2008 Engineering review at UNC

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:

• Carolina Inn, 211 Pittsboro Street, Chapel Hill, NC
• Franklin Hotel, 311 W Franklin St, Chapel Hill, NC

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

• Courtyard Marriott, 100 Marriott Way, Chapel Hill, NC

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

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