** Steve's presentation of small programming sending coords to SlicerDaemon and updating MRML
*** Scenesnapshot can be used as logging. Replay. Crash recovery.

*** State machines may be useful mechanism in Slicer
***

***Connection with commercial navigation system
****MR/T BWH
****Brainlab
****Neuromate
****Medtronics

*3-4pm: List 2
** [[Slicer/Features/Middleware | Inter-communication mechanism to/from Slicer]]
*** Tracker Image
*** Publish subscribe ORB/ACE [Peter]
*** Socket IGSTK [Junichi Patrick]

** Volume rendering
*** Performance and speed continue to be upgraded
*** GPU, fastere volume rendering
*** 4D IGT
*** Real I/O
*** New MRML? Time-series MRML volume?

** (Regulartory approval) (Legal issue/ form / guideline)

=====4:00 Discussion=====

** [[Slicer/Features/GUI | GUI]]
*** GUI-Workflow (David)
*** David's opening statement from Queens' perspective
*** How can we add additional windows?
*** KWWidgets has workflow mechanism
*** Compacting GUI - necessary
*** Single screen? Two screen setup? Two screen setup to be tried by David
*** [http://www.kwwidgets.org/Wiki/KWWidgets/Wizard_Workflow KWWidgets Wizard Workflow] [http://www.kwwidgets.org/Wiki/images/5/53/KWWidgets_-_Wizard_Workflow_-_IGT_-_07%2C_Dec.ppt Powerpoint presentation].

*** Observing events (convenience)

*** Status window is nice
*** short cut
**** pre-defined view point
**** lower left (two complicated)
*** GUI Layout to be stored in MRML (as log)
*** Turning off lower left
*** Status (window) part

*** human interface--
**** Voice
**** configurable GUI using current XML mechanism
***** What's the mechanism for Slicer-IGT

*** Overlay of tools in 2D view of Slicer

*5pm: Review day and plan for Friday (Hata)

*5:30pm: adjourn

[[Image:2007_December_Slicer_IGT_Programming_photo.jpg]]

==Friday, December 14==
----
*9:00am: breakfast, work
*9:30-11:00am

*Review of the meeting
*Discuss how we can continue this effort in what way
**Hands on IGT Week
***Outreaching to animal research community
***Training and simulation
***

*Action Items
**[[2007_Slier_IGTWS_homework_NCIGT| NCIGT]]
**[[2007_Slier_IGTWS_homework_GT| Georgetown]]
**[[2007_Slier_IGTWS_homework_Kitware | Kitware ]]
**[[2007_Slicer_IGTWS_homework_Queens| Queens ]]
**[[2007_Slicer_IGTWS_homework_JHU| JHU ]]
*11:00am-noon: Wrapup/Suggestion to NAC, NCIGT, NAC, and ultimately NIH(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)

2007 December Slicer IGT Programming

2007-12-14T17:47:10Z

Jstoll: /* 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
*Learning IGSK-Slicer
*Interface to scanners

=Agenda=
==Wednesday, December 12 ==
'''Theme: Where are we?'''
*12noon: lunch
*12:55pm: Welcome (Ron Kikinis)
*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]
***IGSTK has time stamping for tracker and event.
***Monitors to ensure the minimal latency between display and data acquisition (possible take away from IGSTK to Slicer).
***works on FLTK, Qt

*215-330pm: Setting goals for meeting: Each IGT group present what they want to achieve at this meeting.
**2:30-3:00pm - [[Media:2007_Slicer_programming_meeting-CIMIT.ppt|NCIGT CIGL Stoll]] and Demo
***Issues for Slicer
****1) Move toward multi-process model, keep idea of GPU capability in mind for future
****2) online/unsupervised segmentation, online/fast registration (almost like tracking)
****3) flexibility in registration techniques - data collection is not perfectly constrained (patient positions vary, imaging qualities vary, fiducials sometimes/not)
**3:00-3:15 - NA-MIC Collaborator Georgetown Cleary/Yaniv
**3:15-3:30 - NA-MIC DBP Queens/JHU Gobbi/Csoma/Kazanzides
*3:30pm-3:45pm: Review of today's progress
** Did you find what the others are doing with Slicer?

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

===9-10:00am Demos:===
*Hata (Tracking at BWH)
*Freudling (Pieper) (Volume rendering)

===1000-10:30am Demonstrations===
**[[Media:Neuro-Dec07.pdf‎|Robot-assisted neurosurgery with Slicer ]] (Kazanzides)
**Robot connected to Slicer via Robot control unit (with Real time OS)
**Slicer CT coords != Stealthstation CT coords
**Needs rasToIjk matrix from xml file
**Inter-computer communication

*Slicer 3 IGT update

===10:30am: Identifying the unmet needs===
(At this point, representatives from each site should start thinking which part of the unment needs they can take primary responsibility, and take home as homework.)

#Queens: NA-MIC DBP
#JHU: BRP
#BWH: NCIGT etc.
#Georgetown: Liver RF
#Kitware-BWH

*Identify the unique needs in IGT
*Identify commonality among the projects
*which one is to be covered by actively funded project?

*Identity and prioritize unmet needs
*Find commonality among the needs, consolidate if necessary
*Identify 2x three focus groups for afternoon

=====Plug-in mechanism=====
[[Slicer/Features/Modules | Plug-in mechanism / Modules]]
*Currently we use CMake + Slicer3
*Compile vs. Run-time -> run-time is current choice for Steve
*Slicer Base version 3.0
*Binary distributed againg Base version
*Firefox extension
*'''How do you balance testing and flexibility.'''
*Version control necessary
*which is module

*'''effort underway in NA-MIC/NAC'''
*Be ready by XXXXXX.

