2006 AHM: Dissemination Update

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

2006 AHM: Dissemination Update

Tina Kapur, Ph.D., Co-PI

Steve Pieper, Ph.D., Co-PI

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

Dissemination Update 2006Kapur, Pieper

Dissemination Update

– Where we want to go– How we plan to get there…– What have we done so far…



Dissemination Goals

• Year 1: – Inward Focus

• Workshops at NA-MIC, for NA-MIC, by NA-MIC – With Service, Engr, Training, Algo, DBP…

• Year 2: – Inward + Outward Focus

• Keep the good • Expand scope to broader research community

– With all the NA-MIC Cores



Dissemination Mechanisms• Facilitate ongoing internal collaboration and

publications– Programming Week– Use of Insight Journal to archive software, test data,

and algorithm descriptions– Advanced ITK/Slicer Workshops– Wiki

• NA-MIC Kit workshops at collaborator sites• Workshops/Tutorials at Research Meetings• Facilitate collaboration grant submissions

– PAR-05-063 Collaboration with NCBC



Dissemination so far…

• Events:– Open Source Workshop at MICCAI, October 30th, Palm Springs, CA– NA-MIC Kit Workshop, October 5-7, EPFL, Lausanne, Switzerland– Programming Week#1, June 27-July 1, MIT

• Growing wiki– 596 pages– 319794 page views/ 12699 page edits

– 4.42 average edits per page/25.18 views per edit. • Strong pipeline of potential external collaborators



MICCAI Open Source Workshop October 30, 2005

• Palm Springs, CA • Guido Gerig, Co-Chair of main MICCAI conference (~600 attendees)• 80 attendees, 72 counted at last talk (~5pm Sunday)• Keynote by Mike Vannier, Radiology, University of Chicago• 37 submissions, 90 reviews• 11 oral and 10 poster presentations. (4 NA-MIC).• Sponsored by

– The Insight Software Consortium – The Insight Journal – The National Library of Medicine – The NA-MIC / NIH Roadmap – The MICCAI Society

• Organized by– Stephen Aylward ([email protected]) – Tina Kapur ([email protected]) – Luis Ibanez ([email protected])



NA-MIC Kit WorkshopOctober 5-7, EPFL, Lausanne, Switzerland

• Advanced ITK course: developer level(new advanced material was created)

• First ITK course not attached to a conference.(participants came just for the course)

• 37 Participants (it was planned to be limited to 30)– Switzerland 14– Spain 7– Belgium 7– Italy 3– France 3 (the group that developed gdcm : ITK DICOM reader)– Germany 1 (a physicist), UK 1, Sweden 1, US 1.

• Hands-on practices (great Swiss organization, computer room standardized)



Programming Week#1, MITJune 27-July 1, 2005

• The Week– 44 participants (including most core and several site PIs)– 5 days (9-5…)– 15 Projects (3 applications, 6 algorithms, 6 software engr)

• Collaborative Wiki-Centric Organization– Historical Snapshots of wiki pages

• Continued Work– 4 submissions to Insight Open Access Journal– Lead to MICCAI Open Source Workshop– Continued Projects at Programming Half Week right after AHM – Programming Week#2 at MIT, Summer 2006

• Side Effect– Symbios (NCBC) Collaboration on Editor for Muscle

Segmentation• Two Projects

– John Melanakos, Georgia Tech– Martin Styner, UNC



Programming Week#1 Projects

• Applications1. Quantitative Fiber Tract Analysis2. Rule-based DLPFC Segmentation3. Non-Rigid EPI Registration

• Algorithms1. Shape Description2. Shape Analysis3. Bayesian Segmentation4. 2d/3d point-landmark Detection 5. Editing 3D Adaptive Tetrahedral Mesh Generation6. Flux Diffusion

• Software Infrastructure1. ITKu2. NRRD IO3. Slicer DTMRI Nightly Testing4. LONI Pipeline Integration of UNC Shape Analysis Pipeline5. Large Scale Algorithm Job Submissions via Condor6. Slicer 3.0 Architecture

• http://www.na-mic.org/Wiki/index.php/Engineering:2005_Programming_Week_Results



• Engineering:Programmers Week Summer 2005• From NAMIC Wiki• (Revision as of 23:26, 31 Mar 2005)• Attendees:

• Known Schedule constraints: – wk of June 6 – wk of June 13 – wk of June 20 – wk of June 27 – wk of July 4 -- probably not – wk of July 11 – wk of July 18 – wk of July 25 – wk of Aug 1 – wk of Aug 8 – (not scheduling in the last two weeks of august due to popular vacation

time)

Didn’t know where, who, what, when….

