2007 Programming/Project Week MIT

Back to Programming/Project Events

Summer 2007

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 capabiliities, integrate Core 1 algorithms, and refine worflows 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-programming-week mailing list
2. May 3, 2007: Kickoff TCON#1 to discuss Engr 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...

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)
   1. Contrasting Tractography Measures (Marek Kubicki, Doug Markant, Doug Terry, Lauren O'Donnell, Katharina Quintus, Jorge Alvarado Harvard)
   2. EPI Distortion correction using field maps (Marek Kubicki BWH)
   3. Dorsolateral Prefrontal Cortex Segmentation in VCFS (John Melonakos, Tauseef Rehman, Brad Davis, Marek Kubicki).
2. Longitudinal MRI Study of Early Brain Development in Autism (UNC: Heather Hazlett, Joseph Piven, PI)
   1. 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)
   1. Lesion Classification in Lupus (Jeremy Bockholt, Mark Scully)
4. Segmentation and Registration Tools for Robotic Prostate Intervention (Queens/JHU: Gabor Fichtinger, PI):
   1. 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, Polina Golland)

Diffusion Image Analysis

1. DTI population analysis (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki 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)

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. Support for Unstructured Grids (Steve, Nicole, Alex, Curt, Will)
5. Python Support in Slicer 3 (Dan, Luca, Steve)
6. CPack, CTest infrastructure Improvements (Bill Hoffman, Katie, Steve)
7. Drafting Human Interface and Slicer Style Guidelines (Wendy,Yumin)
8. Slicer Matlab Pipeline for Tensors (Katharina, Sylvain, Steve)
9. Dendritic Spine Morphometrics (Bryan Smith)
10. Review of Slicer3 CMake Files (Steve, Jim, Luca, Bill)
11. ROIs in Slicer3 (Wendy, Jim, Nicole, Steve, Ron)

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
   1. 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

