Difference between revisions of "2008 Winter Project Week"

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Back to [[Engineering:Programming_Events|Programming/Project Events]], [[AHM_2008]]
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__NOTOC__
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Back to [[Events]]
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To [[AHM_2008| AHM 2008]]
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=Welcome to the web page for the 6th Project Week!=
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==Summary==
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The sixth NA-MIC Project event was held on January 7-11, 2008 in connection with the 2008 NA-MIC AHM. The AHM recorded 104 total attendees. During the project event, 38 projects were actively pursued by the participants.
 +
 
 +
Statistics at a glance:
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* 87 Registered Attendees:  62 NA-MIC participants, 25 collaborators
 +
** 63 NA-MIC Participants breakdown by cores: Core 1 (16), Core 2 (10), Core 3 (31), EABS-NIH (2)
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** 24 Collaborators: Caltech (2), Ohio State University (4), University of Iowa (3), Harvard (1), Negri Institute (1), Washington University School of Medicine (1), Acoustic MedSystems (1), Mayo Clinic (1), Georgetown University (1), AIST (1), College of William and Mary (1), John Hopkins University (1), Queens University (1), UCSD (1), UCLA (1), Kyushu University (1), Knowledge Vis (1), Indiana (1), Cardiovascular Simulation (1), Stony Brook University (1)
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* 38 Projects: DBP Roadmap Projects (5), Other NA-MIC Projects (21), External Collaborations (12)
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A [[Project_Events#Past_Project_Weeks|summary]] of all past Project Events.
  
 
== Logistics ==
 
== Logistics ==
 +
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]
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*[[2007_Programming/Project_Week_MIT#Projects|Last Year's Projects as a reference]]
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*For hosting projects, we are planning to make use of the NITRC resources.  See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]
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*Next Project Week is at MIT -- June 23-27, 2008
  
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'''Dates:''' January 7-11, 2008
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===Introduction to NA-MIC Project Week===
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Please read an introduction about these events [[Project_Events#Introduction|here]].
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===NA-MIC DBP Roadmap Projects===
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Please note that these projects correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem. 
 +
 
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#[[2008_Winter_Project_Week:StochasticTract_Arcuate|Stochastic tractography of the arcuate fasciculus in schizophrenia]] (Marek Kubicki, Tri Ngo, Doug Markant) [[DBP2:Harvard:Brain_Segmentation_Roadmap|[Harvard Roadmap Project: Stochastic Tractography for VCFS]]]
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#[[2008_Winter_Project_Week:Cortical_Thickness|Cortical thickness analysis of pediatric brains]] (Heather Cody Hazlett, Martin Styner, Clement Vachet, Jim Miller) [[DBP2:UNC:Cortical_Thickness_Roadmap|[UNC Roadmap Project: Cortical Thickness Measurement for Autism]]]
 +
#[[2008_Winter_Project_Week:Lesions|Towards an end to end lesion analysis feature in Slicer3]] (Mark Scully, Jeremy Bockholt, Brad Davis, Marcel Prastawa, Sonia Pujol, Vincent Magnotta)[[DBP2:MIND:Roadmap|[MIND Roadmap Project: Brain Lesion Analysis in Lupus]]]
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#[[2008_Winter_Project_Week:Robotic_Prostate_Interventions|Robotic Prostate Interventions]] (David Gobbi, Csaba Csoma, Junichi Tokuda, Katie Hayes)[[DBP2:JHU:Roadmap|[JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]]
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#[[2008_Winter_Project_Week:Prostate_Segmentation|MRI-US Prostate Segmentation]], (Yi Gao, Ponnappan Arumuganainar, John Melonakos, Allen Tannenbaum, Gabor Fichtinger, Xiaodong Tao)
 +
 