Did know that wewould program for

a week in the summer

Wiki Page Snapshot March 31, 2005



Wiki Page Snapshot April 9, 2005• Engineering:Programmers Week Summer 2005• From NAMIC Wiki• (Revision as of 13:04, 9 Apr 2005)• Date: Monday, June 27 - Friday, July 1st, 2005. •

• Location: Boston (where in Boston is TBD) • Goals: This main goal of this week is to move forward the software deliverables of NAMIC. All NAMIC programmers, whether they are faculty,

researcher, student, administrator, engineer, or anything else in their day job, are welcome to join us. Some key points: • You don't need to be in core 1 or 2 to attend, even though most of the attendees are likely to be from these cores. • You do need to be actively programming on a NAMIC project in order to make this investment worthwhile for everyone. • Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend. • Ideal candidates are those who have an algorithm that needs to be moved into the NAMIC Kit, and those who can help make it happen. • This is not an introduction to ITK or Slicer or LONI pipeline. If you have not had any introductory exposure to at least one of these three yet,

and want to attend, please make sure that you have done all the programming exercises that were introduced in the NAMIC dissemination workshops.

• …• Interested Attendees: • Delphine Nain (Georgia Tech, Core 1) • John Melonakos (Georgia Tech, Core 1) • Casey Goodlett (UNC, Core 1) • Ipek Oguz (UNC, Core 1) • Martin Styner (UNC, Core 1) • Tom Fletcher (Utah, Core 1) • Steve Pieper (BWH, Core 2) • Katie Hayes (BWH, Core 2) • Michael Pan (UCLA, Core 2) • Luis Ibanez (Kitware, Core 2) • Alex Yarmarkovich (BWH, Core 2) • Josh Snyder (MGH, Core 1) • Lauren O'Donnell (MIT, Core 1) • Candidate Projects • DTI • Shape Analysis (Martin Styner): General shape analysis framework incorporating descriptions of object populations and general feature

analysis framework. Support needed: ITK • Slicer3.0 Architecture Kickoff

Started to answer when, who, what



Wiki Page Snapshot April 26, 2005• Engineering:Programmers Week Summer 2005• From NAMIC Wiki• (Revision as of 07:16, 26 Apr 2005)• Dates and Schedule• Monday, June 27 - Friday, July 1st, 2005. • Location• Mon-Tue at Star Conference Room at MIT CSAIL, 32-D463 • …• Participants• John Melonakos (Georgia Tech, Core 1) • Casey Goodlett (UNC, Core 1) • Ipek Oguz (UNC, Core 1) • Christine Xu (UNC, Core 1) • Martin Styner (UNC, Core 1) • Tom Fletcher (Utah, Core 1) • Josh Snyder (MGH, Core 1) • Lauren O'Donnell (MIT, Core 1) • Steve Pieper (BWH, Core 2) • Katie Hayes (BWH, Collaborator) • Raul San Jose Estepar (BWH, Collaborator) • Michael Pan (UCLA, Core 2) • Luis Ibanez (Kitware, Core 2) • Andy Cedilnik (Kitware, Core 2) • Alex Yarmarkovich (BWH, Core 2) • Jim Miller (GE, Core 2) • Xiaodong Tao (GE, Core 2) • Nicole Aucoin (BWH, Collaborator) • Bill Lorensen (GE, Core 2 PI) • Sylvain Bouix (Harvard, Core 3) • Besam Khidhir (BWH, Collaborator) • Neculai Archip (BWH, Collaborator) • Bryn Lloyd (BWH) • Sonia Pujol (BWH, Core 5) • Will Schroeder (Kitware, Core 4 PI) • Sebastien Barre (Kitware, Core 2) • Projects• Applications • Non-rigid EPI registration using ITK (Snyder, Tuch, Ibanez)• Prototype ITK system for Quantitative Fiber Tract Analysis (Casey - UNC, Xiaodong - GE)• Processing modules and visualization tools for shape analysis (Ipek Oguz, Christine Xu, Martin Styner - UNC)• Object population desription and general feature analysis framework (Martin Styner, Tom Fletcher)• Addition of Bayesian Segmentation Module to ITK (John M, Ibanez)• Wrap motion robust matching code using ITK (Khidhir, Warfield)•

Infrastructure • Pipelining ITK modules(Mike, )• Slicer3.0 Architecture Kickoff (Pieper, Lorensen, Schroeder, Hayes)•

TBD • TBD: Improve Slicer Tract Clustering Implementation (Lauren)• TBD User Testing and Feature Requests (Sylvain, Katie)

MIT, 20+ people,10+ projects



• Engineering:Programmers Week Summer 2005• From NAMIC Wiki• (Revision as of 19:05, 26 Jun 2005)• Table of contents [hide] 1 Logistics

