2008 Engineering review at UNC

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Date: December 15-16, 2008.

Arrival: Morning of Monday, December 15. Leaving: Afternoon on Tuesday, December 16.

SUMMARY AND ACTION ITEMS


ACTION UPDATE

Minutes

  • General issues:
    • Source / Module handling
      • Current idea: Source updated within UNC NeuroLib - Releases at NITRIC
      • Steve: presentation of ideas to load/unload Slicer extensions
      • It would be important to have easy access to both Nightly and Release versions
      • NAMIC Wiki for roadmap description
      • Slicer Wiki for modules, NITRC links to this documentation
      • Install compilation of Modules for upload/download
    • Population handling
      • XNAT browse within Slicer
      • createx xcat => included in Batchmake for running on population
      • This should be used for the current development of ARCTIC population phase
    • Download of a module
      • Wizard selection
      • SLICER_MODULE_PATHS => for executables & BatchMake bmm files

Suggested Hotels

Nice for walking to campus & Franklin Street, but rather expensive:

Best suggestion (needs taxi to campus/UNC Hospitals & Franklin Street):

Engineering Attendees (projected)

Will Schroeder, Steve Pieper, (possibly) Jim Miller, Julien Jomier

Place

  • University of North Carolin, Chapel Hill
  • Dunphy Conference Room (see also map)
  • 3rd Floor Medical School Wing C (next to Neuro Image Research and Analysis Lab)
  • There is very limited parking on campus for visitors, so car rental is not necessarily encouraged, but nearest parking is in Dogwood UNC Hospital Patient & Visitor Parking House (see map)
  • Transportation from Airport
    • Taxi ride to UNC Hospitals: 30-35 USD, use map or call Martin (919-260-6674) to get to the conference room

DunphyConfRoomLocation.jpg

Proposed discussion items

Schedule

Tentative schedule:

Monday: noon - 5pm

  • Noon - 1 pm: Arrival, Lunch and Meet of the whole group
  • 1pm - 2pm: UNC cortical thickness pipeline and related issues (regional analysis) - Vachet, Mathieu, Styner
  • 2pm - 3pm: UNC cortical thickness pipeline for local analysis - Vachet, Styner, Mathieu
  • 3pm - 4pm: UNC cortical/surface correspondence incorporating DTI - Oguz, Styner, Vachet
  • 4pm - 5pm: Make up time and wrap up for the day
  • 7pm: Dinner on Franklin Street: Restaurant TBA

Tuesday: 9am - 1pm

  • 9am - 10am: UNC shape analysis framework, including MANCOVA based statistical analysis - Styner
  • 10am - 10:45am: DTI prep tool - Liu, Styner
  • 10:45am - 11:30: DTI voxel based analysis - Liu, Styner
  • 11:30am - noon: Mouse brain analysis pipeline and Slicer 3 - Lee, Styner
  • noon - 1pm: Make up time and wrap up
  • General topics: BatchMake, Grid computing, Population tools in Slicer, NITRC and Slicer, Atlases, MRML File Output, Workflow Wizards
  • Saving Parameter sets (save MRML parameters or could be BatchMake config file)

Catering: MEDITERRANEAN DELI Menu

Attendees

  • Martin Styner
  • Clement Vachet
  • Cedric Mathieu
  • Ipek Oguz
  • Zhexing Liu
  • Julien Jomier
  • Will Schroeder
  • Steve Pieper
  • Jim Miller
  • Marc Niethammer (possibly)

Notes

Slicer Items:

  • Scene matrix dialog
    • parse directory tree or use config file
    • show matrix of subjects and QC steps for easy loading
    • ideally with screen captures of mrml scene
  • screen grabs of mrml scenes at load and or save time (or on demand during processing) saved in data dir
  • Model intersection visible in model display gui
  • BatchMake build as part of genlib
  • Slicer3_Module_Paths variable exported to environment for BatchMake to inherit
  • UNC DTI QC module uses in TBI
  • "Decorated" BatchMake to act as Slicer CLI by generating --xml to build gui for configuring script
  • "Open As Template..." for MRML scene file
    • all Storable nodes listed in dialog
    • user can accept default or browse to files to override