NAMIC Wiki - User contributions [en]

2007 Project Half Week

2007-02-01T19:23:58Z

Simond: /* External Collaborations */

Back to [[AHM_2007|AHM_2007]]

== Results ==
Results of this event will be summarized here after it is completed.

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
# Data assimilation for NAMIC (Stephen) [[Media:2007_Project_Half_Week_MIDAS.ppt | 4 block PPT Jan 2007]]
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration]] (Stephen, Jim, Ross) [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
## Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration.ppt| 4-block PPT Jan 2007]]
#Genus Zero Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]
#Thickness Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]
#Shape Analysis of Caudate paper (Jim, Martin, Marc, Sylvain, Martha), [[Media:2007_Project_Half_Week_Caudate_Paper.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]
#ITK Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT), [[Media:2007_Project_Half_Week_StochasticTractography.ppt| 4-block PPT Jan 2007]]

===NA-MIC Kit===
#'''[[Slicer3:Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) [[Media:2007 Programming Half Week SlicerArch.ppt | 4-block ppt]]
#'''[[Slicer3:Data_Model|Slicer3: Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4 block:MRML Feedback]],[[Media:2007_Programming_Half_Week_HierModel.ppt| 4 block:MRML Hierarchy Representation]]
#'''[[Slicer3:Execution_Model|Slicer3: Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
#'''[[Slicer3:Interface_Design|Slicer3: Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Transition_of_Slicer2.x_Modules|Slicer3: Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
##[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI] [[Media:2007_Project_Half_Week_DTI.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:DTMRI|Tractography]] '''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:Editor|Editor]] '''Steve''' [[Media:2007_Programming_Half_Week_Editor.ppt | 4-block ppt]]
##[[Slicer3:ColorsFiducialsFreesurferModelmaker|Slicer3: Colors, Fiducials, FreeSurfer, ModelMaker]] '''Nicole''' [[Media:2007_Project_Half_Week_Slicer3Colors.ppt | 4 block:Colors]],[[Media:2007_Project_Half_Week_Slicer3Fiducials.ppt | 4 block:Fiducials]],[[Media:2007_Project_Half_Week_Slicer3FreeSurfer.ppt | 4 block:FreeSurfer]], [[Media:2007_Project_Half_Week_Slicer3ModelMaker.ppt | 4 block:ModelMaker]]

#'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie) [[media:2007 AHM Programming Half Week PackagingAndDeployment.ppt | 4-block PPT]]
#Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[media:2007 AHM Programming Half Week Slicer3 Launch.ppt | 4-block PPT]]
#'''[[Slicer3:Pipeline_Integration|Slicer3: Pipeline Integration]]''' ('''Jags''') [[media:2007_Project_Half_Week_Loni_Pipeline.ppt| 4-block PPT]]
#'''[[Slicer3:Grid_Interface|Slicer3: Grid Integration]]''' ('''Neil''', Bill, Jim) [[media:2007_Project_Half_Week_GridExecution.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''') [[Media:2007_Programming_Half_Week_Performance_Analysis.ppt| 4-block PPT Jan 2007]] [[Media:2007_Programming_Half_Week_Performance_Analysis_Feb.ppt| 4-block PPT Feb 2007]]
#Matlab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT Jan 2007]]
#[[Slicer3:_Image_Guided_Therapy_%28IGT%29|Slicer3: IGT, Trackers]] '''Haiying''' [[Media:2007_Project_Half_Week_Tracker_New.ppt|4 block PPT Jan 2007]]
#[[IGT|IGT Workflow for Slicer3: Interventional Imaging]] (Simon DiMaio, Raimundo Sierra, Haiying Liu, Noby Hata, Stephen Aylward) [[Media:2007_Project_Half_Week_InterventionalImaging.ppt|4 block PPT Jan 2007]]
#Radiology Workstation Module for Slicer3 (Pat, Steve)
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]]
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]]
##Voxel meshing as an execuation module in Slicer3 - [[Media:2007 AHM Programming Half Week VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Mesh Quality Visualization Development - [[Media:Mesh_Quality_Visualization.ppt|Mapped Quality 4 block PPT Jan 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Bounding Box Projection Meshing - [[Media:Mapped Mesh.ppt|Bounding Box 4 block PPT Jan 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
##Tetrahedral Mesh Generation Tools in VTK - [[Media:Tetmesh_VTK_Tools.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) [[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | 4 block PPT Jan 2007]]

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

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

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# 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]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## 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. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# 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]].

2007 Project Half Week

2007-02-01T19:23:23Z

Simond: /* External Collaborations */

Back to [[AHM_2007|AHM_2007]]

== Results ==
Results of this event will be summarized here after it is completed.

