Difference between revisions of "2008 Winter Project Week"

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Back to [[Project Events]], [[AHM_2008]], [[Events]]
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__NOTOC__
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Back to [[Events]]
  
== Projects ==
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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
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** 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.
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== Logistics ==
 
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]
 
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]
 
*[[2007_Programming/Project_Week_MIT#Projects|Last Year's Projects as a reference]]
 
*[[2007_Programming/Project_Week_MIT#Projects|Last Year's Projects as a reference]]
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*Next Project Week is at MIT -- June 23-27, 2008
 
*Next Project Week is at MIT -- June 23-27, 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]].
  
===DBP Roadmap Projects===
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===NA-MIC DBP Roadmap Projects===
Please note that the first four categories below 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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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.   
====[[DBP2:Harvard:Brain_Segmentation_Roadmap|DBP Harvard Roadmap Project: Stochastic Tractography for Velocardio Facial Syndrome (VCFS)]]====
 
*[[2008_Winter_Project_Week:StochasticTract_Arcuate|Stochastic tractography of the arcuate fasciculus in schizophrenia]] (Marek Kubicki, Tri Ngo, Doug Markant)
 
  
====[[DBP2:UNC:Cortical_Thickness_Roadmap|DBP UNC Roadmap Project: Cortical Thickness Measurement for Autism]]====
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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]]]
*[[2008_Winter_Project_Week:Cortical_Thickness|Cortical thickness analysis of pediatric brains]] (Heather Cody Hazlett, Martin Styner, Clement Vachet, Jim Miller)
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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]]]
 +
#[[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]]]
 +
#[[2008_Winter_Project_Week:Prostate_Segmentation|MRI-US Prostate Segmentation]], (Yi Gao, Ponnappan Arumuganainar, John Melonakos, Allen Tannenbaum, Gabor Fichtinger, Xiaodong Tao)
  
====[[DBP2:MIND:Roadmap|DBP MIND Roadmap Project: Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus]]====
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===Other NA-MIC Projects===
*[[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)
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#[[2008_Winter_Project_Week_GroupwiseReg|Groupwise Registration and Atlas Building]] (Brad Davis, Serdar Balci, Casey Goodlett)
 +
#[[2008_Winter_Project_Week_BSplineReg|Optimization for B-Spline based Registration]] (Serdar Balci, Luis Ibanez, Polina Golland)
 +
#[[2008_Winter_Project_Week:MRISC|Joint Segmentation and Classification of MR Images Based on Structure-specific Affine Registration]] (Mert Sabuncu, Kilian Pohl, Xiaodong Tao)
 +
#[[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)
 +
#[[2008_Winter_Project_Week:Population_DTI|Integrating population based DTI tools into NAMIC Kit]] (Casey Goodlett, Alex Yarmakovich)
 +
#[[2008_Winter_Project_Week:Population_DTI_Application|Application of population based DTI tools to Schizophrenia]] (Casey Goodlett, Alex Yarmakovich, Marek Kubicki)
 +
#[[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)
 +
#[[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)
 +
#[[2008_Winter_Project_Week:PythonSupport|Python Support in Slicer 3]] (Luca Antiga, Dan Blezek)
 +
#[[2008_Winter_Project_Week:MRMLTransformHardening|Transform hardening in MRML]] (Luca Antiga, Steve Pieper)
 +
#[[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)
 +
#[[2008_Winter_Project_Week:EventBrokerInSlicer3|Event broker in Slicer3]] (Jim Miller, Steve Pieper, Alex Yarmakovich, Luca Antiga, Dan Blezek)
 +
#[[2008_Winter_Project_Week:CPack|CPack]], CTest, CMake infrastructure Improvements(Katie Hayes, Steve Pieper, Bill Hoffman, Sebastien Barre, Will Schroeder)
 +
#[[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)
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#[[2008_Winter_Project_Week:KWWidgets|KWWidgets Roadmap]] (Sebastien Barre, Wendy Plesniak, Katie Hayes)
  
