Difference between revisions of "2007 December Slicer IGT Programming"

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__NOTOC__
 
__NOTOC__
 +
 
=Introduction=
 
=Introduction=
<gallery Caption="Sponsored by" widths="120px" heights="75px" perrow="6">
+
<gallery Caption="Sponsored by">
 
image:NAMIC_380x463.jpg|[http://www.na-mic.org NA-MIC]
 
image:NAMIC_380x463.jpg|[http://www.na-mic.org NA-MIC]
 
image:NCIGTlogo.gif|[http://www.ncigt.org NCIGT]
 
image:NCIGTlogo.gif|[http://www.ncigt.org NCIGT]
image:CIMITlogo.gif|IGT program of [http://www.cimit.org CIMIT]
+
image:Logo_CIMIT.png|IGT program of [http://www.cimit.org CIMIT]
 
Image:Logo_nac.gif|[http://nac.spl.harvard.edu/ NAC]
 
Image:Logo_nac.gif|[http://nac.spl.harvard.edu/ NAC]
 
</gallery>
 
</gallery>
  
This is a working meeting for research groups with funding to work on the IGT extensions of the NA-MIC kit. There will be a follow up meeting during the NA-MIC AHM in SLC.
+
This was a working meeting for research groups with funding to work on the IGT extensions of the NA-MIC kit. There will be a follow up meeting during the NA-MIC AHM in SLC.
 +
 
 +
=Summery=
 +
Over 20 researchers attended this meeting.
 +
 
 +
{|
 +
|[[Image:2007_December_Slicer_IGT_Programming_photo.jpg|200px]]
 +
|[[Image:2007_December_Slicer_IGT_Programming_photo01.jpg|200px]]
 +
|[[Image:2007_December_Slicer_IGT_Programming_photo02.jpg|200px]]
 +
|[[Image:2007_December_Slicer_IGT_Programming_photo03.jpg|200px]]
 +
|-
 +
|[[Image:2007_December_Slicer_IGT_Programming_photo05.jpg|200px]]
 +
|[[Image:2007_December_Slicer_IGT_Programming_photo06.jpg|200px]]
 +
|[[Image:2007_December_Slicer_IGT_Programming_photo08.jpg|200px]]
 +
|[[Image:2007_December_Slicer_IGT_Programming_photo09.jpg|200px]]
 +
|-
 +
|[[Image:2007_December_Slicer_IGT_Programming_photo04.jpg|200px]]
 +
|[[Image:2007_December_Slicer_IGT_Programming_photo07.jpg|200px]]
 +
|}
 +
 
  
 
=Dates.Location.Hotels=
 
=Dates.Location.Hotels=
Line 21: Line 41:
 
*Continued [[Leadership:SlicerIGT_2007|'''discussion''']] of Slicer IGT infrastructure, applications, and timelines
 
*Continued [[Leadership:SlicerIGT_2007|'''discussion''']] of Slicer IGT infrastructure, applications, and timelines
 
*Introduce each team's effort in Slicer in the context of IGT
 
*Introduce each team's effort in Slicer in the context of IGT
*active funding&future submissions
+
*Find unmet needs
*on-going technical development
+
*Identify high-priority working items
*find unmet needs
+
*Identify each team's potential contribution to the high-priority tasks
*find how we can share the work
+
 