 +
===Other NA-MIC Projects===
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#[[2008_Winter_Project_Week_GroupwiseReg|Groupwise Registration and Atlas Building]] (Brad Davis, Serdar Balci, Casey Goodlett)
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#[[2008_Winter_Project_Week_BSplineReg|Optimization for B-Spline based Registration]] (Serdar Balci, Luis Ibanez, Polina Golland)
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#[[2008_Winter_Project_Week:MRISC|Joint Segmentation and Classification of MR Images Based on Structure-specific Affine Registration]] (Mert Sabuncu, Kilian Pohl, Xiaodong Tao)
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#[[2008_Winter_Project_Week:Particle_Correspondence_DTI|Incorporating DTI data into entropy-based particle system for cortical correspondence]] (Ipek Oguz, Josh Cates, Tom Fletcher, Martin Styner, Xiaodong Tao)
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#[[2008_Winter_Project_Week:Population_DTI|Integrating population based DTI tools into NAMIC Kit]] (Casey Goodlett, Alex Yarmakovich)
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#[[2008_Winter_Project_Week:Population_DTI_Application|Application of population based DTI tools to Schizophrenia]] (Casey Goodlett, Alex Yarmakovich, Marek Kubicki)
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#[[2008_Winter_Project_Week:Geodesic_Tractography_Segmentation|Geodesic Tractography Segmentation]], (John Melonakos, Luis Ibanez, Marek Kubicki)
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#[[2008_Winter_Project_Week:Fluid_Mechanics_Tractography|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman,Alex Yarmakovich, Jim Miller)
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#[[2008_Winter_Project_Week:MRMLScenesForExecutionModel|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
 +
#[[2008_Winter_Project_Week:UnstructuredGrids|Unstructured Grids and Mesh Support]] (Curt, Alex, Steve, Will, Vince, Bob O'Bara)
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#[[2008_Winter_Project_Week:PythonSupport|Python Support in Slicer 3]] (Luca Antiga, Dan Blezek)
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#[[2008_Winter_Project_Week:MRMLTransformHardening|Transform hardening in MRML]] (Luca Antiga, Steve Pieper)
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#[[2008_Winter_Project_Week:OutOfCoreMRML|MRML support for out of core processing with fMRI and DTI as use cases]] (Steve Pieper, Jim Miller, Wendy Plesniak, Alex Yarmakovich, Will Schroeder)
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#[[2008_Winter_Project_Week:EventBrokerInSlicer3|Event broker in Slicer3]] (Jim Miller, Steve Pieper, Alex Yarmakovich, Luca Antiga, Dan Blezek)
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#[[2008_Winter_Project_Week:CPack|CPack]], CTest, CMake infrastructure Improvements(Katie Hayes, Steve Pieper, Bill Hoffman, Sebastien Barre, Will Schroeder)
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#[[2008_Winter_ProjectWeek:SlicerCookbook|Slicer GUI Style Guide and Cookbook]] (Wendy Plesniak, Sebastien Barre)
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#[[2008_Winter_Project_Week_VolumeRendering|Volume rendering]] (Andy Freudling, Steve Pieper, Benjamin Grauer)
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#[[2008_Winter_Project_Week_VolumeRenderingUsingCuda|Volume rendering using Cuda]] (Benjamin Grauer, Nobuhiko Hata)
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#[[2008_Winter_Project_Week:3DWWidgets|3D W Widgets and Picking]] (Will Schroeder, Nicole Aucoin, Curt Lisle, Kiran Shivana)
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#[[2008_Winter_Project_Week:XNAT_Integration|XNAT Integration]] (Dan Marcus, Steve Pieper, Stephen Aylward, Jeff Grethe, Julien Jomier, Kevin Archie, Misha Milchenko)
 +
#[[2008_Winter_Project_Week:KWWidgets|KWWidgets Roadmap]] (Sebastien Barre, Wendy Plesniak, Katie Hayes)
 +
 
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===External Collaborations===
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#[[2008_Winter_Project_Week:Astronomical_Medicine|Astronomical coordinate system support]] [Harvard IIC] (Mike Halle, Douglas Alan, Steve Pieper)
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#[[2008_Winter_Project_Week:Meshing Techniques into NA-MIC Toolkit|New Meshing Techniques into NA-MIC]] [Univ. of Iowa] (Vince Magnotta and Nicole Grosland, )
 +
#[[2008_Winter_Project_Week:Finite Element Meshing into NA-MIC|Meshing Workflow into Slicer]] [Univ. of Iowa] (Curt Lisle, Nicole Grosland, Vince Magnotta, Kiran Shivana, Steve Pieper, Brad Davis)
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#[[2008_Winter_Project_Week:SmallAnimalEvalNCI|Evaluating NA-MIC Tools for Small Animal Imaging Workflows]] [NCI] (Curt Lisle, Jack Collins, Killian Pohl)
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#[[2008_Winter_Project_Week:IGT_IGSTK_Slicer|IGSTK-Slicer]]  [Georgetown] (Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda, Luis Ibanez, Steve Pieper)
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#[[2008_Winter_Project_Week:IGT_Intelligent_Surgical_Instrument_Projects|Japanese Intelligent Surgical Instrument Project]] [AIST] (Noby Hata, Chinzei, Hong)
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#[[2008_Winter_Project_Week:GoFigure|GoFigure:High-Level Microscopy Image analysis Application and Algorithms]] [CalTech-Harvard Medical School] (Alex G, Sean Megason, Arnaud Gelas?, Stephen Aylward)
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#[[2008_Winter_Project_Week:microslicer_3 |Doing microscopy image analysis with Slicer3]] [The Ohio State University](Kishore Mosaliganti, Raghu Machiraju, Brad Davis,Stephen Aylward, Steve Pieper)
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#[[2008_Winter_Project_Week:fmri_image_analysis|fMRI Analysis with Slicer 3]] [The Ohio State University](Firdaus Janoos,Raghu Machiraju, Luis Ibanez,Steve Pieper, Wendy Plesniak)
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#[[2008_Winter_Project_Week:Resampling_DTIs_with_Slicer3|Resampling DTIs with Slicer 3]] (Francois Budin, Sylvain Bouix, Xiaodong Tao)
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#[[2008_Winter_Project_Week:fmri_eeg_analysis|Analyzing fMRI and concurrent EEG with Slicer and SCIRun]] [BWH] (Padma Sundaram)
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#[[2008_Winter_Project_Week:fmri_var|Bayesian hierarchical models for fMRI variance components analysis]] (Kinh Tieu, Sandy Wells, Jim Miller)
  
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'''Location:''' Marriott City Center, SLC, Utah.
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== Dates.Venue.Registration ==
  
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'''Registration:''' Coming soon.
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'''Dates:'''  
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* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 10th'''. 
 +
* Project Activities will be held rest of the week between '''Monday, January 7th and Friday, January 11th'''.
  
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'''Hotel:''' Same hotel as the AHM.
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'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. To reserve rooms at the meeting rate of $129/night, please call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting.  Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.
  
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([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])
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<big> '''Registration:''' We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click [http://www.sci.utah.edu/namic2008/registration.html '''here'''] for online registration. This registration must be completed by Friday, December 14, 2007. </big>
  
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===Introduction to NA-MIC Project Week===
 
  
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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. 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). 
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Please note that this information can also be found [[AHM_2008#Dates.Venue.Registration|here.]]
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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. 
 
  
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* 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.
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([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])
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* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
 
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* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
 
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* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
 
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* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
 
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* 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.
 
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* 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.
 
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* Everyone should '''bring a laptop'''. We will have four projectors.
 
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* About half the time will be spent working on projects and the other half in project related discussions.
 
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* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
 
  
 
=== Agenda===
 
=== Agenda===
  
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[[AHM_2008#Agenda|Agenda for AHM 2008 and Project Half Week]]
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[[AHM_2008#Agenda|Agenda for AHM 2008 and Project Week]]
  
 
=== Preparation ===
 
=== Preparation ===
  
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# 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]
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# 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]
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# [[Engineering:TCON_2007#2007-11-29|November 29, 2007: Kickoff TCON#1 to discuss Projects and Assign/Verify Teams]]
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# [[Engineering:TCON_2007#2007-11-29|November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams]]
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# [[Engineering:TCON_2007#2007-12-06|December 6, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
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# [[Engineering:TCON_2007#2007-12-06|December 6, 2007: TCON#2 with all participants to Assign/Verify Teams]]
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# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#3 to discuss outstanding projects and teams]]
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# [[Engineering:TCON_2007#2007-12-13|December 13, 2007: TCON#3 with Breakout Session owners to review agendas]]
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# December 6, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
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# [[Engineering:TCON_2007#2007-12-13|December 20, 2007: TCON#4 to discuss outstanding projects and teams]]
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# By December 20, 2008: [[2008_Winter_Project_Week_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.
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# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]
 
# January 3, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
 
# January 3, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
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##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
 
## 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)
 
## 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.)
 
## 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)
 
## 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)
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# By 3pm ET on Jan 3, 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.
 
 
# 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...
 
# 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...
  
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== A History in Wiki Links ==
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== Previous Project Events ==
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A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].
 
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== Projects ==
 
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'''(Last Project Week Projects are listed here as a starting point....)'''
 
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===DBP II===
 
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These are projects by the new set of DBPS:
 
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#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
 
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## [[Projects/Diffusion/2007_Project_Week_EPI Distortion correction using field maps|EPI Distortion correction using field maps]] (Marek Kubicki BWH)
 
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##[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|Dorsolateral Prefrontal Cortex Segmentation in VCFS]] (Nicole Aucoin, John Melonakos, Tauseef Rehman, Brad Davis, Marek Kubicki).
 
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#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
 
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##[[Projects/Structural/2007_Project_Week_Cortical_Thickness_for_Autism|Cortical Thickness Measurement for UNC Autism Study]] (Clement Vachet UNC, Heather Hazlett UNC, Martin Styner UNC)
 
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#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
 
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##[[Projects/Structural/2007_Project_Week_Lesion_Classification_in_Lupus|Lesion Classification in Lupus]] (Jeremy Bockholt, Mark Scully)
 
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#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI):
 
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##[[Collaboration/JHU/Brachytherapy_needle_positioning_robot_integration | Brachytherapy needle positioning robot integration
 
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]] (David Gobbi Queen's U, Csaba Csoma, JHU, Katie Hayes, BWH, Peter Kazanzides JHU)
 
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===Structural Analysis===
 
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#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)
 
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#[[Projects/Structural/2007_Project_Week_Nonrigid_Groupwise_Registration| Non-Rigid Groupwise Registration Tools for ITK]] (Serdar K Balci, Lilla Zollei, Polina Golland, Sandy Wells)
 
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===Diffusion Image Analysis===
 
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# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH, Raul San Jose BWH)
 
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#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
 
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# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
 
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# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)
 
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# [[Projects/Diffusion/2007_Project_Week_DTI_Registration|Distortion Correction in DWI]] (Ran Tao, Utah)
 
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# [[Projects/Diffusion/2007_Project_Week_Fluid_Mechanics_Based_Tractography|Fluid Mechanics Based Tractography]] (Nathan Hagemen UCLA)
 
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# [[Projects/Diffusion/2007_Project_Week_Glyphed_Visualization_For_Volume_Data|Sliced Multiple Glyphed Visualization for Volume Data]] (Demian Wassermann, Raul San Jose, Rachid Deriche, CF Westin)
 
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===Calibration/Validation===
 
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This is a new category of projects jointly led by team members in Core 1, Core 3 and Core 5
 
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#[[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures|Contrasting Tractography Measures]] (Marek Kubicki, Ross Whitaker, Guido Gerig, Randy Gollub)
 
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===NA-MIC Kit - Slicer 3===
 
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#[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
 
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#[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
 
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# [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
 
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# [[Projects/Slicer3/2007_Project_Week_Lightbox|Lightbox]] (James, Jim, Wendy, Alex)
 
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# [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Curt, Nicole, Alex, Steve, Will, Vince)
 
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# [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Dan, Luca, Steve)
 
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# [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Katie, Steve, Bill Hoffman)
 
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# [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
 
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# [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Tensors]] (Katharina, Sylvain, Steve)
 
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# [[Projects/Slicer3/2007_Project_Week_Support for electron microscopy | Dendritic Spine Morphometrics]] (Bryan Smith)
 
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# [[Projects/Slicer3/2007_Project_Week_Review of Slicer3 CMake Files | Review of Slicer3 CMake Files]] (Steve, Jim, Luca, Bill)
 
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# [[Projects/Slicer3/2007_Project_Week_ROIs in Slicer3 | ROIs in Slicer3]] (Wendy, Jim, Nicole, Steve, Ron)
 
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# [[Projects/Slicer3/2007_Project_Week_Lego Mindstorms dissemination for IGT | Lego Mindstorms Dissemination for IGT]] (Danielle Pace)
 
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# [[Projects/Slicer3/2007_Project_Week_EdgeDetection | Edge Detection in Slicer3]] (Elliot Uvero MIT, Lauren O'Donnell BWH, Luis Ibanez Kitware)
 
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===External Collaborations===
 
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# Meshing
 
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## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
 
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## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
 
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# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
 
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# [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
 
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# Registration
 
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## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
 
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## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
 
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## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
 
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# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)
 
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# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
 
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# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)
 
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# MIND Clinical Imaging Study: [[Collaboration/MCIC/DTI:mgh60direction|conversion of mgh 60 direction sequence to nrrd]] (Jeremy Bockholt, Sumner Williams)
 
  
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===Non-Medical Collaborations===
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A history of all the programming/project events in NA-MIC is available by following [[Project Events|this link]].
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#[[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)
 

Latest revision as of 15:52, 30 March 2017

Home < 2008 Winter Project Week

Back to Events

To AHM 2008

Welcome to the web page for the 6th Project Week!

Summary

The sixth NA-MIC Project event was held on January 7-11, 2008 in connection with the 2008 NA-MIC AHM. The AHM recorded 104 total attendees. During the project event, 38 projects were actively pursued by the participants.

Statistics at a glance:

  • 87 Registered Attendees: 62 NA-MIC participants, 25 collaborators
    • 63 NA-MIC Participants breakdown by cores: Core 1 (16), Core 2 (10), Core 3 (31), EABS-NIH (2)
    • 24 Collaborators: Caltech (2), Ohio State University (4), University of Iowa (3), Harvard (1), Negri Institute (1), Washington University School of Medicine (1), Acoustic MedSystems (1), Mayo Clinic (1), Georgetown University (1), AIST (1), College of William and Mary (1), John Hopkins University (1), Queens University (1), UCSD (1), UCLA (1), Kyushu University (1), Knowledge Vis (1), Indiana (1), Cardiovascular Simulation (1), Stony Brook University (1)
  • 38 Projects: DBP Roadmap Projects (5), Other NA-MIC Projects (21), External Collaborations (12)

A summary of all past Project Events.

Logistics

Introduction to NA-MIC Project Week

Please read an introduction about these events here.

NA-MIC DBP Roadmap Projects

Please note that these projects correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.

  1. Stochastic tractography of the arcuate fasciculus in schizophrenia (Marek Kubicki, Tri Ngo, Doug Markant) [Harvard Roadmap Project: Stochastic Tractography for VCFS]
  2. Cortical thickness analysis of pediatric brains (Heather Cody Hazlett, Martin Styner, Clement Vachet, Jim Miller) [UNC Roadmap Project: Cortical Thickness Measurement for Autism]
  3. Towards an end to end lesion analysis feature in Slicer3 (Mark Scully, Jeremy Bockholt, Brad Davis, Marcel Prastawa, Sonia Pujol, Vincent Magnotta)[MIND Roadmap Project: Brain Lesion Analysis in Lupus]
  4. Robotic Prostate Interventions (David Gobbi, Csaba Csoma, Junichi Tokuda, Katie Hayes)[JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]
  5. MRI-US Prostate Segmentation, (Yi Gao, Ponnappan Arumuganainar, John Melonakos, Allen Tannenbaum, Gabor Fichtinger, Xiaodong Tao)

Other NA-MIC Projects

  1. Groupwise Registration and Atlas Building (Brad Davis, Serdar Balci, Casey Goodlett)
  2. Optimization for B-Spline based Registration (Serdar Balci, Luis Ibanez, Polina Golland)
  3. Joint Segmentation and Classification of MR Images Based on Structure-specific Affine Registration (Mert Sabuncu, Kilian Pohl, Xiaodong Tao)
  4. Incorporating DTI data into entropy-based particle system for cortical correspondence (Ipek Oguz, Josh Cates, Tom Fletcher, Martin Styner, Xiaodong Tao)
  5. Integrating population based DTI tools into NAMIC Kit (Casey Goodlett, Alex Yarmakovich)
  6. Application of population based DTI tools to Schizophrenia (Casey Goodlett, Alex Yarmakovich, Marek Kubicki)
  7. Geodesic Tractography Segmentation, (John Melonakos, Luis Ibanez, Marek Kubicki)
  8. Fluid Mechanics Based DTI Tractography (Nathan Hageman,Alex Yarmakovich, Jim Miller)
  9. MRML Scenes for the Execution Model including Transforms (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
  10. Unstructured Grids and Mesh Support (Curt, Alex, Steve, Will, Vince, Bob O'Bara)
  11. Python Support in Slicer 3 (Luca Antiga, Dan Blezek)
  12. Transform hardening in MRML (Luca Antiga, Steve Pieper)
  13. MRML support for out of core processing with fMRI and DTI as use cases (Steve Pieper, Jim Miller, Wendy Plesniak, Alex Yarmakovich, Will Schroeder)
  14. Event broker in Slicer3 (Jim Miller, Steve Pieper, Alex Yarmakovich, Luca Antiga, Dan Blezek)
  15. CPack, CTest, CMake infrastructure Improvements(Katie Hayes, Steve Pieper, Bill Hoffman, Sebastien Barre, Will Schroeder)
  16. Slicer GUI Style Guide and Cookbook (Wendy Plesniak, Sebastien Barre)
  17. Volume rendering (Andy Freudling, Steve Pieper, Benjamin Grauer)
  18. Volume rendering using Cuda (Benjamin Grauer, Nobuhiko Hata)
  19. 3D W Widgets and Picking (Will Schroeder, Nicole Aucoin, Curt Lisle, Kiran Shivana)
  20. XNAT Integration (Dan Marcus, Steve Pieper, Stephen Aylward, Jeff Grethe, Julien Jomier, Kevin Archie, Misha Milchenko)
  21. KWWidgets Roadmap (Sebastien Barre, Wendy Plesniak, Katie Hayes)

