NA-MIC National Alliance for Medical Image Computing http://na-mic.org

The NA-MIC Kit: ITK, VTK, Pipelines, Grids and 3D Slicer as An Open Platform for the Medical Image Computing Community

Steve Pieper 1,5 , Bill Lorensen 2,5 , Will Schroeder 3,5 , Ron Kikinis 4,5

1) Isomics, Inc. 2) GE Corporate R&D 3) Kitware, Inc. 4) Brigham and Women's Hospital, Surgical Planning Lab 5) National Alliance for Medical Image Computing

Overview

• National Alliance for Medical Image Computing (

NA-MIC

) is an NIH National Center for Biomedical Computing (

NCBC

) • The NA-MIC Kit is a Collection of Software and Methodology to Support Image Computing Innovation and Reproducibility • Builds on Existing Efforts

National Alliance for Medical Image Computing http://na-mic.org

NA-MIC Sites

• • • • Leadership: – BWH: Ron Kikinis, (Overall PI) – Steve Wong Core 1 Algorithms – – – – – Utah: Ross Whitaker (Core 1 PI) MIT: Eric Grimson UNC: Guido Gerig MGH: Bruce Fischl, Dave Kennedy GaTech: Allen Tannenbaum Core 2 Engineering – GE: Bill Lorensen (Core 2 PI) – Kitware: Will Schroeder – – – Isomics: Steve Pieper UCSD: Mark Ellisman UCLA: Art Toga Core 3 DBP – BWH: Martha Shenton – – – Dartmouth: Andy Saykin UCI: Steve Potkin UofT: Jim Kennedy

National Alliance for Medical Image Computing http://na-mic.org

• • • • Core 4 Service – Kitware: Will Schroeder Core 5 Training – MGH: Randy Gollub Core 6 Dissemination – Isomics: Steve Pieper, Tina Kapur Core 7 Management – BWH: Steve Wong

NIH NCBC Goals

• http://grants1.nih.gov/grants/guide/rfa-files/

RFA RM-04-003

.html

• …NIH does have

goals for software dissemination

… • …software should be

freely available

… • …

permit the commercialization

of enhanced or customized versions… • …include the ability of researchers outside the center and its collaborating projects to

modify the source code and to share modifications

…

National Alliance for Medical Image Computing http://na-mic.org

Role of NA-MIC Kit Analogy

• NA-MIC, as a Taxpayer Funded Activity is Like a Public Road System – Provides Infrastructure for a Variety of Uses – Driveways can Lead to Anything • a Coop Grocery Store • a Factory • a Park • a Gated Community

National Alliance for Medical Image Computing http://na-mic.org

Translational Medicine Platform

NA-MIC Kit

Industry

National Alliance for Medical Image Computing http://na-mic.org

NA-MIC Kit Licensing Policies

• Technology Base for Research and Commercialization – Okay to build GPL or Closed SW

on top of

NA-MIC Kit – But no GPL or Closed SW

in

NA-MIC Kit • NA-MIC Provides “Reference Standard Distribution” – Maintain Official Releases – Avoid Code Forking, Non-Free Code Creeping into Core • No “Knowing” Addition of Patented Techniques into NA-MIC Kit • Copyright to Substantive Works Remains with Creators – Available under NA-MIC Approved Licenses for Distribution with Kit – Insight Journal is Example of this Process

National Alliance for Medical Image Computing http://na-mic.org

NA MIC Kit is…

• Open Source Software • Targeted for Medical Image Analysis and Data Management • Distributed Under BSD-style License • Supporting Documentation and Training for End Users and Developers • NA-MIC Development/Testing Methodology • Ongoing Maintenance through NIH NCBC •

Conduit for Technology to Flow from Algorithm Developers to Clinicians National Alliance for Medical Image Computing http://na-mic.org

NA-MIC Kit Functionality

• • • • First Driving Biological Project – Schizophrenia Research Quantify Structural and Functional Relationships to Disease and Symptoms Integrated Software Tools – Morphometric MRI, DTI, and fMRI – Segmentation and Registration Kit will Evolve with New DBPs and Community Uses

National Alliance for Medical Image Computing http://na-mic.org

NA-MIC Kit Components

• Software Engineering Tools – CMake, Dart, CTest • Image Analysis, Visualization, and GUI libraries – ITK, VTK, KWWidgets • End User Application – 3D Slicer • Large Scale Data Processing Tools – LONI Pipeline, GRID tools http://www.na-mic.org/Wiki/index.php/SoftwareInventory

National Alliance for Medical Image Computing http://na-mic.org

NA-MIC Kit Architecture

Algorithms ITK Batch Programs VTK VTK Apps Using ITK Slicer Modules Scripts of Slicer Mods Slicer 3.0

Non-NAMIC Cmd tools LONI Pipeline BIRN Grid Data/Compute User Desktop

National Alliance for Medical Image Computing http://na-mic.org

2 months

Development Methodology

Release Extreme lifecycle Patch Nightly

Release X.Y.1

Continuous Testing

Private Sandbox NA-MIC Sandbox Slicer Release X.Y

Release X.Y.2

4 months ITK Release X.Y.3

6 months

National Alliance for Medical Image Computing http://na-mic.org

Dashboard CMake CTest CPack

Dissemination and Training

• National and International Events – MIT, MGH, UNC, EPFL, NIH, UNM, UCSD… • All Materials on Wiki • Project Weeks – Full Week Each Summer – ½ Week at Winter AHM • Workshops – MICCAI 2005, 2006 – Others Planned

National Alliance for Medical Image Computing http://na-mic.org

Practical Implications

• NA-MIC Kit is Available Now – Ready-Made Infrastructure for Medical Image Computing Development • NA-MIC Kit is Usable – Many Examples, Tutorials, Mailing Lists… • NA-MIC Kit Will Continue to Improve – Multi-Year NIH Effort and Community of Users

National Alliance for Medical Image Computing http://na-mic.org

More Information

• Project Overview http://www.na-mic.org

• Day-to-Day Organization, Project Plans, Event Information, Reference Materials, etc, etc.

http://wiki.na-mic.org

National Alliance for Medical Image Computing http://na-mic.org