Engineering:September 12, 2007

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Home < Engineering:September 12, 2007


Catch up on latest developments, set priorities, identify issues. Also brainstorm on competitive renewal.


One day in Clifton Park, 10am to 4pm. Location is the Comfort Suites Hotel in Clifton Park, NY. Please go to for more information.

Boston people can plan for one (somewhat long) day or stay over.

Hot Topics

Review of the needs of the DBPs

  • UNC DBP2:UNC:Cortical_Thickness_Roadmap
  • JHU/Queens
  • MIND
  • Harvard
    • Structural Pipeline (will be done first)
      • bias field correction missing (independent of EM)
      • intensity normalization missing
      • skull stripping (PNL currently using FSL BET)
      • EMSegmentation (still some issues with slicer3 module vs slicer2 -- being worked on, ball in Sylvain's court)
      • Unbiased atlas creation (several people working on it, no finished tool yet)
    • Diffusion Pipeline (deferred until Slicer3 DTI infrastructure is in place)
      • DICOM to NRRD (general solution would be great if it were possible)
      • Eddy Current Correction (also requested by IUPUI; PNL currently using Affine reg in FSL)
      • Outlier rejection (Marc is working on automated detection tool)
      • Filtering : Rician noise model (LMI tool from Santi)
  • Scope: Ongoing

Slicer3 release

  • Technical issues
    • Build process
    • CPack (see below)
  • what are roadblocks?
    • crashes?
    • critical functionality?
    • modules
      • interactive editor
      • EM segmenter
      • DTI functionality
      • data fusion
  • Review of release process and schedule
    • Code freeze, ...
  • Scope: Jan 1 Release (pre-AHM)

Year 4 Workplan

The "next" EM Segmenter

  • Registration (rigid and non-rigid; modules to create statistical atlases)
  • DTI (visualize; advanced queries; rendering performance, Runge-Kutta, etc.)
  • Interactive editing
  • Scope: July 2008


  • NAMIC Kit Overview (as requested by NIH)
  • Practical Software Process
  • Scope: July 2008

BatchMake interface

  • Data sharing
    • Access to MIDAS and other database repositories from within Slicer
  • Batch(Make) modules
    • EMSegmenter
    • OtsuThreshold
    • Registration(?)
  • Scope: Jan 2008 (pre-AHM)


  • rpm, deb
  • na-mic kit available via standard linux distribution sites?
  • visual studio 8 issues
  • other topics from project week
  • Scope: Dec 2007 (pre-release)

Volume rendering in Slicer3


  • "testing mode"
    • avoid the confirmation dialog on exit
    • avoid being influenced by the user's registry
    • avoid polluting the user's registry
    • Seb: easy one :) check all KWW examples, they are run both as examples and as nightly tests. vtkKWApplication::PromptBeforeExitOff() will disable the confirmation dialog, vtkKWApplication::SetRegistryLevel(0) will make sure the registry is not affected.
  • access to events from scripting languages
    • Seb: do you remember where the corresponding meeting notes are? We discussed that item in the past, and I remember it was all good, awaiting implementation...
  • gui tracing for macros and replay (and for creating tests)?
  • file browser multithreading
  • other follow ups from project week discussions
  • Scope: Ongoing, large scope


  • 3D Widgets
  • Level-of-detail?
  • Oblique slice plane specifier?
  • Disambiguating "picking" with mouse
  • Scope: Ongoing, large scope

command line modules

  • passing mrml scenes back and forth
  • Scope: Jan 2008 (pre-AHM)


Competitive Renewal

  • where do we want to be 7 years from now?
  • what is the state of medical image computing likely to be?
  • what is the state of computing likely to be?

wiki 2 web and PublicationDB

  • perl script translation
  • counting downloads
  • integrated license agreement

Databases and GRID

  • Breakout session: 1pm tcon

Webpage Rework

  • TBD


Confirmed (please add your name so we can keep count to estimate room size etc):

  • Steve, Ron, Nicole, Katie, Will, Dan, Jim, Alex, Old Bill, Sebastien, Zack, Luis, Dave Cole, Stephen, Andy Freudling

Meeting Summary

The following summarizes the results of the meeting:

The agenda was as follows:

  • DBP Needs Discussion – 10:30-11:30
  • Slicer3 Releases – 11:30-12:30
  • The “next” EM Segmenter – 12:30-1:00
  • Workplan 2007 – afternoon
  • Technical discussions – afternoon
    • KWWidgets
    • 3D Interactions
    • Build issues / CMake / CPack
    • Command line modules
  • Breakouts
    • Grid discussion / BatchMake / Database
    • PubDB / wiki2web
    • Volume rendering
    • Licensing discussions
    • Slicer Lightbox for pursuing funding opps

Key Deliverables for the coming year

  • DBP Related
  • Slicer Releases
    • Support building a Slicer module from a binary distribution – AHM 2008
    • Support for command-line tutorial (Jim)
    • BatchMake tutorial AHM 2008 (Stephen)
    • Official release v3.0, Code freeze mid-November
      • interactive editor (Steve)
      • EM segmenter (Sylvain/Brad)
      • DTI functionality (Alex)
      • Linear data fusion (Luis –registration, oriented images)