Full Week

1. John Melonakos, Georgia Tech, Core 1 (Registration Fee: Received by DK at MIT)
2. Tauseef Rehman, Georgia Tech, Core 1 (Registration Fee: Received by DK at MIT)
3. Casey Goodlett, UNC, Core 1 (Registration Fee: Received by DK at MIT)
4. Serdar K Balci, MIT, Core 1 (Registration Fee: )
5. Elliot Uvero, MIT, Core 1 (Registration Fee: )
6. Ran Tao, Utah, Core 1 (Registration Fee: )
7. Kevin Teich, MGH, Core 1 (Registration Fee: )
8. W. Bryan Smith, UCSD/NCMIR, Core 2 (Registration Fee: )
9. Jeffrey Grethe, UCSD, Core 2 (Registration Fee: )
10. Marco Ruiz, UCSD, Core 2 (Registration Fee: )
11. Neil Jones, UCSD, Core 2 (Registration Fee: Received by DK at MIT)
12. Jim Miller, GE Core 2 (Registration Fee: )
13. Dan Blezek, GE Core 2 (Registration Fee: Received by DK at MIT)
14. Steve Pieper, Isomics, Core 2 (Registration Fee: )
15. Alex Yarmarkovich, Isomics, Core 2 (Registration Fee: Received by DK at MIT)
16. Katie Hayes, BWH, Core 2 (Registration Fee: BWH Check Attendee 1) - confirmed by Ron
17. Nicole Aucoin, BWH, Core 2 (Registration Fee: BWH Check Attendee 2) - confirmed by Ron
18. Will Schroeder, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 1)
19. Yumin Yuan, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 2)
20. Brad Davis, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 3)
21. Luis Ibanez, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 4)
22. Bill Hoffman, Kitware, Core 2 (Mon, Tue) (Registration Fee: Kitware Check Attendee 5)
23. Sylvain Bouix, BWH, Core 3 (Registration Fee: ) - to be paid by personal check and reimbursed by MS
24. Katharina Quintus, BWH, Core 3 (Registration Fee: )- to be paid by personal check and reimbursed by MS
25. Marc Niethammer, BWH. Core 3 (Registration Fee: )- to be paid by personal check and reimbursed by MS
26. Clement Vachet, UNC Core 3 (II) (Registration Fee: )
27. David Gobbi, Queen's University, Core 3 (II) (Registration Fee: Received by DK at MIT)
28. Csaba Csoma, Johns Hopkins University, Core 3 (II) (Registration Fee: Received by DK at MIT)
29. H. Jeremy Bockholt, The MIND Institute, Core 3 (II) (Registration Fee: )
30. Mark Scully, The MIND Institute, Core 3 (II) (Registration Fee: )
31. Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01 (Registration Fee: )
32. Zack Galbreath, Kitware, Core 4 (Mon, Tue) (Registration Fee: )
33. Tina Kapur, BWH, Core 6 (Registration Fee: BWH Check Attendee 3)- confirmed by Ron
34. Ron Kikinis, Core 7, PI (Registration Fee: BWH Check Attendee 4)- confirmed by Ron
35. Chris Wyatt, Virginia Tech, Collaborator R01 (Registration Fee: Received by DK at MIT)
36. Vincent Magnotta, University of Iowa, Collaborator R01 (Registration Fee: )
37. Kiran Shivanna, University of Iowa, Collaborator R01 (Registration Fee: )
38. Luca Antiga, Mario Negri Institute, Collaborator (Registration Fee: )
39. Stephen Aylward, Kitware, Collaborator (Registration Fee: Kitware CHeck Attendee 6)
40. Douglas Alan, Harvard IIC, Collaborator (Registration Fee: )
41. Michael Halle, BWH/IIC, Collaborator (Registration Fee: BWH Check Attendee 5 ) - confirmed by Ron
42. Wendy Plesniak, BWH, Collaborator (Registration Fee: BWH Check Attendee 6)- confirmed by Ron
43. Kilian Pohl, BWH Collaborator (Registration Fee: BWH Check Attendee 7)- confirmed by Ron
44. Raimundo Sierra, BWH, Collaborator (Registration Fee: BWH Check Attendee 8)- confirmed by Ron
45. Lauren O'Donnell, BWH, Collaborator (Registration Fee: BWH Check Attendee 9)- confirmed by Ron
46. Raul San Jose, BWH, Collaborator (Registration Fee: BWH Check Attendee 10)- confirmed by Ron
47. Haiying Liu, BWH Collaborator (Registration Fee: BWH Check Attendee 11)- confirmed by Ron
48. Hans Johnson, University of Iowa, Collaborator (Registration Fee: Received by DK at MIT)
49. Gary E. Christensen, University of Iowa, Collaborator (Registration Fee: Received by DK at MIT)
50. Joo Hyun (Paul) Song, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
51. Xiujuan Geng, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
52. Jake Nickel, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
53. Nick Kiguta, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
54. Kunlin Cao, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
55. James Harris, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
56. Kai Ding, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
57. Jeff Hawley, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
58. Skip Talbot, Northwestern University, Collaborator (Registration Fee: )
59. Alex Kogan, Northwestern University, Collaborator (Registration Fee: )
60. Vladimir Kleper, Northwestern University, Collaborator (Registration Fee: )
61. Pat Mongkolwat, Northwestern University, Collaborator (Registration Fee: )
62. Greg Sharp, MGH, Collaborator (Registration Fee: )
63. James Ross, GE, Collaborator (Registration Fee: )
64. Alex Gouaillard, CEGS Caltech, Collaborator (Registration Fee: )
65. Sean Megason, CEGS caltech, Collaborator (Registration Fee: )
66. Clif Burdette, Acousticmed, Collaborator (Registration Fee: )
67. Jack Blevins, Acousticmed, Collaborator (Registration Fee: )
68. Curtis Lisle, KnowledgeVis, Collaborator (Registration Fee: )
69. C-F Westin, BWH, Collaborator (Registration Fee: BWH Check Attendee 12)- confirmed by Ron
70. Demian Wassermann, BWH/INRIA , Collaborator (Registration Fee: BWH Check Attendee 13)
71. Danielle Pace, BWH , Summer Intern (Registration Fee: BWH Check Attendee 14)
72. Sandy Wells, BWH, Collaborator (Registration Fee: BWH Check Attendee 15)

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.

One Day

1. Marek Kubicki, BWH, Core 3 (Monday) (Registration Fee: 0)
2. Clare Tempany, BWH Collaborator (Tuesday) (Registration Fee: 0)
3. Noby Hata, BWH Collaborator (Monday) (Registration Fee: 0)
4. Peter Kazanzides, JHU, Collaborator (Wednesday) (Registration Fee: 0)
5. Lilla Zollei, MGH, Collaborator (Tuesday) (Registration Fee: 0)
6. Hong Xiang, BWH Collaborator (Tuesday) (Registration Fee: 0)
7. Kim Lawson, BWH Collaborator (Tuesday) (Registration Fee: 0)
8. Junichi Tokuda, BWH Collaborator (Tuesday) (Registration Fee: 0)

PICTURES! taken by Jeffrey Hawley