2007 Programming/Project Week MIT

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Welcome to the web page for the 5th Project Week!

Photo taken by Jeffrey Hawley. More photos taken by Jeffrey Hawley.

Summary

The fifth NA-MIC Project event was concluded at MIT on June 29, 2007. This was the largest hands-on project event in the three year history of NA-MIC with 41 active projects and peak attendance of 90. Of the 85 registered attendees, 35 were NA-MIC participants, 48 external collaborators, and 2 representatives from the External Advisory Board and the NIH. The external collaborators were from 13 Institutions.

Statistics at a glance:

• 85 Registered Attendees: 35 NA-MIC participants, 48 collaborators, 2 EAB+NIH
  • 35 NA-MIC Participants breakdown by cores: Core 1 (7), Core 2 (14), Core 3 (10), Core 4-5-6-7 (4)
  • 46 Collaborators: Acoustic Med (2), BWH (19), Caltech (2), GE (1), Harvard IIC (1), JHU (1), Kitware (1), Knowledge Vis (1), Mario Negri (1), MGH (2), NWU (4), University of Iowa(12), Virginia Tech (1)
• 41 Projects: DBP-II(6), Structural Analysis (2), Diffusion Image Analysis (7), NA-MIC Kit (14), External Collaborations (12)

A summary of all past NA-MIC Project Events is available here.

Logistics

• Dates: June 25-29, 2007.
• Location: MIT. Grier Rooms A & B: 34-401A & 34-401B.

Registration Fee: $200 (this will cover the cost of breakfast, lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

Hotel: We have a group rate of $209/night at the Hotel at MIT. (Use group code NAM.) Here is some information about several other Boston area hotels that are convenient to NA-MIC events: Boston_Hotels. Summer is tourist season in Boston, so please book your rooms early.

(This is a checklist for the onsite planning items)

Introduction to NA-MIC Project Week

NA-MIC Project Week is a hands on activity -- programming using the NA-MIC Kit, algorithm design, and clinical application -- that has become one of the major events in the NA-MIC Kit calendar. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January). The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

• NA-MIC Members: 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 want to contribute to the NA-MIC Kit, and those who can help make it happen.
• This is not an introduction to the components of the NA-MIC Kit.
• NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
• NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the NA-MIC Kit capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.
• NA-MIC Core 3 (DBP) - bring your data to work on with the NA-MIC Kit and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
• External Collaborators - if you are working on a project that uses the NA-MIC kit, and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
• Everyone should bring a laptop. We will have four projectors.
• About half the time will be spent working on projects and the other half in project related discussions.
• You do need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

Agenda

• Monday June 25
  • noon-1pm lunch
  • 1pm: Welcome (Ron Kikinis)
  • 1:05-3:30pm Introduce Projects using templated wiki pages (all Project Leads) (Wiki Template)
  • 3:30-5:30pm Start project work
  • 4:30-5:30pm Special topic breakout: New DBP Introduction to NA-MIC Engineering
• Tuesday June 26
  • 8:30am breakfast
  • 9:00-9:45am: NA-MIC Software Process (Bill Hoffman, special guest speaker David Abrahams of Boost Consulting)
    • Bill's presentation, David's presentation
  • 10-10:30am Slicer 3.0 Update (Jim Miller, Steve Pieper)
  • 11am Special topic breakout: Grid Computing (Neil Jones, Marco Ruiz, Jeffrey Grethe, Stephen Aylward, Steve Pieper)
  • 11-12pm: Special topic breakout: IGT for Prostate
  • noon lunch
  • 1:30-2:30pm: Special topic breakout: KWWidgets
  • 2:30-3:30pm: Special topic breakout: Non-Linear Registration
  • 3:30-4:30pm: Special topic breakout: Atlases
  • 4:30-5:30pm: Special topic breakout: DWI/DTI
  • 5:30pm adjourn for day
• Wednesday June 27
  • 8:30am breakfast
  • 9:00-12pm Special topic breakout: ITK (Luis Ibanez)
  • noon lunch
  • 4-5pm: Special topic breakout: Plan for Long Lead Time Items
  • 5:30pm adjourn for day
• Thursday June 28
  • 8:30am breakfast
  • noon lunch
  • 5:30pm adjourn for day
• Friday June 29
  • 8:30am breakfast
  • 10am-noon: Project Progress using update Project Wiki pages
  • noon lunch boxes and adjourn. (Next one in Utah the week of Jan 7, 2008)

Preparation

1. Please make sure that you are on the NA-MIC Project Week mailing list.
2. May 3, 2007: Kickoff TCON#1 to discuss Engineer Core Projects and Assign/Verify Teams
3. May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams
4. May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week
5. May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
6. May 31, 2007: Create a directory for each project on the NAMIC Sandbox (Andy)
   1. Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
   2. Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
   3. Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
7. By 3pm ET on June 21, 2007: Complete a templated wiki page for your project. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
8. June 21, 2007: TCON#4 Final Call before showtime...
9. Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

A History in Wiki Links

A history of all the programming/project events in NA-MIC is available by following this link.

