2007 December Slicer IGT Programming
From NAMIC Wiki
Home < 2007 December Slicer IGT Programming
Dates.Location.Hotels
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
- 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
- Slicer Core + Loadable Modules
- 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).
- works on FLTK, Qt
- Slicer: overview of architecture, current status, and future plans (Pieper, Hata)
- 215-330pm: Setting goals for meeting: Each IGT group present what they want to achieve at this meeting.
- 2:30-3:00pm - NCIGT CIGL Stoll and Demo
- 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 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
- 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
List 1
Plug-in mechanism
- 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
- 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
- Data/communication/event...
- GUI
- GUI-Workflow (see possible topics for discussion ) (David)
- human interface
- Overlay of tools in 2D view of Slicer
- GUI
- Testing/Quality assurance, GUI Testing (Slicer), Tracker Testing (Robot)
List 2
- Inter-communication mechanism to/from Slicer
- Volume rendering
- Abdominal registration
- (Regulartory approval) (Legal issue/ form / guideline)
- Module/function dependency
Features | Base | Module |
Visualization | MRML, Arbitary ViewPoint (Pre-defined) | Liver RF |
Filtering | None | Command Line Module |
IGT | Intra-op Image I/O | Liver RF |
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 |
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
1pm: lunch
Afternoon
- 1:30-2:30pm Second round of break-out session (topics to be decided in the morning session)
- 3-4pm: Coffee break (and NA-MIC TCON)
- 3-4pm: session leaders put together reports in wiki
- 4:00 review of outcome from break out sessions
- 5pm: Review day and plan for Friday (Hata)
- 5:30pm: adjourn
Friday, December 14
- 9:00am: breakfast, work
- 9:00-10:00am
- Identify the homework for each team (NCIGT, NA-MIC, Georgetown, Queens, JHU)
- Identify the new initiative, i.e. new funding: who will do what
- review this meeting
- discuss how we can continue this effort in what way.
- Plan for Hands on IGT Week
- 11:15am-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)