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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

Na mic structure

NA-MIC Structure

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


Enjoy !

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