*Learning IGSK-Slicer
+
=Meeting summery=
*Interface to scanners
+
Twenty three investigators using Slicer for their IGT research supported by NIH gathered in Brigham and Women's Hospital from December 12 to 14, 2007.
 +
We discussed current status, unmet needs, future direction, and resource sharing in Slicer engineering. Four live demonstrations using real tracking device
 +
and phantoms were performed to facilitate the discussion.  In summery, we concluded that the 3D Slicer, which currently centers around medical image
 +
processing and visualization,  definitely has proven to be also useful for IGT and has potential to become enabling tool for new domain of research in IGT.
 +
However, we also agreed that Slier still has gap in its in feature list to meet requirements of the investigators goals in their own clinical targets as well as innovative IGT applications.  These unmet needs are
 +
*Plug-in mechanism to develop a high-performance software specifically tailored to a target clinical application
 +
*Controlled and fast Data/communication/event management
 +
*Inter-device communication mechanism to/from Slicer
 +
*Fast Volume rendering for 4D IGT
 +
*Flexible GUI design
 +
Objective evidence for existence of these needs derives from our own assessment as well as our extensive discussion during the meeting. Continued existence of these need represents an important problem because, until the needs are met, new and innovative IGT procedures using state-of-art imaging and treatment device may not be available due to lack of guiding and navigation software.
 +
As the next step in IGT research using Slicer, we decided to collaboratively develop the above mentioned mechanism through resource sharing, frequent communication, and if necessary additional funding support.
  
 
=Agenda=
 
=Agenda=
 
==Wednesday, December 12 ==
 
==Wednesday, December 12 ==
 
'''Theme:  Where are we?'''
 
'''Theme:  Where are we?'''
*12noon: lunch
+
===12noon: Lunch===
*12:55pm: Welcome (Ron Kikinis)
+
===12:55pm: Welcome (Ron Kikinis)===
*1-2pm:
+
===1-2pm:Slicer and IGSTK presentation===
**Slicer: overview of architecture, current status, and future plans (Pieper, Hata)
+
*Slicer: overview of architecture, current status, and future plans (Pieper, Hata)
***History
+
**History
***Clinical applications
+
**Clinical applications
***transition from 2.6 to 3
+
**transition from 2.6 to 3
***resource
+
**resource
***[[media:Pieper-IGT-retreat-2007-12-12.ppt | Slicer Core]] + [[Slicer3:Loadable_Modules | Loadable Modules]]  
+
**[[media:Pieper-IGT-retreat-2007-12-12.ppt | Slicer Core]] + [https://www.slicer.org/wiki/Slicer3:Loadable_Modules Loadable Modules]
**IGSTK
+
*IGSTK
*** [[Media:IGSTK-Architecture-IGT-Meeting-Dec-12-2007.ppt‎|Architecture Overview]] (Ibanez)
+
** [[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]
+
** 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.
+
**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).
+
**Monitors to ensure the minimal latency between display and data acquisition (possible take away from IGSTK to Slicer).
***works on FLTK, Qt
+
**GUI tools for sample programs are FLTK and Qt
 
 
 
 
 
 
  
 +
===215-330pm: Presentation by Slicer Developers===
  
*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
**2:30-3:00pm - [[Media:2007_Slicer_programming_meeting-CIMIT.ppt|NCIGT CIGL Stoll]] and Demo
+
**Issues for Slicer
***Issues for Slicer
 
 
#Move toward multi-process model, keep idea of GPU capability in mind for future
 
#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
 
#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
 
#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
+
*3:00-3:15 - NA-MIC Collaborator Georgetown Cleary/Yaniv
**3:15-3:30 - NA-MIC DBP Queens/JHU Gobbi/Csoma/Kazanzides
+
*3:15-3:30 - NA-MIC DBP Queens/JHU Gobbi/Csoma/Kazanzides
 
*3:30pm-3:45pm: Review of today's progress
 
*3:30pm-3:45pm: Review of today's progress
** Did you find what the others are doing with Slicer?
 
  
 
+
===400pm: Adjourn===
Adjourn
+
===4-6pm (optional) MRI Demonstration ===
*4-6pm (optional) demonstration of Slicer for control and display of MRI scanner (prostate module) @Advanced MRI center, 221 Longwood
+
*Use of Slicer for control and display with MRI (prostate module) presented by Junichi Tokuda. Location: Advanced MRI center, 221 Longwood, Boston
 
**See [[2007_December_Slicer_IGT_Programming_MRI_DEMO| slicer-MRI demo]]
 
**See [[2007_December_Slicer_IGT_Programming_MRI_DEMO| slicer-MRI demo]]
  
 
==Thursday, December 13==
 
==Thursday, December 13==
===Morning===
+
'''Theme:  Where are we?'''
 
 
Theme:  Where are we?'''
 
*9:00am breakfast, start work
 
 
 
 
===9-10:00am Demos:===
 
===9-10:00am Demos:===
 
*Hata (Tracking at BWH)
 
*Hata (Tracking at BWH)
Line 98: Line 121:
 
*Identify commonality among the projects
 
*Identify commonality among the projects
 
*which one is to be covered by actively funded project?
 
*which one is to be covered by actively funded project?
 
 
*Identity and prioritize unmet needs  
 
*Identity and prioritize unmet needs  
 
*Find commonality among the needs, consolidate if necessary
 
*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]]
+
===Unmet needs #1: Plug-in mechanism===
 +
Related wiki page -> [https://www.slicer.org/wiki/Slicer/Features/Events_and_communication Plug-in mechanism / Modules]
 
*Currently we use CMake + Slicer3
 
*Currently we use CMake + Slicer3
 
*Compile vs. Run-time -> run-time is current choice for Steve
 
*Compile vs. Run-time -> run-time is current choice for Steve
Line 113: Line 135:
 
*'''How do you balance testing and flexibility.'''
 
*'''How do you balance testing and flexibility.'''
 
*Version control necessary
 
*Version control necessary
*which is module
 
 
 
*'''effort underway in NA-MIC/NAC'''
 
*'''effort underway in NA-MIC/NAC'''
*Be ready by XXXXXX.
 
 
 
*Module/function dependency
 
*Module/function dependency
  
*Tracker I/O (BWH Hata)
+
*Common functions to be implemented in Base
**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)
 
  
  
Line 162: Line 162:
 
|-
 
|-
 
| align="left" | IGT  
 
| align="left" | IGT  
| align="left" | Intra-op Image I/O
+
| align="left" |  
| align="left" | Liver RF
+
*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)
 +
| align="left" | BWH, Georgetown, JHU, Queens applications
 
|-
 
|-
 
| align="left" | Registration  
 
| align="left" | Registration  
Line 191: Line 212:
 
|}
 
|}
  
===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
+
===Unmet needs #2 Data/communication/event ===
 +
Related wiki page [https://www.slicer.org/wiki/Slicer/Features/Events_and_communication Events / Data transfer]
  
[[Slicer/Features/Events_and_communication | Events / Data transfer]]
+
* Data Workflow I/O
** Data/communication/event...
+
* ticking and latency management
*** Data Workflow I/O
+
* Threads to read-in tracker info
*** ticking and latency management
+
* Special DICOM and PACS
*** Threads to read-in tracker info
+
* Priority control of events?  -> Event Manager
*** Special DICOM and PACS
+
* Realtime needs
*** Priority control of events?  -> Event Manager
+
* Inter-communication mechanism to/from Slicer
*** Realtime needs
 
*** Inter-communication mechanism to/from Slicer
 
  
*** '''Socket mechanism in SlicerDaemon'''
+
* '''Socket mechanism in SlicerDaemon'''
*** Steve's presentation of small programming sending coords to SlicerDaemon and updating MRML
+
* Steve's presentation of small programming sending coords to SlicerDaemon and updating MRML
*** Scenesnapshot can be used as logging. Replay. Crash recovery.
+
* Scenesnapshot can be used as logging. Replay. Crash recovery
 +
* State machines may be useful mechanism in Slicer
 +
** follow up activities in the related wiki page [https://www.slicer.org/wiki/Slicer/Features/Events_and_communication Events / Data transfer] '''
 +
*Connection with commercial navigation system
 +
**MR/T BWH
 +
**Brainlab
 +
**Neuromate
 +
**Medtronics
  
*** State machines may be useful mechanism in Slicer
 
***
 
  
***Connection with commercial navigation system
+
===Unmet needs #4: Inter-device communication mechanism to/from Slicer ===
****MR/T BWH
+
** [https://www.slicer.org/wiki/Slicer/Features/Middleware Inter-device communication mechanism to/from Slicer]
****Brainlab
 
****Neuromate
 
****Medtronics
 
 
 
 
 
*3-4pm: List 2
 
** [[Slicer/Features/Middleware | Inter-communication mechanism to/from Slicer]]
 
 
*** Tracker Image
 
*** Tracker Image
 
*** Publish subscribe ORB/ACE [Peter]
 
*** Publish subscribe ORB/ACE [Peter]
 
*** Socket IGSTK [Junichi Patrick]
 
*** Socket IGSTK [Junichi Patrick]
  
 +
===Unmet needs #5: Volume rendering===
 
** Volume rendering
 
** Volume rendering
 
*** Performance and speed continue to be upgraded
 
*** Performance and speed continue to be upgraded
Line 248: Line 254:
 
** (Regulartory approval) (Legal issue/ form / guideline)
 
** (Regulartory approval) (Legal issue/ form / guideline)
  
 +
*[[2007_December_Slicer_IGT_Programming_IGSTK_Slicer_Integration|December 12-14, 2007, Slicer IGT Programming - IGSTK Slicer Integration]]
  
  
=====4:00 Discussion=====
+
===Unmet needs #3: GUI ===
  
** [[Slicer/Features/GUI | GUI]]
+
* [https://www.slicer.org/wiki/Slicer/Features/GUI GUI]
*** GUI-Workflow (David)
+
** GUI-Workflow (David)
*** David's opening statement from Queens' perspective
+
** David's opening statement from Queens' perspective
*** How can we add additional windows?
+
** How can we add additional windows?
*** KWWidgets has workflow mechanism
+
** KWWidgets has workflow mechanism
*** Compacting GUI - necessary
+
** Compacting GUI - necessary
*** Single screen? Two screen setup? Two screen setup to be tried by David
+
** 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].
+
** [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)  
+
** Observing events (convenience)  
 
+
** Status window is nice
*** Status window is nice
+
** short cut
*** short cut
+
*** pre-defined view point
**** pre-defined view point
+
*** lower left (two complicated)
**** lower left (two complicated)
+
** GUI Layout to be stored in MRML (as log)
*** GUI Layout to be stored in MRML (as log)
+
** Turning off lower left
*** Turning off lower left
+
** Status (window) part
*** Status (window) part
+
** human interface--
 
+
*** '''configurable GUI using current XML mechanism'''
 
 
*** 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)
 
*5pm: Review day and plan for Friday (Hata)
  
 
*5:30pm: adjourn
 
*5:30pm: adjourn
 
[[Image:2007_December_Slicer_IGT_Programming_photo.jpg]]
 
  
 
==Friday, December 14==
 
==Friday, December 14==
----
+
===9:00am: breakfast, work===
*9:00am: breakfast, work
+
===9:30-11:00am Review of the meeting===
*9:30-11:00am
 
 
 
*Review of the meeting
 
 
*Discuss how we can continue this effort in what way
 
*Discuss how we can continue this effort in what way
 
**Hands on IGT Week
 
**Hands on IGT Week
***Outreaching to animal research community
+
**Outreaching to animal research community
***Training and simulation
+
**Training and simulation
  
  
Line 307: Line 301:
 
*11:00am-noon: Wrapup/Suggestion to NAC, NCIGT, NAC, and ultimately NIH(Hata)  
 
*11:00am-noon: Wrapup/Suggestion to NAC, NCIGT, NAC, and ultimately NIH(Hata)  
 
*noon: adjourn and head out to group lunch
 
*noon: adjourn and head out to group lunch
 
----
 
 
=Photos=
 
[[Image:2007_December_Slicer_IGT_Programming_photo01.jpg]]
 
[[Image:2007_December_Slicer_IGT_Programming_photo02.jpg]]
 
[[Image:2007_December_Slicer_IGT_Programming_photo03.jpg]]
 
[[Image:2007_December_Slicer_IGT_Programming_photo04.jpg]]
 
[[Image:2007_December_Slicer_IGT_Programming_photo05.jpg]]
 
[[Image:2007_December_Slicer_IGT_Programming_photo06.jpg]]
 
[[Image:2007_December_Slicer_IGT_Programming_photo07.jpg]]
 
[[Image:2007_December_Slicer_IGT_Programming_photo08.jpg]]
 
[[Image:2007_December_Slicer_IGT_Programming_photo09.jpg]]
 
  
 
==Confirmed Attendees==
 
==Confirmed Attendees==
Line 342: Line 323:
 
#Neculai Archip, BWH (Wed only) (NCIGT)
 
#Neculai Archip, BWH (Wed only) (NCIGT)
 
#Nicholas Ayache (NCIGT) (Wed only)
 
#Nicholas Ayache (NCIGT) (Wed only)
 +
#Andy Freudling, (NAMIC)
 +
#Henrik Keller (NCIGT)
 +
#Benjamin Grauer (NCIGT)

Latest revision as of 19:45, 11 April 2023

Home < 2007 December Slicer IGT Programming


Introduction

This was a working meeting for research groups with funding to work on the IGT extensions of the NA-MIC kit. There will be a follow up meeting during the NA-MIC AHM in SLC.

Summery

Over 20 researchers attended this meeting.

2007 December Slicer IGT Programming photo.jpg 2007 December Slicer IGT Programming photo01.jpg 2007 December Slicer IGT Programming photo02.jpg 2007 December Slicer IGT Programming photo03.jpg
2007 December Slicer IGT Programming photo05.jpg 2007 December Slicer IGT Programming photo06.jpg 2007 December Slicer IGT Programming photo08.jpg 2007 December Slicer IGT Programming photo09.jpg
2007 December Slicer IGT Programming photo04.jpg 2007 December Slicer IGT Programming photo07.jpg


Dates.Location.Hotels

Date: December 12-14, 2007

SPL at 1249 Boylston Street, Boston MA. (Directions)

Area hotels: Boston_Hotels

Goal

  • Continued discussion of Slicer IGT infrastructure, applications, and timelines
  • Introduce each team's effort in Slicer in the context of IGT
  • Find unmet needs
  • Identify high-priority working items
  • Identify each team's potential contribution to the high-priority tasks

Meeting summery

Twenty three investigators using Slicer for their IGT research supported by NIH gathered in Brigham and Women's Hospital from December 12 to 14, 2007. We discussed current status, unmet needs, future direction, and resource sharing in Slicer engineering. Four live demonstrations using real tracking device and phantoms were performed to facilitate the discussion. In summery, we concluded that the 3D Slicer, which currently centers around medical image processing and visualization, definitely has proven to be also useful for IGT and has potential to become enabling tool for new domain of research in IGT. However, we also agreed that Slier still has gap in its in feature list to meet requirements of the investigators goals in their own clinical targets as well as innovative IGT applications. These unmet needs are

  • Plug-in mechanism to develop a high-performance software specifically tailored to a target clinical application
  • Controlled and fast Data/communication/event management
  • Inter-device communication mechanism to/from Slicer
  • Fast Volume rendering for 4D IGT
  • Flexible GUI design

Objective evidence for existence of these needs derives from our own assessment as well as our extensive discussion during the meeting. Continued existence of these need represents an important problem because, until the needs are met, new and innovative IGT procedures using state-of-art imaging and treatment device may not be available due to lack of guiding and navigation software. As the next step in IGT research using Slicer, we decided to collaboratively develop the above mentioned mechanism through resource sharing, frequent communication, and if necessary additional funding support.

Agenda

Wednesday, December 12

Theme: Where are we?

12noon: Lunch

12:55pm: Welcome (Ron Kikinis)

1-2pm:Slicer and IGSTK presentation

  • Slicer: overview of architecture, current status, and future plans (Pieper, Hata)
  • IGSTK
    • Architecture Overview (Ibanez)
    • Current status, and future plans (Cheng) 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).
    • GUI tools for sample programs are FLTK and Qt

215-330pm: Presentation by Slicer Developers

  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); can trade some accuracy for speed
  3. 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

400pm: Adjourn

4-6pm (optional) MRI Demonstration

  • Use of Slicer for control and display with MRI (prostate module) presented by Junichi Tokuda. Location: Advanced MRI center, 221 Longwood, Boston

Thursday, December 13

Theme: Where are we?

9-10:00am Demos:

  • Hata (Tracking at BWH)
  • Freudling (Pieper) (Volume rendering)

1000-10:30am Demonstrations

    • 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.)

  1. Queens: NA-MIC DBP
  2. JHU: BRP
  3. BWH: NCIGT etc.
  4. Georgetown: Liver RF
  5. 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


Unmet needs #1: Plug-in mechanism

Related wiki page -> 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
  • effort underway in NA-MIC/NAC
  • Module/function dependency
  • Common functions to be implemented in Base




  • Module/function dependency
Features Base Module
Visualization MRML, Arbitary ViewPoint (Pre-defined) Liver RF
Filtering None Command Line Module
IGT
  • 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)
BWH, Georgetown, JHU, Queens applications
Registration Transform Display, Edit and Save/Resotre Calculae Transforms, Resample Data
Segmentation Label Maps, Parcellated Surface Segmentation Algorighms
Quantification Label, Image, Volume Statistics; Numpy access to MRML Applications in Python or MATLAB
Real-time Integration VTK Rendering, KWWidgets framework, Tracker Support (as Transforms) Direct Manipulation of the MRL Scene; 2D/3D Widgets; Device Interface
Diffusion Imaging DWI, DTI, Fiber Bundles Tractography, Clustering, Atlases
Application Bundles of Modules in Distribution: Registration Editor, some Filters Customized Extensions, Domain specific code, optimized Interface



Unmet needs #2 Data/communication/event

Related wiki page Events / Data transfer

  • 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


Unmet needs #4: Inter-device communication mechanism to/from Slicer

Unmet needs #5: Volume rendering

    • 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)


Unmet needs #3: 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
    • KWWidgets Wizard Workflow 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--
      • configurable GUI using current XML mechanism
  • 5pm: Review day and plan for Friday (Hata)
  • 5:30pm: adjourn

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


Confirmed Attendees

  1. Noby Hata, BWH (NCIGT)
  2. Steve Pieper, Isomics - (All Days) (NAMIC, NAC)
  3. Patrick Cheng, Georgetown (NAMIC Collab)
  4. Ziv Yaniv, Georgetown (NAMIC Collab)
  5. Kevin Cleary, Georgetown (Wed only) (NAMIC Collab)
  6. Luis Ibanez, Kitware (NAMIC)
  7. Sebastien Barre, Kitware (NCIGT)
  8. Stephen Aylward, Kitware (NCIGT)
  9. Jeff Stoll (except Thursday), BWH/CIMIT (NCIGT)
  10. Haiying Liu, BWH (NCIGT)
  11. Katie Hayes, BWH (NAC)
  12. Peter Kazanzides (except Friday), JHU (NAMIC Collab)
  13. Csaba Csoma, JHU (NAMIC/NCIGT Collab)
  14. David Gobbi, Queens (NAMIC/NCIGT Collab)
  15. Tina Kapur,BWH (NAMIC/NCIGT)
  16. Ron Kikinis, BWH (NAMIC/NCIGT)
  17. Junichi Tokuda, BWH (NCIGT)
  18. Raul San Jose, BWH (NAC)
  19. Neculai Archip, BWH (Wed only) (NCIGT)
  20. Nicholas Ayache (NCIGT) (Wed only)
  21. Andy Freudling, (NAMIC)
  22. Henrik Keller (NCIGT)
  23. Benjamin Grauer (NCIGT)