*Module/function dependency

*Tracker I/O (BWH Hata)
**Tracker On/Off
*Real-Image I/O (BWH Hata)
**'''Video capturing'''
**Simple loading image
**Imager control for each modality
***MRI (NCIGT Tokuda)

*Image re-slicing based on tracker (BWH Hata Liu)

*GUI configuration control (XXX)

*Human interface control
**Foot pedal (BWH Liu)

*Stereo
*Output to outside display

*Logging replay and saving
**IGSTK has fast version
**MRML scene recorder (Georgetown)

*Module/function dependency
{| border="1" cellpadding="5" cellspacing="0" align="center"
|-
| align="left" | Features
| align="left" | Base
| align="left" | Module
|-
| align="left" | Visualization
| align="left" | MRML, Arbitary ViewPoint (Pre-defined)
| align="left" | Liver RF
|-
| align="left" | Filtering
| align="left" | None
| align="left" | Command Line Module
|-
| align="left" | IGT
| align="left" | Intra-op Image I/O
| align="left" | Liver RF
|-
| align="left" | Registration
| align="left" | Transform Display, Edit and Save/Resotre
| align="left" | Calculae Transforms, Resample Data
|-
| align="left" | Segmentation
| align="left" | Label Maps, Parcellated Surface
| align="left" | Segmentation Algorighms
|-
| align="left" | Quantification
| align="left" | Label, Image, Volume Statistics; Numpy access to MRML
| align="left" | Applications in Python or MATLAB
|-
| align="left" | Real-time Integration
| align="left" | VTK Rendering, KWWidgets framework, Tracker Support (as Transforms)
| align="left" | Direct Manipulation of the MRL Scene; 2D/3D Widgets; Device Interface
|-
| align="left" | Diffusion Imaging
| align="left" | DWI, DTI, Fiber Bundles
| align="left" | Tractography, Clustering, Atlases
|-
| align="left" | Application
| align="left" | Bundles of Modules in Distribution: Registration Editor, some Filters
| align="left" | Customized Extensions, Domain specific code, optimized Interface
|-
|}

===12:00-1pm First round of break out session===
(topics to be decided in the morning session)

Report template

http://wiki.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming:report-template

Reports

*[[2007_December_Slicer_IGT_Programming_IGSTK_Slicer_Integration|December 12-14, 2007, Slicer IGT Programming - IGSTK Slicer Integration]]

===1pm: lunch===

===Afternoon===

*1:30-2:30pm Discussion continues

[[Slicer/Features/Events_and_communication | Events / Data transfer]]
** Data/communication/event...
*** Data Workflow I/O
*** ticking and latency management
*** Threads to read-in tracker info
*** Special DICOM and PACS
*** Priority control of events? -> Event Manager
*** Realtime needs
*** Inter-communication mechanism to/from Slicer

*** '''Socket mechanism in SlicerDaemon'''
*** Steve's presentation of small programming sending coords to SlicerDaemon and updating MRML
*** Scenesnapshot can be used as logging. Replay. Crash recovery.

*** State machines may be useful mechanism in Slicer
***

***Connection with commercial navigation system
****MR/T BWH
****Brainlab
****Neuromate
****Medtronics

*3-4pm: List 2
** [[Slicer/Features/Middleware | Inter-communication mechanism to/from Slicer]]
*** Tracker Image
*** Publish subscribe ORB/ACE [Peter]
*** Socket IGSTK [Junichi Patrick]

** Volume rendering
*** Performance and speed continue to be upgraded
*** GPU, fastere volume rendering
*** 4D IGT
*** Real I/O
*** New MRML? Time-series MRML volume?

** (Regulartory approval) (Legal issue/ form / guideline)

=====4:00 Discussion=====

** [[Slicer/Features/GUI | GUI]]
*** GUI-Workflow (David)
*** David's opening statement from Queens' perspective
*** How can we add additional windows?
*** KWWidgets has workflow mechanism
*** Compacting GUI - necessary
*** Single screen? Two screen setup? Two screen setup to be tried by David
*** [http://www.kwwidgets.org/Wiki/KWWidgets/Wizard_Workflow KWWidgets Wizard Workflow] [http://www.kwwidgets.org/Wiki/images/5/53/KWWidgets_-_Wizard_Workflow_-_IGT_-_07%2C_Dec.ppt Powerpoint presentation].

*** Observing events (convenience)

*** Status window is nice
*** short cut
**** pre-defined view point
**** lower left (two complicated)
*** GUI Layout to be stored in MRML (as log)
*** Turning off lower left
*** Status (window) part

*** human interface--
**** Voice
**** configurable GUI using current XML mechanism
***** What's the mechanism for Slicer-IGT

*** Overlay of tools in 2D view of Slicer

*5pm: Review day and plan for Friday (Hata)

*5:30pm: adjourn

[[Image:2007_December_Slicer_IGT_Programming_photo.jpg]]

==Friday, December 14==
----
*9:00am: breakfast, work
*9:30-11:00am

*Review of the meeting
*Discuss how we can continue this effort in what way
**Hands on IGT Week
***Outreaching to animal research community
***Training and simulation
***

*Action Items
**[[2007_Slier_IGTWS_homework_NCIGT| NCIGT]]
**[[2007_Slier_IGTWS_homework_GT| Georgetown]]
**[[2007_Slier_IGTWS_homework_Kitware | Kitware ]]
**[[2007_Slicer_IGTWS_homework_Queens| Queens ]]
**[[2007_Slicer_IGTWS_homework_JHU| JHU ]]
*11:00am-noon: Wrapup/Suggestion to NAC, NCIGT, NAC, and ultimately NIH(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)

File:2007 Slicer programming meeting-CIMIT.ppt

2007-12-14T17:39:06Z

Jstoll: