Difference between revisions of "2006 Programming/Project Week MIT"

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 +
== Summary ==
 +
 +
This event was successfully concluded on June 30, 2006. The results of this week are summarized [[Engineering:2006_Project_Week_Results|here]].
 +
 +
Some statistics:
 +
 +
* 56 total attendees: 38 NA-MIC participants, 18 collaborators
 +
** 38 NA-MIC Participants breakdown by cores: Core 1 (11), Core 2 (13), Core 3 (9), Core 4 (2), Core 5 (2), Core 6 (1)
 +
** 18 Collaborators: Northwestern (3), Iowa (1), JHU (1), Harvard IIC (1), Canary Islands (2), MIT(3), BWH (7)
 +
* 22 Projects: Structural Analysis (4), Diffusion Image Analysis (4), fMRI analysis (2), NA-MIC Kit (10), Astronomy Data(1)
 +
 
== Logistics ==
 
== Logistics ==
  
−
* Dates: June 26-30, 2006
+
'''Dates:''' June 26-30, 2006
−
* Location: MIT Stata Center
 
−
* Hotel: We are not booking a block of rooms at any hotel. Here is some information about Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
 
  
−
== Agenda Draft ==
+
'''Location:''' MIT.
  
−
* Monday: start at noon
+
Please note that Monday lunch will be in the Allen Room, 36-462 (due to water damage in previously planned location). Entrance is still at 50 Vassar St., turn left inside the lobby (building 34), proceed to the elevators in building 36. Go to the 4th floor and exit to the RIGHT. Follow around the corner and the conference room is just a few steps down the hall.
−
* Tue: 9-5
+
 
−
* Wed: 9-5
+
Rest of the activities are in [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
−
* Thurs: 9-5
+
 
−
* Fri: 9-noon
+
'''Registration Fee:''' $75 (to subsidize the cost of breakfast and lunch for the week). Due by Tuesday, June 20, 2006. Please make checks out to "Massachusetts Institute of Technology" and mail to: <br />Donna Kaufman <br />MIT <br />77 Massachusetts Ave., 38-409b <br />Cambridge, MA 02139
 +
 
 +
If you are attending for one day only, the registration fee is not required.
 +
 
 +
'''Hotel:''' There is no official hotel for the meeting. Here is some information about Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
 +
 
 +
== Agenda ==
  
 
<br />
 
<br />
 +
 +
* Monday
 +
** noon-1pm lunch (Allen Room, 36-462)
 +
** 1-3:30pm Introduce Projects using 4-block slides (all Project Leads)
 +
** 3:30-5:30pm Start project work
 +
* Tuesday
 +
** 8:30am breakfast
 +
** 9-10:30am Slicer 3.0 [[Slicer3:Execution_Model_Documentation|Execution Model]] (Jim Miller, Steve Pieper)
 +
** noon lunch
 +
** 1-2pm: Special topic: [[IGT_Software_Architecture_at_JHU|IGT Software Architecture at JHU]] (Peter Kazanzides)
 +
** 2-3pm: Special topic: [[Slicer3:FeatureRequests|Slicer UI Feature Request & Usability discussion ]] (Wendy Plesniak)
 +
** 5:30pm adjourn for day
 +
* Wednesday
 +
** 8:30am breakfast
 +
** 9-10am [[Insight_Journal_Submission_Q%26A|Insight Journal Submission Q&A]] (Luis Ibanez)
 +
** noon lunch
 +
** 1-2pm: Special topic: [[Calibrating_Slicer%27s_EM_Segmenter|Calibrating Slicer's EM Segmenter]] (Kilian Pohl)
 +
** 5:30pm adjourn for day
 +
** 7:00pm [[2006_Programming/Wednesday_Evening_Dinner_and_Music|Dinner and Music]]
 +
* Thursday
 +
** 8:30am breakfast
 +
** noon lunch
 +
** 3:30-5pm [[Genetics_101|Genetics 101]] (Jim Kennedy, Aristotle Voineskos - UToronto/CAMH)
 +
** 5:30pm adjourn for day
 +
* Friday
 +
** 8:30am breakfast
 +
** 10am-noon: Project Progress using 4-block slides
 +
** noon lunch boxes and adjourn
  
 
== Background and Preparation ==
 
== Background and Preparation ==
  
−
A difference between previous such weeks and this one is that we have decided to call it "Project Week" to reflect what actually goes on in these sessions - along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and we'd like the name to reflect that. What does this mean to you: if you are participating in a NA-MIC project by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.
+
A difference between previous such weeks and this one is that we have decided to call it "Project Week" rather than "Programming Week" to better reflect the activity during the event - along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.
  