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
# Data assimilation for NAMIC (Stephen) [[Media:2007_Project_Half_Week_MIDAS.ppt | 4 block PPT Jan 2007]]
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration]] (Stephen, Jim, Ross) [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
## Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration.ppt| 4-block PPT Jan 2007]]
#Genus Zero Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]
#Thickness Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]
#Shape Analysis of Caudate paper (Jim, Martin, Marc, Sylvain, Martha), [[Media:2007_Project_Half_Week_Caudate_Paper.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]
#ITK Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT), [[Media:2007_Project_Half_Week_StochasticTractography.ppt| 4-block PPT Jan 2007]]

===NA-MIC Kit===
#'''[[Slicer3:Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) [[Media:2007 Programming Half Week SlicerArch.ppt | 4-block ppt]]
#'''[[Slicer3:Data_Model|Slicer3: Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4 block:MRML Feedback]],[[Media:2007_Programming_Half_Week_HierModel.ppt| 4 block:MRML Hierarchy Representation]]
#'''[[Slicer3:Execution_Model|Slicer3: Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
#'''[[Slicer3:Interface_Design|Slicer3: Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Transition_of_Slicer2.x_Modules|Slicer3: Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
##[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI] [[Media:2007_Project_Half_Week_DTI.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:DTMRI|Tractography]] '''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:Editor|Editor]] '''Steve''' [[Media:2007_Programming_Half_Week_Editor.ppt | 4-block ppt]]
##[[Slicer3:ColorsFiducialsFreesurferModelmaker|Slicer3: Colors, Fiducials, FreeSurfer, ModelMaker]] '''Nicole''' [[Media:2007_Project_Half_Week_Slicer3Colors.ppt | 4 block:Colors]],[[Media:2007_Project_Half_Week_Slicer3Fiducials.ppt | 4 block:Fiducials]],[[Media:2007_Project_Half_Week_Slicer3FreeSurfer.ppt | 4 block:FreeSurfer]], [[Media:2007_Project_Half_Week_Slicer3ModelMaker.ppt | 4 block:ModelMaker]]

#'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie) [[media:2007 AHM Programming Half Week PackagingAndDeployment.ppt | 4-block PPT]]
#Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[media:2007 AHM Programming Half Week Slicer3 Launch.ppt | 4-block PPT]]
#'''[[Slicer3:Pipeline_Integration|Slicer3: Pipeline Integration]]''' ('''Jags''') [[media:2007_Project_Half_Week_Loni_Pipeline.ppt| 4-block PPT]]
#'''[[Slicer3:Grid_Interface|Slicer3: Grid Integration]]''' ('''Neil''', Bill, Jim) [[media:2007_Project_Half_Week_GridExecution.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''') [[Media:2007_Programming_Half_Week_Performance_Analysis.ppt| 4-block PPT Jan 2007]] [[Media:2007_Programming_Half_Week_Performance_Analysis_Feb.ppt| 4-block PPT Feb 2007]]
#Matlab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT Jan 2007]]
#[[Slicer3:_Image_Guided_Therapy_%28IGT%29|Slicer3: IGT, Trackers]] '''Haiying''' [[Media:2007_Project_Half_Week_Tracker_New.ppt|4 block PPT Jan 2007]]
#[[IGT|IGT Workflow for Slicer3: Interventional Imaging]] (Simon DiMaio, Raimundo Sierra, Haiying Liu, Noby Hata, Stephen Aylward) [[image:2007_Project_Half_Week_InterventionalImaging.ppt|4 block PPT Jan 2007]]
#Radiology Workstation Module for Slicer3 (Pat, Steve)
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]]
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]]
##Voxel meshing as an execuation module in Slicer3 - [[Media:2007 AHM Programming Half Week VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Mesh Quality Visualization Development - [[Media:Mesh_Quality_Visualization.ppt|Mapped Quality 4 block PPT Jan 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Bounding Box Projection Meshing - [[Media:Mapped Mesh.ppt|Bounding Box 4 block PPT Jan 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
##Tetrahedral Mesh Generation Tools in VTK - [[Media:Tetmesh_VTK_Tools.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) [[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | 4 block PPT Jan 2007]]

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

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

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# 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]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## 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. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# 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]].

2007 Project Half Week

2007-02-01T18:08:52Z

Simond: /* External Collaborations */

Back to [[AHM_2007|AHM_2007]]

== Results ==
Results of this event will be summarized here after it is completed.