====[[DBP2:JHU:Roadmap|DBP JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]====
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===External Collaborations===
#[[2008_Winter_Project_Week:Robotic_Prostate_Interventions | Robotic Prostate Interventions]] (David Gobbi, Csaba Csoma, Junichi Tokuda, Katie Hayes)
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#[[2008_Winter_Project_Week:Astronomical_Medicine|Astronomical coordinate system support]] [Harvard IIC] (Mike Halle, Douglas Alan, Steve Pieper)
#[[2008_Winter_Project_Week:Prostate_Segmentation|Prostate Segmentation]], (Yi Gao, Ponnappan Arumuganainar, John Melonakos, Allen Tannenbaum, Gabor Fichtinger)
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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, )
 
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#[[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)
===All Other Projects===
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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)
# [[2008_Winter_Project_Week_GroupwiseReg | Groupwise Registration and Atlas Building]] (Brad Davis, Serdar Balci, Casey Goodlett)
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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)
# [[2008_Winter_Project_Week:MRISC|Joint Segmentation and Classification of MR Images Based on Structure-specific Affine Registration]] (Mert Sabuncu, Kilian Pohl)
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#[[2008_Winter_Project_Week:IGT_Intelligent_Surgical_Instrument_Projects|Japanese Intelligent Surgical Instrument Project]] [AIST] (Noby Hata, Chinzei, Hong)
# [[2008_Winter_Project_Week:CorPar|Cortical Surface Parcellation]] (Thomas Yeo, Mert Sabuncu)
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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)
# [[2008_Winter_Project_Week:Dorsolateral_Prefrontal_Cortex_Segmentation|Dorsolateral Prefrontal Cortex Segmentation]] (Marek Kubicki, Sylvain Bouix, John Melonakos, Brad Davis, Polina Golland)
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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)
#[[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)
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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)
#[[2008_Winter_Project_Week:Population_DTI|Integrating population based DTI tools into NAMIC Kit]] (Casey Goodlett)
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#[[2008_Winter_Project_Week:Resampling_DTIs_with_Slicer3|Resampling DTIs with Slicer 3]] (Francois Budin, Sylvain Bouix, Xiaodong Tao)
#[[2008_Winter_Project_Week:Population_DTI_Application|Application of population based DTI tools to Schizophrenia]] (Casey Goodlett, Marek Kubicki)
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#[[2008_Winter_Project_Week:fmri_eeg_analysis|Analyzing fMRI and concurrent EEG with Slicer and SCIRun]] [BWH] (Padma Sundaram)
#[[2008_Winter_Project_Week:Geodesic_Tractography_Segmentation|Geodesic Tractography Segmentation]], (John Melonakos, Allen Tannenbaum, Marek Kubicki)
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#[[2008_Winter_Project_Week:fmri_var|Bayesian hierarchical models for fMRI variance components analysis]] (Kinh Tieu, Sandy Wells, Jim Miller)
#[[2008_Winter_Project_Week:Fluid_Mechanics_Tractography|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman)
 
#[[2008_Winter_Project_Week:MRMLScenesForExecutionModel |MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
 
#Unstructured Grids and Mesh Support(Curt, Alex, Steve, Will, Vince, Bob O'Bara)
 
#[[2008_Winter_Project_Week:PythonSupport |Python Support in Slicer 3]] (Luca, Bryan Smith, Dan Blezek)
 
#[[2008_Winter_Project_Week:MRMLTransformHardening |Transform hardening in MRML]] (Luca Antiga, Steve Pieper)
 
#[[2008_Winter_Project_Week:EventBrokerInSlicer3 |Event broker in Slicer3]] (Jim, Steve, Alex Y, Luca, Dan Blezek)
 
#[[2008_Winter_Project_Week:CPack |CPack]], CTest, CMake infrastructure Improvements(Katie, Steve, Bill Hoffman, Sebastien)
 