 
=== Goals ===
 
=== Goals ===
Line 42: Line 85:
 
# [[Engineering:TCON_04_06_2006|April 6: Kickoff TCON]]
 
# [[Engineering:TCON_04_06_2006|April 6: Kickoff TCON]]
 
# April 19: Create a Wiki page per project (the participants must do this, hopefully jointly)
 
# April 19: Create a Wiki page per project (the participants must do this, hopefully jointly)
−
# May: TCON#2 to discuss projects and assign teams
+
# May 25: TCON#2 to discuss projects and assign teams
−
# May ?: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
+
# May 30: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
 
# June:
 
# June:
 
## 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)
 
## 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)
Line 59: Line 102:
 
== Projects ==
 
== Projects ==
  
−
'''Instructions''' Please use the following protocol to add your project(s) to this list, under the appropriate category:
+
All the project pages are available [[Engineering:2006_Project_Week_Results|here]].
−
 
 
−
Project Title (Team Names) [[2006_Project_Week_MIT_ProjectName]], [[Media:2006_Project_Week_MIT_ProjectName.ppt|1-slide summary]]
 
−
 
 
−
i.e.
 
−
 
 
−
* create a line for each project with the above text
 
−
* create a page for your project named 2006_Project_Week_MIT_<Project Name> and link it to the text "project page"
 
−
* download [[Image:2006_Summer_Project_Week_Template.ppt|Image:2006 Summer Project Week Template.ppt]], summarize the project in it, and upload it to the wiki under the filename 2006_Project_Week_MIT_<ProjectName>.ppt
 
−
 
 
−
'''List of Projects'''
 
−
 
 
−
=== Structural Analysis ===
 
−
 
 
−
# ITK Spherical Wavelet Transform Filter (Xavier Le Faucheur, GT, Delphine Nain, GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez, Kitware): [[NA-MIC/Projects/Structural/Shape_Analysis/3D_Shape_Analysis_Using_Spherical_Wavelets|3D Shape Analysis Using Spherical Wavelets]], <4-block ppt>
 
−
 
 
−
=== Diffusion Image Analysis ===
 
−
 
 
−
# ITK DTI Image Processing Modules (Casey Goodlett UNC), [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software and Algorithm Infrastructure]], <4-block ppt>
 
−
 
 
−
=== FMRI Image Analysis ===
 
−
 
 
−
# ITK Conformal Flattening Filter (Yi Gao GT, Delphine Nain GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez Kitware): [[NA-MIC/Projects/fMRI_Analysis/Conformal_Flattening_for_fMRI_Visualization|Conformal Flattening for fMRI Visualization]]. <4-block ppt>
 
−
 
 
−
=== NA-MIC Kit ===
 
−
 
 
−
# NA-MIC cluster package (Jeff Grethe), <Project Page>, <4-block ppt>
 
−
# MRML Lib (Alex Yarmarkovich, Mathieu Malaterre, Xiaodong Tao), <Project Page>, <4-block ppt>
 
−
# Slicer3 Interface (Wendy Plesniak, Sebastient Barre), <Project Page>, <4-block ppt>
 
−
# Slicer3 Execution Model (Dan Blezek, Mike Halle, Jim Miller), <Project Page>, <4-block ppt>
 
−
# Migrating Slicer2.x Modules to Slicer3 (Nicole Aucoin, Mathieu Malaterre, Katie Hayes), <Project Page>, <4-block ppt>
 
−
# Slicer3 Build/Test/Pack (Andy Cedilnik, Katie Hayes), <Project Page>, <4-block ppt>
 