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
# Data assimilation for NAMIC (Stephen) [[Media:2007_Project_Half_Week_MIDAS.ppt | 4 block PPT Jan 2007]]
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration]] (Stephen, Jim, Ross) [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
## Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration.ppt| 4-block PPT Jan 2007]]
#Genus Zero Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]
#Thickness Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]
#Shape Analysis of Caudate paper (Jim, Martin, Marc, Sylvain, Martha), [[Media:2007_Project_Half_Week_Caudate_Paper.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]
#ITK Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT), [[Media:2007_Project_Half_Week_StochasticTractography.ppt| 4-block PPT Jan 2007]]

===NA-MIC Kit===
#'''[[Slicer3:Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) [[Media:2007 Programming Half Week SlicerArch.ppt | 4-block ppt]]
#'''[[Slicer3:Data_Model|Slicer3: Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4 block:MRML Feedback]],[[Media:2007_Programming_Half_Week_HierModel.ppt| 4 block:MRML Hierarchy Representation]]
#'''[[Slicer3:Execution_Model|Slicer3: Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
#'''[[Slicer3:Interface_Design|Slicer3: Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Transition_of_Slicer2.x_Modules|Slicer3: Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
##[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI] [[Media:2007_Project_Half_Week_DTI.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:DTMRI|Tractography]] '''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:Editor|Editor]] '''Steve''' [[Media:2007_Programming_Half_Week_Editor.ppt | 4-block ppt]]
##[[Slicer3:ColorsFiducialsFreesurferModelmaker|Slicer3: Colors, Fiducials, FreeSurfer, ModelMaker]] '''Nicole''' [[Media:2007_Project_Half_Week_Slicer3Colors.ppt | 4 block:Colors]],[[Media:2007_Project_Half_Week_Slicer3Fiducials.ppt | 4 block:Fiducials]],[[Media:2007_Project_Half_Week_Slicer3FreeSurfer.ppt | 4 block:FreeSurfer]], [[Media:2007_Project_Half_Week_Slicer3ModelMaker.ppt | 4 block:ModelMaker]]

#'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie) [[media:2007 AHM Programming Half Week PackagingAndDeployment.ppt | 4-block PPT]]
#Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[media:2007 AHM Programming Half Week Slicer3 Launch.ppt | 4-block PPT]]
#'''[[Slicer3:Pipeline_Integration|Slicer3: Pipeline Integration]]''' ('''Jags''') [[media:2007_Project_Half_Week_Loni_Pipeline.ppt| 4-block PPT]]
#'''[[Slicer3:Grid_Interface|Slicer3: Grid Integration]]''' ('''Neil''', Bill, Jim) [[media:2007_Project_Half_Week_GridExecution.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''') [[Media:2007_Programming_Half_Week_Performance_Analysis.ppt| 4-block PPT Jan 2007]]
#Matlab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT Jan 2007]]
#[[Slicer3:_Image_Guided_Therapy_%28IGT%29|Slicer3: IGT, Trackers]] '''Haiying''' [[Media:2007_Project_Half_Week_Tracker_New.ppt|4 block PPT Jan 2007]]
#[[IGT|IGT Workflow for Slicer3: Interventional Imaging]] (Simon DiMaio, Raimundo Sierra, Haiying Liu, Noby Hata, Stephen Aylward) [[Media:2007_Project_Half_Week_InterventionalImaging.ppt|4 block PPT Jan 2007]]
#Radiology Workstation Module for Slicer3 (Pat, Steve)
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]]
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]]
##Voxel meshing as an execuation module in Slicer3 - [[Media:2007 AHM Programming Half Week VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Mesh Quality Visualization Development - [[Media:Mesh_Quality_Visualization.ppt|Mapped Quality 4 block PPT Jan 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Bounding Box Projection Meshing - [[Media:Mapped Mesh.ppt|Bounding Box 4 block PPT Jan 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
##Tetrahedral Mesh Generation Tools in VTK - [[Media:Tetmesh_VTK_Tools.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) [[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | 4 block PPT Jan 2007]]

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

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

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# 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]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## 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. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# 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]].

IGT:October 2006 IGT Workshop

2007-01-22T22:08:52Z

Simond: /* Thursday, October 19, 2006 */

==Summary==

This meeting was successfully concluded with over 75 registered attendees. A summary white paper will be made available here in February 2007.

== Registration and Attendee List ==

'''Registration Fee'''<nowiki>: US $250.00 payable onsite only by check payable to "BWPO Radiology" or cash. We can not accept credit cards, or payments before the meeting. </nowiki>

'''Registration'''<nowiki>: Registration for this workshop is quite simple. To register, please follow two steps: </nowiki>

# Create an account for yourself on this wiki by clicking here [[Special:Userlogin|Special:Userlogin]]
# After creating the account, go to the [[2006_IGT_Workshop_Attendee_List|2006 IGT Workshop Attendee List]] and add your name, Institution, an email address, and the name of the breakout session you will be attending on Friday.

