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Back to [[Engineering:Programming_Events|Programming/Project Events]]
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__NOTOC__
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Back to [[Events]]
  
[[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]
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[[image:ProjectWeek-2008.png|300px]]
  
== Logistics ==
+
=Welcome to the web page for the 7th Project Week!=
 
+
==Summary==
'''Dates:''' June 23-27, 2008
+
The seventh NA-MIC Project event was held on June 23-27, 2008 at MIT. There were 114 registered participants for this meeting who worked on 58 projects.  14 of these projects were directly related to the NA-MIC DBPs, 19 to External Collaborations, and 15 to NA-MIC Infrastructure.  
 
 
'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
 
  
 +
A [[Project_Events#Past_Project_Weeks|summary]] of all past Project Events.
  
'''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139
+
<gallery perrow="3" widths="200px">
 +
Image:2008MITDay1-349.jpg|Welcome
 +
Image:2008MITProjectWeekOpening-353.jpg|Opening Session
 +
Image:2008MITDay3-030.jpg|Lively Discussions
 +
Image:2008MITDay3-038.jpg|Hard at Work
 +
Image:2008MITDay3-089.jpg|Breakout Session
 +
Image:2008MITDay3-080.jpg|Modern Architecture
 +
Image:2008MITDay3-106.jpg|IGT Breakout
 +
Image:2008MITDay4-016.jpg|Lunchtime
 +
Image:Nuts2008.jpg|Say no more...
 +
</gallery>
  
If you are attending for one day only, the registration fee is not required.
+
[http://woofton.rivendel.net/gallery2/main.php?g2_itemId=33261 More pictures] (taken by Jeffrey Hawley).
  
'''Hotel:''' We have a group rate of TBD/night at the [http://www.hotelatmit.com 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|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
 
 
([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])
 
  
 
==Introduction to NA-MIC Project Week==
 
==Introduction to NA-MIC Project Week==
 +
Please read an introduction about these events [[Project_Events#Introduction|here]].
  
NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. 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). 
+
== Agenda==
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|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 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|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|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|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  
 
* Monday  
 
** noon-1pm lunch  
 
** noon-1pm lunch  
**1pm: Welcome (Ron Kikinis)
+
**1pm: [[2008-Project-Week-Welcome|Welcome]] (Ron Kikinis)
 
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])  
 
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])  
 
** 3:30-5:30pm Start project work
 
** 3:30-5:30pm Start project work
 
* Tuesday  
 
* Tuesday  
 
** 8:30am breakfast
 
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process
+
** 10-10:30am [https://www.slicer.org/wiki/Announcements:Slicer3.2 Slicer 3.2 Update] (Jim Miller, Steve Pieper)
** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
+
** 11-12noon [[Project Week 2008 Slicer Tuning| Performance tuning for Slicer 3.2]] (Jackson Room 38-466) (Ron Kikinis)
 
** noon lunch
 
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]]  
+
** 1pm: [[2008-Project-Week-SVN-Change|Cut over to a new version of the NA-MIC SVN]].
 +
** 1:00-4:00pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Stata 32-D451) (Daniel Marcus)
 
** 5:30pm adjourn for day
 
** 5:30pm adjourn for day
 
* Wednesday  
 
* Wednesday  
 
** 8:30am breakfast
 
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)
+
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Stata Kiva Conference Room) (Luis Ibanez)
 
** noon lunch
 
** noon lunch
** 4-5pm: Special topic breakout: [[NA-MIC:2008 Plan for Long-Lead Time Items|  Plan for Long Lead Time Items]]
+
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-rigid Registration]] (Stata Kiva Conference Room) (Stephen Aylward)
 +
** 4:00-5:30pm: Project Week 2008 Special topic breakout: CMake/CPack/CTest/CDash, KWWidgets (Stata Kiva Conference Room) (Julien Jomier, Sebastien Barre)
 
** 5:30pm adjourn for day
 
** 5:30pm adjourn for day
 
* Thursday
 
* Thursday
 
** 8:30am breakfast
 
** 8:30am breakfast
 
** noon lunch
 
** noon lunch
 +
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Stata Kiva Conference Room) (Marco Ruiz)
 
** 5:30pm adjourn for day
 
** 5:30pm adjourn for day
 
* Friday  
 
* Friday  
 
** 8:30am breakfast
 
** 8:30am breakfast
 
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
 
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn.  (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])
+
** Misc:
 
+
*** Noon: Lunch boxes and adjourn by 1:30pm.
=== Preparation ===
+
***We need to empty room by 1:30You are welcome to use wireless in Stata.
 