−
# Slicer3 Grid Integration (Jeff Grethe, Brendan Faherty), [[2006_Project_Week_MIT_Grid_Integration|2006_Project_Week_MIT_Grid_Integration]], <4-block ppt>
 
−
# Slicer3 Pipeline Integration (Jagadeeswaran Rajendiran), <Project Page>, <4-block ppt>
 
  
 
== Attendees ==
 
== Attendees ==
Line 101: Line 111:
 
# Ipek Oguz, UNC Core 1
 
# Ipek Oguz, UNC Core 1
 
# Casey Goodlett, UNC Core 1
 
# Casey Goodlett, UNC Core 1
−
# Kilian Pohl, BWH Core 1
+
# Tom Fletcher, Utah Core 1
 +
# Ross Whitaker, Utah Core 1 (Wed-Fri - off and on)
 +
# Gheorghe Postelnicu, MGH Core 1
 +
# Polina Golland, MIT Core 1 (Wed-Thur)
 +
# Lauren O'Donnell, MIT Core 1 (Thur-Fri)
 +
# Wanmei Ou, MIT Core 1
 
# Xavier Le Faucheur, GT Core 1
 
# Xavier Le Faucheur, GT Core 1
−
# Delphine Nain, GT Core 1 (for some of the week)
 
 
# Yi Gao, GT Core 1
 
# Yi Gao, GT Core 1
 
# John Melonakos, GT/GE Core 1,2
 
# John Melonakos, GT/GE Core 1,2
 
# Bill Lorensen, GE Core 2
 
# Bill Lorensen, GE Core 2
 
# Jim Miller, GE Core 2
 
# Jim Miller, GE Core 2
−
# Dan Blezek, GE Core 2
 
−
# Xiaodong Tao, GE Core 2
 
 
# Luis Ibanez, Kitware Core 2
 
# Luis Ibanez, Kitware Core 2
 
# Will Schroeder, Kitware Core 2,4
 
# Will Schroeder, Kitware Core 2,4
 
# Mathieu Malaterre, Kitware Core 2
 
# Mathieu Malaterre, Kitware Core 2
−
# Andy Cedilnik, Kitware Core 4
+
# Andy Cedilnik, Kitware Core 4 (Tue, Wed, Thu, Fri)
 
# Sebastien Barre, Kitware Core 2
 
# Sebastien Barre, Kitware Core 2
 
# Steve Pieper, Isomics Core 2,6
 
# Steve Pieper, Isomics Core 2,6
 +
# Alex Yarmarkovich, Isomics Core 2 (Tue, Wed, Thu)
 
# Katie Hayes, BWH Core 2
 
# Katie Hayes, BWH Core 2
 
# Nicole Aucoin, BWH Core 2
 
# Nicole Aucoin, BWH Core 2
 
# Wendy Plesniak, BWH Core 2
 
# Wendy Plesniak, BWH Core 2
 +
# Brendan Faherty, UCSD Core 2
 +
# Jagadeeswaran Rajendiran, UCLA - Core 2
 +
# Katharina Quintus, PNL Core 3.1 (Tue)
 +
# Doug Markant, PNL Core 3.1 (Tue)
 +
# Lillian Hsu, PNL Core 3.1 (Tue)
 +
# Marc Niethammer, PNL Core 3.1 (Mon, Thurs)
 +
# Sylvain Bouix, PNL core 3.1 (Mon, Tue, Thurs)
 +
# Marek Kubicki, PNL core 3.1
 +
# John West, Dartmouth Medical School, Core 3.1 (Wed)
 +
# Aristotle Voineskos, University of Toronto, Core 3.2 (Thursday)
 +
# James Kennedy, University of Toronto, Core 3.2 (Thursday)
 
