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Introduction. Ron Kikinis. Logistics. Wireless Network available Presenters: Please upload to the wiki AHM: Thursday morning: Present Thursday afternoon: Future Friday morning: EAB Project week: Wednesday through Friday. [email protected]'s Bar & Grill. 160 South Main St. Phone: 801-359-7271

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Ron Kikinis

  • Wireless Network available
  • Presenters: Please upload to the wiki
  • AHM:
    • Thursday morning: Present
    • Thursday afternoon: Future
    • Friday morning: EAB
  • Project week: Wednesday through Friday
bill@murphy s bar grill
[email protected]'s Bar & Grill

160 South Main St. Phone: 801-359-7271

6:00pm-9:00pm: Thursday Evening

  • Year 3: organized around four themes
    • NA-MIC Kit
    • Structural Analysis
    • DTI
    • fMRI
  • Reports this morning
namic kit update
NAMIC Kit Update
  • Slicer 3
    • Significant progress
    • Modules now beingcontributed
  • Foundational Software
    • KWWidgets
    • CPack
    • DART, CMake
    • VTK, ITK
    • BIRN, InsightJournal
structural analysis update
Structural Analysis Update
  • New methods segmentation & shape leading to tools
  • Slicer integration
  • MGH Freesurfer
  • Coherent, joint effort across groups and cores for shape
dwi dti analysis
Expert Labels

Clustered Data

DWI/DTI Analysis
  • Algorithms
    • Low-level
      • Filtering and estimation
      • Segmentation
    • Higher-level
      • Tracts/paths
      • Altases
  • Software
    • Slicer/Slicer3
  • Clinical results
core 1
Core 1:
  • Ross is Core 1 PI
  • Polina is now site-PI for MIT, Eric serves as senior advisor
  • Guido is moving to Utah
core 2
Core 2:
  • Will replaces Bill as Core 2 PI,
  • Jim takes over the site PI function
  • Slicer3 beta is released
core 3
Core 3:
  • Current DBP's
    • NA-MIC funding for current DBP’s ends 07-31-2007.
    • No follow-up grant applications until now!!!
  • New DBP's will use NA-MIC funding to transition into NA-MIC kit and develop application portfolio
    • Harvard
    • UNC
    • JHU/Queens
    • UNM
velo cardio facial syndrome vcfs as a genetic model for schizophrenia
Velo-Cardio-Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia.


Marek Kubicki, MD, PhD


Martha Shenton, PhD

Zora Kikinis, PhD

Sylvain Bouix, PhD

Marc Niethammer, PhD


Doug Markant, BA


  • VCFS is a rare genetic syndrome (single copies of 30-45 genes on chromosome 22 are missing)
  • 30% of patients with VCFS develop schizophrenia


  • To characterize anatomical similarities and dissimilarities between VCFS and Schizophrenia
  • To find “schizophrenia” genes


  • DTI, MRI, haplotypes, neuropsychology
unc autism study
UNC Autism Study

Longitudinal MRI study of early brain development in neuropsychiatric disorder:

Heather Cody Hazlett, PhD (Co-PI Joseph Piven, MD)

UNC Chapel Hill, Department of Psychiatry

& the Neurodevelopmental Disorders Research Center

  • Possible projects for NA-MIC:
  • Substructure segmentation – automate existing protocols
  • (2) Cortical thickness – localized analysis, longitudinal
  • (3) DTI atlas – regional & localized analysis
  • (4) Shape analysis – automated, longitudinal

Data: sMRI, DTI, behavioral /clinical

Group age 2 age 4

Autism 56 28

DevDelay 10 6

TypDev 18 8

The MIND Institute / UNMThe Analysis of Brain Lesions in Neuropsychiatric Systemic Lupus Erythematosis


H. Jeremy Bockholt

Charles Gasparovic, Ph.D.


Vincent Magnotta, Ph.D.

Vince Calhoun, Ph.D.

Dominic Meier, Ph.D.


Sumner Williams, M.S.


  • NPSLE is an autoimmune disorder that causes neurological and psychiatric complications
  • Afflicted patients have distinct white matter lesions that vary over time
  • To understand the etiology of brain lesions in NPSLE, accurate measurement of lesion location, size, and time course must be achieved
  • AIMS:
  • Evaluate existing tools and develop new tools useing the NA-MIC kit for time series analysis of brain lesions found in NPSLE


  • MRI, DTI, perfusion, transcranial ultrasound, echocardiography, and neuropsychology

Data collected under R01-NS35708-04

cores 4 7
Cores 4-7
  • Web: move to new infrastructure
  • Training Core: Outreach events for 2007: Suggestions, Requests?
  • Leadership Core:
    • Steve Wong has moved to other activities.
    • Rachana Manandhar joins the administration team.
collaboration grants
Collaboration grants:
  • PAR's have been reissued.
  • NIH removed the restriction on prior collaborators.
  • Electronic submission required.
  • PAR-07-249 (R01)PAR-07-250 (R21)
  • Iowa funded to do FEM Mesh Generation
  • Several other applications are being submitted or are pending
strategic planning
Strategic Planning
  • Competitive renewal is looming (if we are allowed to submit)
  • We need to identify NIH institutes who might co-sponsor NA-MICs competitive renewal: NIBIB, NLM, NCRR, NIMH, NCI….
define na mic s strength
Define NA-MIC’s Strength
  • Mark Ellisman: What is our “Moonshot”?
    • We need a story that will be understood by people on the outside, including NIH and congress
  • Who are we relative to:
    • other software efforts such as SPM, Mathlab, FSL, LONI, Freesurfer, SCI, Paraview, BIRN etc.
    • other NCBC’s
what is our offering
What is our offering?
  • Algorithm researchers: Toolkits and developers environment
  • Biomedical Engineers: we need scripting capabilities
  • Application scientists: we need turn-key solutions
to do list for 2007
To-Do List for 2007
  • Your NA-MIC funding is intended for NA-MIC relevant work
  • Use and improve the NA-MIC kit
  • Move to Slicer 3!
  • Cores 1 and 2 should work with the current DBP’s to exploit the NA-MIC kit:
    • Use-Scenarios
    • “Portable” Solutions
    • Collaboration Grants
  • Identify projects with the new DBP’s
project week june 25 29 mit
Project Week: June 25-29, MIT
  • Computer Scientists: Work on your source code using the NA-MIC kit
    • Produce Modules
  • DBP’s: Work on your data using the NA-MIC kit
    • Produce Procedure Manuals