+
***Please sign up for the Slicer developer [http://www.slicer.org/pages/Mailinglist mailing list].
# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
+
***[http://grants.nih.gov/grants/guide/pa-files/PAR-08-184.html Collaborator RFA has been renewed]
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss Engr Core Projects and Assign/Verify Teams
+
***[[Events:TutorialContestJan2009]]
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss Projects and Assign/Verify Teams
+
***Next Project Week [[AHM_2009| in Utah, January 5-9, 2009]])
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss outstanding projects and teams from previous week
 
# June 12: Create a Wiki page per project (the participants must do this, hopefully jointly)
 
# June 12, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
 
## 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)
 
## 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.)
 
## 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. (Zack)
 
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/Template|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.
 
# [[Engineering:TCON_2008|3pm ET on June 19, 2008: TCON#4 Final Call before showtime...]]
 
# 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 [[Engineering:Programming_Events|this link]].
 
  
 
== Projects ==
 
== Projects ==
  
 
===DBP II===
 
===DBP II===
These are projects by the new set of DBPS:
+
These are projects by the current DBPS:
 
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
 
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
 +
##[[2008_Summer_Project_Week:DWIRegistrationOMT|DWI Registration using Optimal Mass Transport]]  (Sylvain Bouix BWH, Tauseef Rehman GATech)
 +
##[[2008_Summer_Project_Week:EddyCurrentCorrection|EPI-DWI Eddy Current distortion correction]] (Sylvain Bouix BWH, Ran Tao Utah)
 +
##[[2008_Summer_Project_Week:LobeParcellation| Parcellation of 3T MR data]](Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
 +
##[[2008_Summer_Project_Week:GMLongDistanceTractography|GM Long Distance Tractography]] (John Melonakos GATech, Marek Kubicki BWH)
 +
##[[2008_Summer_Project_Week:PopulationDTIApplication|Group Analysis of DTI]] (Casey Goodlett Utah, Serdar Balci MIT, Sylvain Bouix BWH, Marek Kubicki BWH)
 
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
 
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
 +
##[[2008_Summer_Project_Week:RegionalCorticalThicknessTool|Work Flow Tool for regional cortical thickness pipeline]] (Clement Vachet UNC)
 +
##[[2008_Summer_Project_Week:NITRCRegistration|NITRC registration of cortical thickness modules]] (Clement Vachet UNC)
 +
##[[2008_Summer_Project_Week:DWI-DTI_PrepTools|DWI DTI Prep Tools]] (Zhexing Liu UNC)
 
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
 
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
 +
##[[DBP2:MIND:RoadmapProject|Lesion Classification Module]] (Mark Scully MIND)
 +
##[[DBP2:MIND:LongitudinalRegistrationProject|Longitudinal Registration and time course analyses in white matter lesions]] (Mark Scully and Jeremy Bockholt, MIND)
 +
##[[DBP2:MIND:BeyondLesionsProject|Enhancements and extension of white matter lesion classification using DTI scalars]] (Jeremy Bockholt, MIND)
 
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)
 
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)
 +
##[[2008_Summer_Project_Week:TransRectal_Prostate_Biopsy_Module|Trans-Rectal Prostate Biopsy module]] (David Gobbi, Gabor Fichtinger, Queens/JHU)
 +
##[[2008_Summer_Project_Week:ProstateSegReg|Prostate Segmentation and Registration]] (Yi Gao GATech, Gabor Fichtinger JHU)
 +
##[[2008_Summer_Project_Week:PerkStation|Hardware/software overlay for percutaneous intervention (PERK Station)]] (Siddharth Vikal, Gabor Fichtinger, Queens/JHU)
  
===Structural Analysis===
+
===Other Projects===
 
+
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
===Diffusion Image Analysis===
+
#[[2008_Summer_Project_Week:GroupwisePortingToNamicKit| Porting groupwise registration project into NAMIC-kit]] (Serdar Balci, Brad Davis)
 
+
# [[2008_Summer_Project_Week:CVS_SVN_Synchronization|CVS / SVN auto synchronization]] (Sebastien, Steve, Jim, Will, Bill)
===Calibration/Validation===
+
# [[2008_Summer_Project_Week:3DWidgetsInSlicer|3D Widgets in Slicer]] (Nicole Aucoin, Will Schroeder)
This is a new category of projects jointly led by team members in Core 1, Core 3 and Core 5
+
## Issues with existing widgets
 