Projects

DBP II

These are projects by the new set of DBPS:

1. Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia (Harvard: Marek Kubicki, PI)
   • EPI Distortion correction using field maps (Marek Kubicki BWH)
   • Dorsolateral Prefrontal Cortex Segmentation in VCFS (Nicole Aucoin, John Melonakos, Tauseef Rehman, Brad Davis, Marek Kubicki).
2. Longitudinal MRI Study of Early Brain Development in Autism (UNC: Heather Hazlett, Joseph Piven, PI)
   • Cortical Thickness Measurement for UNC Autism Study (Clement Vachet UNC, Heather Hazlett UNC, Martin Styner UNC)
3. Analysis of Brain Lesions in Lupus (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
   • Lesion Classification in Lupus (Jeremy Bockholt, Mark Scully)
4. Segmentation and Registration Tools for Robotic Prostate Intervention (Queens/JHU: Gabor Fichtinger, PI):
   • Brachytherapy needle positioning robot integration (David Gobbi Queen's U, Csaba Csoma, JHU, Katie Hayes, BWH, Peter Kazanzides JHU)

Structural Analysis

1. EMSegmentation Validation (Brad Davis Kitware, Sylvain Bouix BWH)
2. Non-Rigid Groupwise Registration Tools for ITK (Serdar K Balci, Lilla Zollei, Polina Golland, Sandy Wells)

Diffusion Image Analysis

1. DTI population analysis (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH, Raul San Jose BWH)
2. Geodesic Tractography (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
3. Slicer3 Whole brain Seeding platform: data representation and pipeline execution (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
4. Slicer 3 Tractography Editor (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)
5. Distortion Correction in DWI (Ran Tao, Utah)
6. Fluid Mechanics Based Tractography (Nathan Hagemen UCLA)
7. Sliced Multiple Glyphed Visualization for Volume Data (Demian Wassermann, Raul San Jose, Rachid Deriche, CF Westin)

Calibration/Validation

This is a new category of projects jointly led by team members in Core 1, Core 3 and Core 5

1. Contrasting Tractography Measures (Marek Kubicki, Ross Whitaker, Guido Gerig, Randy Gollub)

NA-MIC Kit - Slicer 3

1. QDEC Integration into Slicer3(Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
2. Display Optimization (Raimundo Sierra, David Gobbi, Steve Pieper)
3. MRML Scenes for the Execution Model including Transforms (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
4. Lightbox (James, Jim, Wendy, Alex)
5. Support for Unstructured Grids (Curt, Nicole, Alex, Steve, Will, Vince)
6. Python Support in Slicer 3 (Dan, Luca, Steve)
7. CPack, CTest infrastructure Improvements (Katie, Steve, Bill Hoffman)
8. Drafting Human Interface and Slicer Style Guidelines (Wendy,Yumin)
9. Slicer Matlab Pipeline for Tensors (Katharina, Sylvain, Steve)
10. Dendritic Spine Morphometrics (Bryan Smith)
11. Review of Slicer3 CMake Files (Steve, Jim, Luca, Bill)
12. ROIs in Slicer3 (Wendy, Jim, Nicole, Steve, Ron)
13. Lego Mindstorms Dissemination for IGT (Danielle Pace)
14. Edge Detection in Slicer3 (Elliot Uvero MIT, Lauren O'Donnell BWH, Luis Ibanez Kitware)

External Collaborations

1. Meshing
   1. Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3 (Will, Vince, Kiran, Curt)
   2. Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK (Vince, Stephen)
2. Applying EMSegmenter to NonHuman Primate Neuroimaging(Chris Wyatt VT, Kilian Pohl BWH)
3. Collaboration/MGH/Radiation Therapy Radiation Therapy Planning (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
4. Registration
   1. Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
   2. Developing Electronic Atlas Software using NA-MIC Kit (Gary Christensen UIowa, Jeff Grethe, Wendy)
   3. Developing a GUI for non-rigid image registration programs using NA-MIC Kit (Gary Christensen UIowa, Yumin Kitware)
5. vmtk (vmtk.sourceforge.net) integration within Slicer3 (Luca Antiga, MNI, Dan Blezek GE)
6. A Translation Station(Skip, Alex, Vlad, Pat, Alex, Steve)
7. 3D+t Cells Lineage:GoFigure (Alex G, Yumin)
8. MIND Clinical Imaging Study: conversion of mgh 60 direction sequence to nrrd (Jeremy Bockholt, Sumner Williams)

Non-Medical Collaborations

1. Collaboration/Harvard IIC/AstroMed (Michael Halle, Douglas Alan)

Attendee List

Core1

1. John Melonakos, Georgia Tech, Core 1
2. Tauseef Rehman, Georgia Tech, Core 1
3. Casey Goodlett, UNC, Core 1
4. Serdar K Balci, MIT, Core 1
5. Elliot Uvero, MIT, Core 1
6. Ran Tao, Utah, Core 1
7. Kevin Teich, MGH, Core 1

