View source for 2008 Engineering review at UNC

Date: December 15-16, 2008.  

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

'''[[2008_Engineering_review_at_UNC:Summary | SUMMARY AND ACTION ITEMS]]'''


'''[[2008_Engineering_review_at_UNC:FollowUp | 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:
* [http://www.carolinainn.com/ Carolina Inn], 211 Pittsboro Street, Chapel Hill, NC  
* [http://www.franklinhotelnc.com/ Franklin Hotel], 311 W Franklin St, Chapel Hill, NC 

Best suggestion (needs taxi to campus/UNC Hospitals & Franklin Street):
* [http://www.courtyardchapelhill.com/ 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

[[Image:DunphyConfRoomLocation.jpg|400px]]

===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 [http://www.mediterraneandeli.com/Catering_Menu/catering_menu.html 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