+
## Design of new widgets
===NA-MIC Kit - Slicer 3===
+
# [[2008_Summer_Project_Week:Batch_Processing|Batch processing in the NAMIC Kit]] (Julien, Marco, Steve, Jim)
 +
#[[2008_Summer_Project_Week:ModuleChaining|Module Chaining]] (Marco, Jim, Steve, Dan B., Luca)
 +
# [[2008_Summer_Project_Week:Nonlinear transforms | Nonlinear transforms]] (Jim, Steve, Luis)
 +
## TransformToWorld/TransformFromWorld, integration with slice viewing
 +
# [[2008_Summer_Project_Week:XNATandXCEDE| Slicer3, XNAT integration and XCEDE Web Services ]] (Dan M., Wendy, Steve, Julien, Dan B.)
 +
## Review and enrich use cases [[Media: XCEDE-Use-Cases-2008-06-25.ppt | (developing use case ppt)]]
 +
# [[2008_Summer_Project_Week:PythonInSlicer| Python in Slicer]] (Dan B., Michael Halle, Steve, Luca)
 +
# [[2008_Summer_Project_Week:PerformanceTuningFiducials|Performance Tuning of Fiducials]] using the EventBroker and other tools (Nicole Aucoin, Alex Yarmarkovich, Steve Pieper, Will Schroeder)
 +
# [[2008_Summer_Project_Week:FocusedGUIRefinement|Focused GUI Refinement and Strategies for Consistency]] (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]
 +
# [[2008_Summer_Project_Week:fMRIconnectivity|fMRI connectivity]]  (Bryce Kim, MIT)
 +
# [[2008_Summer_Project_Week:AtlasFreeSegmentation|Atlas free Segmentation]]  (Tammy Riklin-Raviv, MIT)
 +
#[[NA-MIC/Projects/Collaboration/EM Bias Field Correction | New Bias Field Correction in EM]] (Carlos Sánchez Mendoza, Kilian Pohl - SPL, Brad Davis - Kitware)
 +
# [[2008_Summer_Project_Week:FluidMechanicsTractographyUCLA|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman, UCLA)
  
 
===External Collaborations===
 
===External Collaborations===
 +
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
 +
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
 +
#[[NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation]] (Gary Christensen Group)
 +
#[[NA-MIC/Projects/Collaboration/Lung Atlas]] (Gary Christensen Group)
 +
#[[NA-MIC/Projects/Collaboration/Non-rigid image registration]] (Gary Christensen Group)
 +
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
 +
#[[FMA (Protege) links to Slicer]] (Vish, Mike, Florin, Jim, Steve, Wendy)
 +
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]] (Vidya Rajagopalan, Chris Wyatt, Kilian Pohl)
 +
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga, Dan Blezek, Mike Halle, Steve Pieper)
 +
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)
 +
#[[NA-MIC/Projects/Collaboration/Carto_scar_BIDMC|Carto Scar BIDMC]] (Dana Peters Group)
 +
#[[NA-MIC/Projects/Collaboration/3D Ultrasound Module in Slicer3]] (Junichi, Haiying and Noby - SPL, David and Siddharth - Queen's, Danielle - Robarts)
 +
#[[NA-MIC/Projects/Collaboration/MGH RadOnc_Summer_2008|RadOnc]] (Greg Sharp, MGH)
 +
#[[NA-MIC/Projects/External Collaboration/W&M CRTC]] Non-rigid Registration for Neurosurgery (Nikos Chrisochoides, Andriy Fedorov, College of William&Mary)
 +
#[[NA-MIC/Projects/Collaboration/SBIA UPenn]] DTI and HARDI Analysis Tools (Ragini Verma, SBIA Upenn)
 +
#[[Projects/Diffusion/2008 Project Week DiffusionMRI QBall|Diffusion QBall Framework Integration]] (Demian Wassermann, Rachid Deriche, Odyssée INRIA, CF Westin, LMI
 +
#[[IGT_Projects_Discussion|IGT Projects Discussion]]
 +
#[[NA-MIC/Projects/Collaboration/Slicer3 Theme]] (Iowa Group)
  
 
===Non-Medical Collaborations===
 
===Non-Medical Collaborations===
#[[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)
+
#[[NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine|Astronomical Medicine]] (Harvard IIC: Douglas Alan, Michael Halle)
 +
 
 +
== Preparation ==
 +
# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week NA-MIC Project Week mailing list].
 +
# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
 +
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
 +
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects.  Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
 +
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations.  All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]].  Projects will be discussed in order of the signups.
 +
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations.  All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]].  Projects will be discussed in order of the signups.
 +
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends.  Anyone with un-addressed questions should call.
 +
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/Template|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.
 +
# By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
 +
## 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)
 +
## 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.)
 +
## 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. (Zack)
 +
# 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...
  