Core2

1. W. Bryan Smith, UCSD/NCMIR, Core 2
2. Jeffrey Grethe, UCSD, Core 2
3. Marco Ruiz, UCSD, Core 2
4. Neil Jones, UCSD, Core 2
5. Jim Miller, GE Core 2
6. Dan Blezek, GE Core 2
7. Steve Pieper, Isomics, Core 2
8. Alex Yarmarkovich, Isomics, Core 2
9. Will Schroeder, Kitware, Core 2
10. Yumin Yuan, Kitware, Core 2
11. Brad Davis, Kitware, Core 2
12. Luis Ibanez, Kitware, Core 2
13. Bill Hoffman, Kitware, Core 2 (Mon, Tue)
14. Nathan Hageman, UCLA, Core 2 (Tue, Wed)

Core3-I&II

1. Sylvain Bouix, BWH, Core 3
2. Katharina Quintus, BWH, Core 3
3. Marc Niethammer, BWH. Core 3
4. Marek Kubicki, BWH, Core 3 (II) (One-day)
5. Clement Vachet, UNC Core 3 (II)
6. David Gobbi, Queen's University, Core 3 (II)
7. Csaba Csoma, Johns Hopkins University, Core 3 (II)
8. H. Jeremy Bockholt, The MIND Institute, Core 3 (II)
9. Mark Scully, The MIND Institute, Core 3 (II)
10. Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01

Core 4,5,6,7

1. Zack Galbreath, Kitware, Core 4 (Mon, Tue)
2. Randy Gollub, MGH, COre 5
3. Tina Kapur, BWH, Core 6
4. Ron Kikinis, Core 7, PI

Collaborators

1. Chris Wyatt, Virginia Tech, Collaborator R01
2. Vincent Magnotta, University of Iowa, Collaborator R01
3. Kiran Shivanna, University of Iowa, Collaborator R01
4. Hans Johnson, University of Iowa, Collaborator
5. Gary E. Christensen, University of Iowa, Collaborator
6. Joo Hyun (Paul) Song, University of Iowa, Gary's student
7. Xiujuan Geng, University of Iowa, Gary's student
8. Jake Nickel, University of Iowa, Gary's student
9. Nick Kiguta, University of Iowa, Gary's student
10. Kunlin Cao, University of Iowa, Gary's student
11. James Harris, University of Iowa, Gary's student
12. Kai Ding, University of Iowa, Gary's student
13. Jeffrey Hawley, University of Iowa, Gary's student
14. Luca Antiga, Mario Negri Institute, Collaborator
15. Stephen Aylward, Kitware, Collaborator
16. Peter Kazanzides, JHU, Collaborator (One-day)
17. Skip Talbot, Northwestern University, Collaborator
18. Alex Kogan, Northwestern University, Collaborator
19. Vladimir Kleper, Northwestern University, Collaborator
20. Pat Mongkolwat, Northwestern University, Collaborator
21. Greg Sharp, MGH, Collaborator
22. Lilla Zollei, MGH, Collaborator (One-day)
23. James Ross, GE, Collaborator
24. Alex Gouaillard, CEGS Caltech, Collaborator
25. Sean Megason, CEGS caltech, Collaborator
26. Clif Burdette, Acousticmed, Collaborator
27. Jack Blevins, Acousticmed, Collaborator
28. Curtis Lisle, KnowledgeVis, Collaborator
29. Douglas Alan, Harvard IIC, Collaborator
30. Michael Halle, BWH/IIC, Collaborator
31. Katie Hayes, BWH, Core 2
32. Nicole Aucoin, BWH, Core 2
33. Wendy Plesniak, BWH, Collaborator
34. Kilian Pohl, BWH Collaborator
35. Raimundo Sierra, BWH, Collaborator
36. Lauren O'Donnell, BWH, Collaborator
37. Raul San Jose, BWH, Collaborator
38. C-F Westin, BWH, Collaborator
39. Demian Wassermann, BWH/INRIA , Collaborator
40. Danielle Pace, BWH , Summer Intern
41. Sandy Wells, BWH, Collaborator
42. Haiying Liu, BWH Collaborator
43. Clare Tempany, BWH Collaborator (One-day)
44. Noby Hata, BWH Collaborator (One-day)
45. Hong Xiang, BWH Collaborator (One-day)
46. Kim Lawson, BWH Collaborator (One-day)
47. Junichi Tokuda, BWH Collaborator (One-day)
48. Robert Cormack, BWH Collaborator (One-day)

NIH, EAB

1. Zohara Cohen, NIH (One-day)
2. Bill Lorensen, EAB (One-day)

We have reached capacity of this workshop. Any changes made to this list at this point do not translate into space at this meeting. Apologies. If you are interested, check back here for dates of the next NA-MIC event and sign up in advance.

Pictures

PICTURES! taken by Jeffrey Hawley