# Randy Gollub, MGH Core 5- as needed to develop supporting materials and/or teach neuro and/or help with fMRI
 
# Randy Gollub, MGH Core 5- as needed to develop supporting materials and/or teach neuro and/or help with fMRI
 
# Sonia Pujol, BWH Core 5- as needed to develop supporting materials
 
# Sonia Pujol, BWH Core 5- as needed to develop supporting materials
 
# Tina Kapur, Epiphany Medical, Core 6
 
# Tina Kapur, Epiphany Medical, Core 6
−
# Haiying Liu, BWH IGT Collaborator
 
−
# Brendan Faherty, UCSD Core 2
 
 
# Pat Mongkolwat, Northwestern Collaborator
 
# Pat Mongkolwat, Northwestern Collaborator
−
# Vincent Magnotta, Iowa Collaboration
+
# Thomas Lechner, Northwestern Collaborator
 +
# Alex Kogan, Northwestern Collaborator
 
# Kiran Shivanna, Iowa Collaboration
 
# Kiran Shivanna, Iowa Collaboration
−
# Tom Fletcher + student, Utah Core 1
+
# Peter Kazanzides, Johns Hopkins University Collaborator (Tuesday)
 +
# Haiying Liu, BWH IGT Collaborator
 +
# C-F Westin, LMI, NAC, BWH, Collaborator
 +
# AW de Vries, LMI, BWH, Collaborator
 +
# Raul San Jose, BWH, Collaborator
 +
# Gordon Kindlmann, BWH, Collaborator (Wed+Thu)
 +
# Michael Halle, BWH, Harvard Initiative in Innovative Computing
 +
# Kilian Pohl, BWH Collaborator (Mon, Tue, Wed)
 +
# Douglas Alan, Harvard IIC, Collaborator
 +
# Rafael Nebot, Canary Islands Technological Institute Collaborator (Tue-Thu)
 +
# Eduardo Suárez, Canary Islands Technological Institute Collaborator (Tue-Thu)
 +
# Lilla Zollei, MIT Collaborator
 +
# Clare Poynton, MIT, BWH Collaborator
 +
# Ulas Ziyan, MIT Collaborator

Revision as of 19:22, 18 December 2006

Home < 2006 Programming < Project Week MIT

Summary

This event was successfully concluded on June 30, 2006. The results of this week are summarized here.

Some statistics:

  • 56 total attendees: 38 NA-MIC participants, 18 collaborators
    • 38 NA-MIC Participants breakdown by cores: Core 1 (11), Core 2 (13), Core 3 (9), Core 4 (2), Core 5 (2), Core 6 (1)
    • 18 Collaborators: Northwestern (3), Iowa (1), JHU (1), Harvard IIC (1), Canary Islands (2), MIT(3), BWH (7)
  • 22 Projects: Structural Analysis (4), Diffusion Image Analysis (4), fMRI analysis (2), NA-MIC Kit (10), Astronomy Data(1)

Logistics

Dates: June 26-30, 2006

Location: MIT.

Please note that Monday lunch will be in the Allen Room, 36-462 (due to water damage in previously planned location). Entrance is still at 50 Vassar St., turn left inside the lobby (building 34), proceed to the elevators in building 36. Go to the 4th floor and exit to the RIGHT. Follow around the corner and the conference room is just a few steps down the hall.

Rest of the activities are in Grier Rooms A & B: 34-401A & 34-401B.

Registration Fee: $75 (to subsidize the cost of breakfast and lunch for the week). Due by Tuesday, June 20, 2006. 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: There is no official hotel for the meeting. Here is some information about Boston area hotels that are convenient to NA-MIC events: Boston_Hotels. Summer is tourist season in Boston, so please book your rooms early.

Agenda


Background and Preparation

A difference between previous such weeks and this one is that we have decided to call it "Project Week" rather than "Programming Week" to better reflect the activity during the event - along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

Goals

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

  • Members of all cores are welcome. In contrast to previous years, this event will involve programming, algorithm design, and clinical application development/testing.
  • You do need to be actively working on a NA-MIC related 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 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.
  • Submit any projects that you would like to work on during this week, and what type of help you might need for it.

How will this week work?

Please note that:

  • Everyone should bring a laptop. We will have three or four projectors.
  • It looks like about half the time will be spent working on projects and the other half in project related discussions.