#[[2008_Winter_ProjectWeek:SlicerCookbook | Slicer Interface Style Guide and Cookbook]] (Wendy Plesniak, Sebastien Barre)
 
#Shape Descriptor Functions for Dendritic Spine Morphometrics (Bryan Smith, Padma, Martin Styner)
 
#[[2008_Winter_Project_Week_VolumeRendering|Volume rendering]] (Andy Freudling, Steve Pieper, Grauer)
 
#[[2008_Winter_Project_Week_VolumeRenderingUsingCuda|Volume rendering using Cuda]] (Andy Freudling, Steve Pieper, Grauer)
 
#[[2008_Winter_Project_Week:3DWWidgets |3D W Widgets and Picking]] (Will Schroeder, Nicole Aucoin, Curt Lisle, Kiran Shivana)
 
#[[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)
 
#[[2008_Winter_Project_Week:XNAT_Integration | XNAT Integration]] ([http://www.xnat.org XNAT], [http://www.slicer.org Slicer], [http://www.Xcede.org XCEDE], [http://www.batchmake.org Batchmake]) (Dan Marcus, Steve Pieper, Stephen Aylward, Jeff Grethe, Julien Jomier)
 
#KWWidgets Roadmap (Sebastien Barre, Wendy Plesniak, Katie Hayes)
 
#Circuit Annotation Capability (for example drawing arrows above regions that are connected functionally, structurally, etc), (Mark Scully, others)
 
#Astronomical coordinate system support (Mike Halle, Doug Alan)
 
#[[2008_Winter_Project_Week:Meshing Techniques into NA-MIC Toolkit|New Meshing Techniques into NA-MIC]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta)
 
#[[2008_Winter_Project_Week:Finite Element Meshing into NA-MIC|Meshing Workflow into Slicer]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta, Kiran Shivana, Steve Pieper, Curt Lisle, Brad Davis)
 
#[[2008_Winter_Project_Week:SmallAnimalEvalNCI |Evaluating NA-MIC Tools for Small Animal Imaging Workflows]] [NCI] (Curt Lisle, Jack Collins, Killian Pohl)
 
#[[2008_Winter_Project_Week:GoFigure |GoFigure:High-Level Microscopy Image analysis Application and Algorithms]] [CalTech-Harvard Medical School] (Alex G, Sean Megason, Arnaud Gelas?)
 
#[[2008_Winter_Project_Week:IGT_IGSTK_Slicer| IGSTK-Slicer]]  [Georgetown] (Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda)
 
#[[2008_Winter_Project_Week:IGT_Intelligent_Surgical_Instrument_Projects| Japanese Intelligent Surgical Instrument Project]] [AIST] (Noby Hata, Chinzei, Hong)
 
#[[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)
 
#[[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)
 
#[[2008_Winter_Project_Week:Resampling_DTIs_with_Slicer3|Resampling DTIs with Slicer 3]] (Francois Budin, Sylvain Bouix)
 
  
 
== Dates.Venue.Registration ==
 
== Dates.Venue.Registration ==
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([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])
 
([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])
 
===Introduction to NA-MIC Project Week===
 
 
Please read the introduction to these events [[Project_Events#Introduction|here]].
 
  
 
=== Agenda===
 
=== Agenda===
Line 90: Line 98:
 
# [[Engineering:TCON_2007#2007-12-13|December 13, 2007: TCON#3 with Breakout Session owners to review agendas]]
 
# [[Engineering:TCON_2007#2007-12-13|December 13, 2007: TCON#3 with Breakout Session owners to review agendas]]
 
# [[Engineering:TCON_2007#2007-12-13|December 20, 2007: TCON#4 to discuss outstanding projects and teams]]
 
# [[Engineering:TCON_2007#2007-12-13|December 20, 2007: TCON#4 to discuss outstanding projects and teams]]
 +
# 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.
 
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]
 
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]
# December 20, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
 
 
# 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)
 
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
 
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
Line 97: Line 105:
 
## 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)
# By December 17, 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.
 
 
# 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...
  

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.