1.1 Dates and Schedule1.2 Location1.3 Hotel1.4 Registration Fee1.5 Tuesday dinner List2 Goals3 How will this week work?4 Preparation for the workshop5 Agenda6 Participants7 Projects7.1 Non-rigid EPI registration using ITK (Snyder, Tuch, Ibanez)7.2 Prototype ITK system for Quantitative Fiber Tract Analysis (Casey - UNC, Xiaodong - GE), Isabelle - UNC7.3 Processing modules and visualization tools for shape analysis (Ipek Oguz, Christine Xu, Martin Styner - UNC, Jim Miller - GE Research)7.4 Object population desription and general feature analysis framework (Martin Styner - UNC, Tom Fletcher - Utah, Jim Miller - GE Research)7.5 Addition of Bayesian Segmentation Module to ITK (John Melonakos, Ibanez)7.6 Wrap motion robust matching code using ITK (Khidhir, Warfield, Archip, Lorensen)7.7 DLPFC Semi-Automatic Segmentor (Ramsey Al-Hakim, Alex Yarmakovich)7.8 Flux Diffusion in ITK (Karl Krissian)7.9 ITKu, minimalist commandline tools using ITK (Raul San Jose, Gordon Kindlmann)7.10 nrrd ITK IO, read and write nrrd tensor data with ITK (Gordon Kindlmann)7.11 Slicer DTMRI module nightly testing (Lauren O'Donnell, Raul San Jose Estepar, Andy Cedilnik)7.12 Spectral Clustering in ITK (Lauren O'Donnell, Luis Ibanez)7.13 ITK Wrap Intensity Correction and Normalization Methods (Weisenfeld, Warfield)7.14 LONI pipeline for UNC script based shape analysis pipeline (Martin Styner, Ipek Oguz - UNC, Jags Rajendiran - UCLA)7.15 3D Adaptive Tetrahedral Mesh Generation in ITK (Fedorov, Chrisochoides, Warfield)7.16 2D/3D Point landmark detection in ITK (Lloyd, Warfield)7.17 Large Scale Algorithm Job Submission via Condor(Jason, Jeff, Pieper)7.18 Pipelining ITK modules(Jags, Pieper)8 Slicer3.0 Architecture Kickoff9 Computer Resources

Wiki Page Snapshot June 27, 2005

19 Projects, 44 people,One wiki page!



Programming Week#1, MITJune 27-July 1, 2005

• The Week– 44 participants (including most core and several site PIs)– 5 days (9-5…)– 15 Projects (3 applications, 6 algorithms, 6 software engr)

• Collaborative Wiki-Centric Organization– Historical Snapshots of wiki pages

• Continued Work– 4 submissions to Insight Open Access Journal– Lead to MICCAI Open Source Workshop– Continued Projects at Programming Half Week right after AHM – Programming Week#2 at MIT, Summer 2006

• Side Effect– Symbios (NCBC) Collaboration on Editor for Muscle

Segmentation• Two Projects

– John Melanakos, Georgia Tech– Martin Styner, UNC



John Melonakos



Programming Week Project: Bayesian Segmentation of MRI

• Collaboration between– Georgia Tech (Algorithms)– UC Irvine (DBP)– Kitware (Engineering)

• John Melonakos (Advisor: Allen Tannenbaum)• Timeline:

– 2005 Nov: Bayesian algorithm prototyped in Matlab– 2005 Dec: attended NA-MIC ITK workshop– 2005 Mar: signed up for programming week project to transfer

prototype code into NA-MIC kit– 2005 Apr-May: started working with Luis: sandbox, data…– 2005 Jun: worked with Jim Fallon at UCI to understand neuroanatomy– 2005 Jun-Jul: worked on it at prog week with Luis– 2005 Aug: IJ submission (algorithm and software)– 2005 Nov: spent two days at Kitware to tie loose ends– 2006 Jan: continuing work at programming half-week…



Martin Styner



Programming week I:UNC Shape Analysis

• LONI pipeline integration of old tools – With LONI people (only processing)

• New Programs with Core 2 (Jim Miller)– Processing, Analysis, and Visualization– Interaction with Core 2 was crucial

• Good design & style, ITK classes, testing• Open Source, now available and stable• Used at other sites (BWH, GT, NIMH)• Interaction with Core 3 necessary

– BWH data, additional visit

• Education for students, senior personnel



Programming week II:UNC shape analysis

• This week, next step • Full integration in LONI

pipeline– Necessary for use by non-

engineers, Core 3

• Visualization enhancement– KW-Widgets

• Methodology standardization• Continued education



UNC Shape Analysis: Studies

• Harvard VA SPD study of caudates

• Dartmouth hippocampus data

• At BWH: 2nd SPD caudate study

lateral

R RL L

medialGroupdifference

Asymmetrydifference



Done

Documents

2006 AHM: Dissemination Update