 
==Attendee List==
 
==Attendee List==
# Gary Christensen, The University of Iowa
 
# Jeffrey Hawley, Gary Christensen's student
 
# Kate Raising, Gary Christensen's student
 
# Nathan Fritze, Gary Christensen's student
 
# Paul Song, Gary Christensen's student
 
# Cheng Zhang, Gary Christensen's student
 
# Ying Wei, Gary Christensen's student
 
# Nathan Burnette, The University of Iowa
 
# Steve Pieper, Isomics, Core 2/6
 
# Dana C. Peters, BIDMC Harvard Medical
 
# Jason Taclas, Student, BIDMC Harvard Medical
 
# Nicole Aucoin, BWH, Core 2
 
# Will Schroeder, Kitware, Cores 2/4
 
# Sebastien Barre, Kitware, Core 2
 
  
==Pictures==
+
# Purang Abolmaesumi :: Queen's University
 +
# Douglas Alan :: Harvard Medical School
 +
# Mark Anderson :: Brigham and Women's Hospital
 +
# Luca Antiga :: Mario Negri Institute
 +
# Kevin Archie :: Washington University in St. Louis
 +
# Neculai Archip :: Brigham and Women's Hospital
 +
# Nicole Aucoin :: Brigham and Women's Hospital
 +
# Viswanath Avasarala :: General Electric
 +
# Stephen Aylward :: Kitware, Inc.
 +
# Serdar K Balci :: Massachusetts Institute of Technology
 +
# Sebastien Barre :: Kitware, Inc.
 +
# Jamie Berger :: University of Western Australia
 +
# Jack Blevins :: Acoustic Med
 +
# Daniel Blezek :: Isomics, Inc.
 +
# Luke Bloy :: University of Pennsylvania
 +
# Jeremy Bockholt :: The MIND Institute
 +
# Sylvain Bouix :: Brigham and Women's Hospital
 +
# Nathan Burnette :: University of Iowa
 +
# Carling Cheung :: University of Western Ontario
 +
# Nikos Chrisochoides :: College of William and Mary
 +
# Gary E. Christensen :: University of Iowa
 +
# Chris Churas :: UCSD
 +
# Csaba Csoma :: Johns Hopkins University
 +
# Andriy Fedorov :: College of William and Mary
 +
# Gabor Fichtinger :: Queen's University
 +
# Nathan Fritze :: University of Iowa
 +
# Yi Gao :: Georgia Institute of Technology
 +
# Arnaud Gelas :: Harvard Medical School
 +
# David Gobbi :: Queen's University
 +
# Polina Golland :: Massachusetts Institute of Technology
 +
# Randy Gollub :: Massachusetts General Hospital
 +
# Casey Goodlett :: University of Utah
 +
# Alexandre Gouaillard :: Harvard Medical School
 +
# Jeffrey Grethe :: UCSD
 +
# Keith Gunderson :: University of Iowa
 +
# Nathan Hageman :: UCLA
 +
# John Hale :: University of Tulsa
 +
# Michael Halle :: Brigham and Women's Hospital
 +
# Nobuhiko Hata :: Brigham and Women's Hospital
 +
# Jeffrey Hawley :: University of Iowa
 +
# Kathryn Hayes :: Brigham and Women's Hospital
 +
# Toru Higaki :: Hiroshima
 +
# Bill Hoffman :: Kitware, Inc.
 +
# Scott Hoge :: Brigham and Women's Hospital
 +
# Luis Ibanez :: Kitware, Inc.
 +
# Marianna Jakab :: Brigham and Women's Hospital
 +
# Yifeng Jiang :: Yale University
 +
# Hans Johnson :: University of Iowa
 +
# Grand Joldes :: University of Western Australia
 +
# Julien Jomier :: Kitware, Inc.
 +
# Tina Kapur :: Brigham and Women's Hospital
 +
# Peter Kazanzides :: Johns Hopkins University
 +
# Ron Kikinis :: Brigham and Women's Hospital
 +
# Bryce Kim :: Massachusetts Institute of Technology
 +
# Jacek Kukluk :: Brigham and Women's Hospital
 +
# Yang Li :: University of Pennsylvania
 +
# Curtis Lisle :: Isomics, Inc.
 +
# Haying Liu :: Brigham and Women's Hospital
 +
# Zhexing Liu :: University of North Carolina
 +
# Vincent Magnotta :: University of Iowa
 +
# Silas Mann :: Massachusetts General Hospital
 +
# Daniel Marcus :: Washington University in St. Louis
 +
# Sean Megason :: Harvard Medical School
 +
# John Melonakos :: Georgia Institute of Technology
 +
# Carlos Sánchez Mendoza :: Brigham and Women's Hospital
 +
