NA-MIC National Alliance for Medical Image Computing Programming Week Kickoff MIT, June 27, 2005

National Alliance for Medical Image Computing Setting the Stage… NAMIC Background – –The “Alliance Diagram”, the sites… –Who is here today (numbers) This week –Goals: What do we want to accomplish? –Mechanics: How are we going to get there? –Measuring Success: How will we know if we have arrived?

National Alliance for Medical Image Computing Structure

National Alliance for Medical Image Computing NAMIC Algorithms Core Harvard Georgia TechUNC UtahMIT Segmentation Registration Foundational Methods Structural Features and Statistics Connective Features and Statistics

National Alliance for Medical Image Computing NAMIC Engineering Core Isomics UCLA Software Integration Software Engineering Software Quality Software Engineering Tools Data Access Tools Distributed Computing Applications

National Alliance for Medical Image Computing NAMIC DBP Core Harvard Toronto Dartmouth UCI Segmentation Registration Foundational Methods Structural Features and Statistics Connective Features and Statistics

National Alliance for Medical Image Computing Number for Today: 44 People –32 NA-MIC 12 Core 1 (Algorithms) 14 Core 2 (Engineering) 1 Core 3 (Driving Biological Projects) 1 Core 4 (Service) 2 Core 5 (Training) 1 Core 6 (Dissemination) 1 Core 7 (Leadership) –12 Collaborators (BWH, Stanford, SRI)

National Alliance for Medical Image Computing Number for Today: 17 Projects 1.Non-rigid EPI registration using ITK (Snyder, Tuch, Ibanez) 2.Prototype ITK system for Quantitative Fiber Tract Analysis (Goodlett, Tao, Corouge,Maddah,Mewes) 3.Processing modules and visualization tools for shape analysis (Oguz, Xu, Styner, Miller) 4.Object population description and general feature analysis framework (Styner,Fletcher,Miller) 5.Addition of Bayesian Segmentation Module to ITK (Melonakos, Ibanez) 6.Wrap motion robust matching code using ITK (Khidhir, Warfield, Archip, Lorensen) 7.DLPFC Semi-Automatic Segmentor (Al-Hakim, Yarmakovich) 8.Flux Diffusion in ITK (Krissian) 9.ITKu, minimalist command line tools using ITK (San-Jose Estepar) 10.nrrd ITK IO, read and write nrrd tensor data with ITK (Kindlmann) 11.Slicer DTMRI module nightly testing (O'Donnell, San-Jose Estepar, Cedilnik) 12.ITK Wrap Intensity Correction and Normalization Methods (Weisenfeld, Warfield) 13.LONI pipeline for UNC script based shape analysis pipeline (Styner, Oguz, Rajendiran) 14.3D Adaptive Tetrahedral Mesh Generation in ITK (Fedorov, Chrisochoides, Warfield, Schroeder) 15.2D/3D Point landmark detection in ITK (Lloyd, Warfield) 16.Large Scale Algorithm Job Submission via Condor (Gerk, Grethe, Pieper) 17.Pipelining ITK modules (Rajendiran, Pieper) 18.Slicer 3.0 (Pieper)

National Alliance for Medical Image Computing This Week: Goals Individual Project Goals NA-MIC Goals –Establish cross-core working teams –Share results, plan publications –Plan software architecture improvements –Follow-up at All-hands-meeting, Jan , 2006.

National Alliance for Medical Image Computing This Week: Mechanics Where –Mon-Tue: Building 32 (Star, Kiva) –Wed-Thurs-Friday: Building 34 (4 th floor, Grier) Time –8:30am breakfast, 9am session,5:30pm wrap up –coffee 10:30am, lunch noon, coffee 3:30pm –Tuesday 6:30-8:30pm Dinner/Discussion (Bldg 32, R&D Dining) –Wednesday afternoon: tour Boston (optional) –End of meeting: Friday at 12:30pm. Every day: –All meet at 9am, then breakout into teams, meet again at 5pm Thursday 9am: highlights

National Alliance for Medical Image Computing This Week: Mechanics (contd) Projectors Ring the bell Slicer 3.0 Discussion People to bug: Bill, Will, Steve, Luis, Jim, Tina

National Alliance for Medical Image Computing This week: Measuring Success Short-term (Yr1-2) –Each team member aware of what scientific questions we are trying to answer in NA-MIC… –Add “NA-MIC” modules to ITK/Slicer Medium term (Yr2-3) –Employ these modules to study scientific questions… –Publish results –Improve the software infrastructure to aid the answering of these questions Longer term (Yr 3-5) –Repeat with a new set of clinical questions (DBP)

National Alliance for Medical Image Computing Rest of today: (~10 min) Dave Tuch – Gathering Requirements… (~10 min) Sonia Pujol – Training Documents (~5 min each) Individual Project 3-Block Summary 3:30-4pm Coffee 4-5:30pm Setup programming environment 5:30-6pm Meet back here for wrap-up