Engineering:Core 3 Programming Week

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Location: 1249 Boylston St, Boston, MA directions

Monday September 26th: Engineering and DBP Discussion


Goal: Core 3 to give feedback on how they are using the NAMIC Kit in their daily work.

  • noon-1pm: Meet and greet
  • 1-2:15pm Feedback from UCI on NAMIC Kit ppt presentation
  • 2:15-3:30pm Feedback from Dartmouth on NAMIC Kit ppt presentation
  • 3:30-3:50pm break
  • 3:50-5:00pm Discussion of features required going forward, Conclusion
  • Dinner

Tuesday September 27th Engineering Discussion

9am-noon: Slicer 3.0 Architecure decision making

  • Agenda Creation
  • Summarize Goals of Slicer 3
    • Serve as Application for Core 3 users of Core 1 Algorithms implemented in ITK
    • Enforce Modularity
    • Broader Development Base (interoperate with different languages, GUI toolkits)
  • Technology Discussions
    • Slicer Protocol (Steve)
    • MRML / Coordinate / Publish and Subscribe (Mike)
    • KWWidgets / Widgets / VolView Update (Will)

  • Implementation Issues
    • Wrapping ITK Algorithms as Modules
      • Filter Watcher, Build as Standalone Executable or Linked Library
    • UI Definition (GUI and CLI)
      • Command line introspection
      • Progress reporting
    • Process Control (Abort, Sync/Async)
    • Communication
      • Serialization of the Scene, Semantics, Coordinate Systems
      • RPC-like back and forth exchanges (what capabilities are provided by Slicer Base?)
    • Provenance
    • Exporting Scene description to text and binary files

  • Timelines and Action Items
  • ** By All Hands Meeting
      • ITK I/O Factory communicating over sockets to slicer 2.x (Steve, Alex)
        • Example executable-based modules:
          • Smooth and image
          • Segmentation
          • Registration
      • TCLAP based XML version of help/interface (Dan, Jim)

  • ** At All Hands Meeting


fMRI in slicer review (Wendy, Haiying, Bill, Will, Jim, Steve, Sandy) Background discussion before Polina and Wanmei arrive.

2-5pm: fMRI statistics

Bill, Jim, Will, Sandy, Steve, Wendy, Carsten, Haiying, Polina, Wanmei

  • ** *** Current VTK (EMSegmenter) and Matlab (Eric Cosman, Wanmei) based implementations
      • Migration to ITK and/or improved VTK methods
        • Discuss existing and planned MRF infrastructure [see this discussion on the ITK mailing list]
          • ICM based filters in current ITK
          • Need: MF, Min-Cut/Max-Flow
        • Review existing MI infrastructure and discuss its applicability to activation detection
        • Migrating GLM from GSL to VNL (vtkITK wrapper)
      • Estimates of amount of effort, action items

Wednesday September 28th Engineering Discussion

  • 9:15-10:15 Misc:
    • MICCAI Workshop talk (NAMIC Kit: Jim 30 min, NAMIC Overview: Ron 10 min, Slicer: Steve 20 min)
    • BugTracker
    • NIH Forge
  • 10:30-noon non-linear ITK registration, widgets