# Bjoern Menze :: Brigham and Women's Hospital
 +
# Mikhail Milchenko :: Washington University in St. Louis
 +
# James Miller :: General Electric
 +
# Kishore Mosaliganti :: Ohio State University
 +
# Timothy Olsen :: Washington University in St. Louis
 +
# John Onofrey :: Yale University
 +
# Danielle Pace :: University of Western Ontario
 +
# Dirk Padfield :: General Electric
 +
# Xenophon Papademetris :: Yale University
 +
# Pratik Patel :: Brainlab
 +
# Marta Peroni :: Massachusetts General Hospital
 +
# Dana Peters :: Harvard Medical School
 +
# Steve Pieper :: Isomics, Inc.
 +
# Wendy Plesniak :: Brigham and Women's Hospital
 +
# Kilian Pohl :: Brigham and Women's Hospital
 +
# Cody Pollet :: University of Tulsa
 +
# Clare Poynton :: Massachusetts Institute of Technology
 +
# Marcel Prastawa :: University of Utah
 +
# Sonia Pujol :: Brigham and Women's Hospital
 +
# Zhen Qian :: Rutgers University
 +
# Kate Raising :: University of Iowa
 +
# Vidya Rajagopalan :: Virginia Tech
 +
# Tauseef Rehman :: Georgia Institute of Technology
 +
# Tammy Riklin Raviv :: Massachusetts Institute of Technology
 +
# Marco Ruiz :: UCSD
 +
# Dustin Scheinost :: Yale University
 +
# Nikeisha Schimke :: University of Tulsa
 +
# William Schroeder :: Kitware, Inc.
 +
# Mark Scully :: The MIND Institute
 +
# Gregory Sharp :: Massachusetts General Hospital
 +
# Paul Song :: University of Iowa
 +
# Priya Srinivasan :: Brigham and Women's Hospital
 +
# Jason Taclas :: Harvard Medical School
 +
# Florin Talos :: Brigham and Women's Hospital
 +
# Ran Tao :: University of Utah
 +
# Xiaodong Tao :: General Electric
 +
# Junichi Tokuda :: Brigham and Women's Hospital
 +
# Clement Vachet :: University of North Carolina
 +
# Ragini Verma :: University of Pennsylvania
 +
# Siddharth Vikal :: Queen's University
 +
# Demian Wassermann :: Brigham and Women's Hospital
 +
# Ying Wei :: University of Iowa
 +
# Carl-Fredrik Westin :: Brigham and Women's Hospital
 +
# Ross Whitaker :: University of Utah
 +
# Adam Wittek :: University of Western Australia
 +
# Alexander Yarmarkovich :: Isomics, Inc.
 +
# Cheng Zhang :: University of Iowa
 +
# Jinghao Zhou :: Rutgers University
 +
 
 +
== Logistics ==
 +
*'''Dates:''' June 23-27, 2008
 +
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
 +
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139.  Receipts will be provided by email as checks are received.  Please send questions to dkauf at mit.edu. If you are attending for one day only, the registration fee is not required.
 +
*'''Registration Method''' The event is full. [[User:Tkapur|Tkapur]] 18:12, 17 June 2008 (UTC)
 +
*'''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&key=4FD1B  Please click here to reserve.] This rate is good only through June 1.
 +
*Here is some information about several other 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.
 +
*2008 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
 +
*[[2007_Programming/Project_Week_MIT#Projects|Last Year's Projects as a reference]]
 +
*For hosting projects, we are planning to make use of the NITRC resources.  See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

Latest revision as of 13:44, 10 July 2017

Home < 2008 Summer Project Week

Back to Events

ProjectWeek-2008.png

Welcome to the web page for the 7th Project Week!

Summary

The seventh NA-MIC Project event was held on June 23-27, 2008 at MIT. There were 114 registered participants for this meeting who worked on 58 projects. 14 of these projects were directly related to the NA-MIC DBPs, 19 to External Collaborations, and 15 to NA-MIC Infrastructure.