Preparation for the workshop

  1. Please make sure that you are on the na-mic-programming-week mailing list
  2. April 6: Kickoff TCON
  3. April 19: Create a Wiki page per project (the participants must do this, hopefully jointly)
  4. May 25: TCON#2 to discuss projects and assign teams
  5. May 30: Create a directory for each project on the NAMIC Sandbox (Andy)
  6. June:
    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 June 22nd:Complete the top half of this powerpoint template for each project. Upload and link to the right place.
  8. June 22: TCON#3 last preparation tcon
  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

Projects

All the project pages are available here.

Attendees

If you are interested in attending this week, please note your name here:

  1. Martin Styner, UNC Core 1
  2. Ipek Oguz, UNC Core 1
  3. Casey Goodlett, UNC Core 1
  4. Tom Fletcher, Utah Core 1
  5. Ross Whitaker, Utah Core 1 (Wed-Fri - off and on)
  6. Gheorghe Postelnicu, MGH Core 1
  7. Polina Golland, MIT Core 1 (Wed-Thur)
  8. Lauren O'Donnell, MIT Core 1 (Thur-Fri)
  9. Wanmei Ou, MIT Core 1
  10. Xavier Le Faucheur, GT Core 1
  11. Yi Gao, GT Core 1
  12. John Melonakos, GT/GE Core 1,2
  13. Bill Lorensen, GE Core 2
  14. Jim Miller, GE Core 2
  15. Luis Ibanez, Kitware Core 2
  16. Will Schroeder, Kitware Core 2,4
  17. Mathieu Malaterre, Kitware Core 2
  18. Andy Cedilnik, Kitware Core 4 (Tue, Wed, Thu, Fri)
  19. Sebastien Barre, Kitware Core 2
  20. Steve Pieper, Isomics Core 2,6
  21. Alex Yarmarkovich, Isomics Core 2 (Tue, Wed, Thu)
  22. Katie Hayes, BWH Core 2
  23. Nicole Aucoin, BWH Core 2
  24. Wendy Plesniak, BWH Core 2
  25. Brendan Faherty, UCSD Core 2
  26. Jagadeeswaran Rajendiran, UCLA - Core 2
  27. Katharina Quintus, PNL Core 3.1 (Tue)
  28. Doug Markant, PNL Core 3.1 (Tue)
  29. Lillian Hsu, PNL Core 3.1 (Tue)
  30. Marc Niethammer, PNL Core 3.1 (Mon, Thurs)
  31. Sylvain Bouix, PNL core 3.1 (Mon, Tue, Thurs)
  32. Marek Kubicki, PNL core 3.1
  33. John West, Dartmouth Medical School, Core 3.1 (Wed)
  34. Aristotle Voineskos, University of Toronto, Core 3.2 (Thursday)
  35. James Kennedy, University of Toronto, Core 3.2 (Thursday)
  36. Randy Gollub, MGH Core 5- as needed to develop supporting materials and/or teach neuro and/or help with fMRI
  37. Sonia Pujol, BWH Core 5- as needed to develop supporting materials
  38. Tina Kapur, Epiphany Medical, Core 6
  39. Pat Mongkolwat, Northwestern Collaborator
  40. Thomas Lechner, Northwestern Collaborator
  41. Alex Kogan, Northwestern Collaborator
  42. Kiran Shivanna, Iowa Collaboration
  43. Peter Kazanzides, Johns Hopkins University Collaborator (Tuesday)
  44. Haiying Liu, BWH IGT Collaborator
  45. C-F Westin, LMI, NAC, BWH, Collaborator
  46. AW de Vries, LMI, BWH, Collaborator
  47. Raul San Jose, BWH, Collaborator
  48. Gordon Kindlmann, BWH, Collaborator (Wed+Thu)
  49. Michael Halle, BWH, Harvard Initiative in Innovative Computing
  50. Kilian Pohl, BWH Collaborator (Mon, Tue, Wed)
  51. Douglas Alan, Harvard IIC, Collaborator
  52. Rafael Nebot, Canary Islands Technological Institute Collaborator (Tue-Thu)
  53. Eduardo Suárez, Canary Islands Technological Institute Collaborator (Tue-Thu)
  54. Lilla Zollei, MIT Collaborator
  55. Clare Poynton, MIT, BWH Collaborator
  56. Ulas Ziyan, MIT Collaborator
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