External Collaborations

  1. Astronomical coordinate system support [Harvard IIC] (Mike Halle, Douglas Alan, Steve Pieper)
  2. New Meshing Techniques into NA-MIC [Univ. of Iowa] (Vince Magnotta and Nicole Grosland, )
  3. Meshing Workflow into Slicer [Univ. of Iowa] (Curt Lisle, Nicole Grosland, Vince Magnotta, Kiran Shivana, Steve Pieper, Brad Davis)
  4. Evaluating NA-MIC Tools for Small Animal Imaging Workflows [NCI] (Curt Lisle, Jack Collins, Killian Pohl)
  5. IGSTK-Slicer [Georgetown] (Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda, Luis Ibanez, Steve Pieper)
  6. Japanese Intelligent Surgical Instrument Project [AIST] (Noby Hata, Chinzei, Hong)
  7. GoFigure:High-Level Microscopy Image analysis Application and Algorithms [CalTech-Harvard Medical School] (Alex G, Sean Megason, Arnaud Gelas?, Stephen Aylward)
  8. Doing microscopy image analysis with Slicer3 [The Ohio State University](Kishore Mosaliganti, Raghu Machiraju, Brad Davis,Stephen Aylward, Steve Pieper)
  9. fMRI Analysis with Slicer 3 [The Ohio State University](Firdaus Janoos,Raghu Machiraju, Luis Ibanez,Steve Pieper, Wendy Plesniak)
  10. Resampling DTIs with Slicer 3 (Francois Budin, Sylvain Bouix, Xiaodong Tao)
  11. Analyzing fMRI and concurrent EEG with Slicer and SCIRun [BWH] (Padma Sundaram)
  12. Bayesian hierarchical models for fMRI variance components analysis (Kinh Tieu, Sandy Wells, Jim Miller)

Dates.Venue.Registration

Dates:

  • The All Hands Meeting and External Advisory Board Meeting will be held on Thursday, January 10th.
  • Project Activities will be held rest of the week between Monday, January 7th and Friday, January 11th.

Venue: The venue for the meeting is Marriot City Center, Salt Lake City, Utah Mariott City Center, Salt Lake City, Utah. (Floorplan). To reserve rooms at the meeting rate of $129/night, please call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

Registration: We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click here for online registration. This registration must be completed by Friday, December 14, 2007.


Please note that this information can also be found here.

(This is a checklist for the onsite planning items)

Agenda

Agenda for AHM 2008 and Project Week

Preparation

  1. Please make sure that you are on the na-mic-project-week mailing list
  2. November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams
  3. December 6, 2007: TCON#2 with all participants to Assign/Verify Teams
  4. December 13, 2007: TCON#3 with Breakout Session owners to review agendas
  5. December 20, 2007: TCON#4 to discuss outstanding projects and teams
  6. By December 20, 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.
  7. January 3, 2008: TCON#5 to discuss outstanding projects and teams
  8. January 3, 2008: Create a directory for each project on the NAMIC Sandbox (Zack)
    1. Ask Zack for a Sandbox account
    2. 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)
    3. 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.)
    4. 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)
  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...

Previous Project Events

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

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