A summary of all past Project Events.

More pictures (taken by Jeffrey Hawley).


Introduction to NA-MIC Project Week

Please read an introduction about these events here.

Agenda

Projects

DBP II

These are projects by the current DBPS:

  1. Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia (Harvard: Marek Kubicki, PI)
    1. DWI Registration using Optimal Mass Transport (Sylvain Bouix BWH, Tauseef Rehman GATech)
    2. EPI-DWI Eddy Current distortion correction (Sylvain Bouix BWH, Ran Tao Utah)
    3. Parcellation of 3T MR data(Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
    4. GM Long Distance Tractography (John Melonakos GATech, Marek Kubicki BWH)
    5. Group Analysis of DTI (Casey Goodlett Utah, Serdar Balci MIT, Sylvain Bouix BWH, Marek Kubicki BWH)
  2. Longitudinal MRI Study of Early Brain Development in Autism (UNC: Heather Hazlett, Joseph Piven, PI)
    1. Work Flow Tool for regional cortical thickness pipeline (Clement Vachet UNC)
    2. NITRC registration of cortical thickness modules (Clement Vachet UNC)
    3. DWI DTI Prep Tools (Zhexing Liu UNC)
  3. Analysis of Brain Lesions in Lupus (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
    1. Lesion Classification Module (Mark Scully MIND)
    2. Longitudinal Registration and time course analyses in white matter lesions (Mark Scully and Jeremy Bockholt, MIND)
    3. Enhancements and extension of white matter lesion classification using DTI scalars (Jeremy Bockholt, MIND)
  4. Segmentation and Registration Tools for Robotic Prostate Intervention (Queens/JHU: Gabor Fichtinger, PI)
    1. Trans-Rectal Prostate Biopsy module (David Gobbi, Gabor Fichtinger, Queens/JHU)
    2. Prostate Segmentation and Registration (Yi Gao GATech, Gabor Fichtinger JHU)
    3. Hardware/software overlay for percutaneous intervention (PERK Station) (Siddharth Vikal, Gabor Fichtinger, Queens/JHU)

Other Projects

  1. Eddy current and head motion correction of DWIs (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
  2. Porting groupwise registration project into NAMIC-kit (Serdar Balci, Brad Davis)
  3. CVS / SVN auto synchronization (Sebastien, Steve, Jim, Will, Bill)
  4. 3D Widgets in Slicer (Nicole Aucoin, Will Schroeder)
    1. Issues with existing widgets
    2. Design of new widgets
  5. Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
  6. Module Chaining (Marco, Jim, Steve, Dan B., Luca)
  7. Nonlinear transforms (Jim, Steve, Luis)
    1. TransformToWorld/TransformFromWorld, integration with slice viewing
  8. Slicer3, XNAT integration and XCEDE Web Services (Dan M., Wendy, Steve, Julien, Dan B.)
    1. Review and enrich use cases (developing use case ppt)
  9. Python in Slicer (Dan B., Michael Halle, Steve, Luca)
  10. Performance Tuning of Fiducials using the EventBroker and other tools (Nicole Aucoin, Alex Yarmarkovich, Steve Pieper, Will Schroeder)
  11. Focused GUI Refinement and Strategies for Consistency (Wendy, Sebastien) [1]
  12. fMRI connectivity (Bryce Kim, MIT)
  13. Atlas free Segmentation (Tammy Riklin-Raviv, MIT)
  14. New Bias Field Correction in EM (Carlos Sánchez Mendoza, Kilian Pohl - SPL, Brad Davis - Kitware)
  15. Fluid Mechanics Based DTI Tractography (Nathan Hageman, UCLA)

External Collaborations

  1. NA-MIC/Projects/Collaboration/UWA-Perth (Adam Wittek)
  2. NA-MIC/Projects/Collaboration/MRSI Module for Slicer (Bjoern Menze)
  3. NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation (Gary Christensen Group)
  4. NA-MIC/Projects/Collaboration/Lung Atlas (Gary Christensen Group)
  5. NA-MIC/Projects/Collaboration/Non-rigid image registration (Gary Christensen Group)
  6. NA-MIC/Projects/Collaboration/SARP phantom (Keith Gunderson)
  7. FMA (Protege) links to Slicer (Vish, Mike, Florin, Jim, Steve, Wendy)
  8. NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction (Vidya Rajagopalan, Chris Wyatt, Kilian Pohl)
  9. NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration (Luca Antiga, Dan Blezek, Mike Halle, Steve Pieper)
  10. NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008 (Iowa Group)
  11. Carto Scar BIDMC (Dana Peters Group)
  12. NA-MIC/Projects/Collaboration/3D Ultrasound Module in Slicer3 (Junichi, Haiying and Noby - SPL, David and Siddharth - Queen's, Danielle - Robarts)
  13. RadOnc (Greg Sharp, MGH)
  14. NA-MIC/Projects/External Collaboration/W&M CRTC Non-rigid Registration for Neurosurgery (Nikos Chrisochoides, Andriy Fedorov, College of William&Mary)
  15. NA-MIC/Projects/Collaboration/SBIA UPenn DTI and HARDI Analysis Tools (Ragini Verma, SBIA Upenn)
  16. Diffusion QBall Framework Integration (Demian Wassermann, Rachid Deriche, Odyssée INRIA, CF Westin, LMI
  17. IGT Projects Discussion
  18. NA-MIC/Projects/Collaboration/Slicer3 Theme (Iowa Group)

Non-Medical Collaborations

  1. Astronomical Medicine (Harvard IIC: Douglas Alan, Michael Halle)

Preparation

  1. Please make sure that you are on the NA-MIC Project Week mailing list.
  2. May 08 and May 15 TCON DBPs ONLY at 3pm ET to discuss NA-MIC DBP Projects ONLY.
  3. May 22 TCON#1 at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
  4. May 29 TCON#2 at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot here. Projects will be discussed in order of the signups.
  5. June 5 TCON#3 at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot here. Projects will be discussed in order of the signups.
  6. June 12 TCON#4 at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot here. Projects will be discussed in order of the signups.
  7. June 19 TCON#5 at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
  8. By 3pm ET on June 12, 2008: 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.
  9. By 3pm on June 19, 2008: Create a directory for each project on the NAMIC Sandbox (Zack)
    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. (Zack)
  10. 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...

Attendee List

  1. Purang Abolmaesumi :: Queen's University
  2. Douglas Alan :: Harvard Medical School
  3. Mark Anderson :: Brigham and Women's Hospital
  4. Luca Antiga :: Mario Negri Institute
  5. Kevin Archie :: Washington University in St. Louis
  6. Neculai Archip :: Brigham and Women's Hospital
  7. Nicole Aucoin :: Brigham and Women's Hospital
  8. Viswanath Avasarala :: General Electric
  9. Stephen Aylward :: Kitware, Inc.
  10. Serdar K Balci :: Massachusetts Institute of Technology
  11. Sebastien Barre :: Kitware, Inc.
  12. Jamie Berger :: University of Western Australia
  13. Jack Blevins :: Acoustic Med
  14. Daniel Blezek :: Isomics, Inc.
  15. Luke Bloy :: University of Pennsylvania
  16. Jeremy Bockholt :: The MIND Institute
  17. Sylvain Bouix :: Brigham and Women's Hospital
  18. Nathan Burnette :: University of Iowa
  19. Carling Cheung :: University of Western Ontario
  20. Nikos Chrisochoides :: College of William and Mary
  21. Gary E. Christensen :: University of Iowa
  22. Chris Churas :: UCSD
  23. Csaba Csoma :: Johns Hopkins University
  24. Andriy Fedorov :: College of William and Mary
  25. Gabor Fichtinger :: Queen's University
  26. Nathan Fritze :: University of Iowa
  27. Yi Gao :: Georgia Institute of Technology
  28. Arnaud Gelas :: Harvard Medical School
  29. David Gobbi :: Queen's University
  30. Polina Golland :: Massachusetts Institute of Technology
  31. Randy Gollub :: Massachusetts General Hospital
  32. Casey Goodlett :: University of Utah
  33. Alexandre Gouaillard :: Harvard Medical School
  34. Jeffrey Grethe :: UCSD
  35. Keith Gunderson :: University of Iowa
  36. Nathan Hageman :: UCLA
  37. John Hale :: University of Tulsa
  38. Michael Halle :: Brigham and Women's Hospital
  39. Nobuhiko Hata :: Brigham and Women's Hospital
  40. Jeffrey Hawley :: University of Iowa
  41. Kathryn Hayes :: Brigham and Women's Hospital
  42. Toru Higaki :: Hiroshima
  43. Bill Hoffman :: Kitware, Inc.
  44. Scott Hoge :: Brigham and Women's Hospital
  45. Luis Ibanez :: Kitware, Inc.
  46. Marianna Jakab :: Brigham and Women's Hospital
  47. Yifeng Jiang :: Yale University
  48. Hans Johnson :: University of Iowa
  49. Grand Joldes :: University of Western Australia
  50. Julien Jomier :: Kitware, Inc.
  51. Tina Kapur :: Brigham and Women's Hospital
  52. Peter Kazanzides :: Johns Hopkins University
  53. Ron Kikinis :: Brigham and Women's Hospital
  54. Bryce Kim :: Massachusetts Institute of Technology
  55. Jacek Kukluk :: Brigham and Women's Hospital
  56. Yang Li :: University of Pennsylvania
  57. Curtis Lisle :: Isomics, Inc.
  58. Haying Liu :: Brigham and Women's Hospital
  59. Zhexing Liu :: University of North Carolina
  60. Vincent Magnotta :: University of Iowa
  61. Silas Mann :: Massachusetts General Hospital
  62. Daniel Marcus :: Washington University in St. Louis
  63. Sean Megason :: Harvard Medical School
  64. John Melonakos :: Georgia Institute of Technology
  65. Carlos Sánchez Mendoza :: Brigham and Women's Hospital
  66. Bjoern Menze :: Brigham and Women's Hospital
  67. Mikhail Milchenko :: Washington University in St. Louis
  68. James Miller :: General Electric
  69. Kishore Mosaliganti :: Ohio State University
  70. Timothy Olsen :: Washington University in St. Louis
  71. John Onofrey :: Yale University
  72. Danielle Pace :: University of Western Ontario
  73. Dirk Padfield :: General Electric
  74. Xenophon Papademetris :: Yale University
  75. Pratik Patel :: Brainlab
  76. Marta Peroni :: Massachusetts General Hospital
  77. Dana Peters :: Harvard Medical School
  78. Steve Pieper :: Isomics, Inc.
  79. Wendy Plesniak :: Brigham and Women's Hospital
  80. Kilian Pohl :: Brigham and Women's Hospital
  81. Cody Pollet :: University of Tulsa
  82. Clare Poynton :: Massachusetts Institute of Technology
  83. Marcel Prastawa :: University of Utah
  84. Sonia Pujol :: Brigham and Women's Hospital
  85. Zhen Qian :: Rutgers University
  86. Kate Raising :: University of Iowa
  87. Vidya Rajagopalan :: Virginia Tech
  88. Tauseef Rehman :: Georgia Institute of Technology
  89. Tammy Riklin Raviv :: Massachusetts Institute of Technology
  90. Marco Ruiz :: UCSD
  91. Dustin Scheinost :: Yale University
  92. Nikeisha Schimke :: University of Tulsa
  93. William Schroeder :: Kitware, Inc.
  94. Mark Scully :: The MIND Institute
  95. Gregory Sharp :: Massachusetts General Hospital
  96. Paul Song :: University of Iowa
  97. Priya Srinivasan :: Brigham and Women's Hospital
  98. Jason Taclas :: Harvard Medical School
  99. Florin Talos :: Brigham and Women's Hospital
  100. Ran Tao :: University of Utah
  101. Xiaodong Tao :: General Electric
  102. Junichi Tokuda :: Brigham and Women's Hospital
  103. Clement Vachet :: University of North Carolina
  104. Ragini Verma :: University of Pennsylvania
  105. Siddharth Vikal :: Queen's University
  106. Demian Wassermann :: Brigham and Women's Hospital
  107. Ying Wei :: University of Iowa
  108. Carl-Fredrik Westin :: Brigham and Women's Hospital
  109. Ross Whitaker :: University of Utah
  110. Adam Wittek :: University of Western Australia
  111. Alexander Yarmarkovich :: Isomics, Inc.
  112. Cheng Zhang :: University of Iowa
  113. Jinghao Zhou :: Rutgers University

Logistics

  • Dates: June 23-27, 2008
  • Location: MIT. Grier Rooms A & B: 34-401A & 34-401B.
  • Registration Fee: $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. If you are attending for one day only, the registration fee is not required.
  • Registration Method The event is full. Tkapur 18:12, 17 June 2008 (UTC)
  • Hotel: We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the Hotel at MIT (now called Le Meridien). Please click here to reserve. This rate is good only through June 1.
  • 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.
  • 2008 Summer Project Week Template
  • Last Year's Projects as a reference
  • For hosting projects, we are planning to make use of the NITRC resources. See Information about NITRC Collaboration