== Goal ==

The goal of this workshop is to bring together researchers developing Image-Guided Therapy (IGT) systems for a 2-day workshop to share their recent advances and to identify synergies in future strategy. The intent of the workshop is to foster community-based development, to share best practices in engineering such systems, to identify gaps in the engineering infrastructure available to IGT researchers, and ultimately to facilitate the transfer of technology among NIH-sponsored research centers.

In this program, we define IGT systems as the integrated devices for therapy delivery that incorporate intra-operative medical imaging, navigation, or robotics. In the lectures and breakout groups of this two-day workshop, we plan to:

# discuss system architectures currently used in IGT systems
# identify challenges in the design and implementation of IGT systems
# identify gaps in the engineering infrastructure available to IGT researchers
# identify opportunities and mechanisms for sharing low-level components and high-level architectural design patterns, and
# identify opportunities for the National Center for Image Guided Therapy (NCIGT, http://www.ncigt.org) to help address these challenges and develop an open system architecture as part of its function as a biotechnology resource for the Image-Guided Therapy community.

The workshop will concentrate on the computer science and engineering aspects of such systems, as the clinical aspects have been covered in previous NIH-related workshops. The agenda will include plenary talks that will review technical aspects of IGT as well as breakout sessions in which the participants will concentrate on issues raised by the talks.

 '''Background on this workshop'''<nowiki>: The initial idea of this workshop was developed in ad-hoc meetings with collaborators across institutions including Georgetown, Johns Hopkins, UNC, NIH, GE Global Research, Kitware Inc., and Brigham and Women's Hospital. The Program Committee welcomed and encouraged suggestions from the IGT community on the content of this workshop until mid July, 2006, when the program was finalized. </nowiki>

== Sponsors ==

We would like to gratefully acknowledge our industry sponsors whose financial support is helping us keep the registration fee low.

* '''GE Healthcare'''
* '''Siemens Corporate Research (SCR)'''
* '''Northern Digital (NDI)'''
* '''Medtronic Navigation'''
* '''Brainlab'''
* '''Acoustic Med'''

If your company would like to sponsor the workshop, please send an email to tkapur at bwh.harvard.edu for additional information.

== Hotel Logistics ==

'''Date'''<nowiki>: October 19-20 (Thursday-Friday), 2006. </nowiki>

'''Location/Hotel'''<nowiki>: The </nowiki>[http://rockvillehotel.com/ Doubletree Hotel & Executive Meeting Center], 1750 Rockville Pike, Rockville, Maryland 20852. Phone number: +1 (301) 468-1100. Room rates for the meeting were US $166/night (+ applicable taxes) for reservations made prior to September 29, 2006 12am using the group code "BRI". After that date, rates revert to the regular ($300+/nt) and we are unable to get the hotel to release additional rooms at the lower rate.

Please note that the conference hotel only has rooms blocked for October 19th night. If you are need accommodation for additional nights, a conveniently located area hotel is the Ramada Inn, 1775 Rockville Pike, Rockville, MD 20852. Phone (301) 881-2300.

== Subway Information ==

[http://www.wmata.com/metrorail/systemmap.cfm Subway Map]

* Directions from Washington Reagan International Airport (DCA) to the Doubletree Hotel:
** Take the Yellow Line to Gallery Place 
** At Gallery Place, switch to the Red Line (going toward Shady Grove) 
** Get off at Twinbrook; the Doubletree is across the street 

== Program Committee ==

Ferenc Jolesz, M.D., Brigham and Women's Hospital, is the Workshop Chair. The program committee includes:

* Kevin Cleary, Ph.D., Georgetown
* Peter Kazanzides, Ph.D, Johns Hopkins
* Keyvan Farahani, Ph.D., NIH
* Bill Lorensen, M.S, GE Global Research
* Stephen Aylward, Ph.D., UNC, Kitware Inc.
* Randy Ellis, Ph.D., Brigham and Women's Hospital
* Ron Kikinis, M.D., Brigham and Women's Hospital
* Clare Tempany, M.D., Brigham and Women's Hospital

== Organizing Committee ==

* Simon DiMaio, Ph.D., Brigham and Women's Hospital
* Noby Hata, Ph.D., Brigham and Women's Hospital
* Dan Kacher, M.S., Brigham and Women's Hospital
* Eigil Samset, Ph.D., Brigham and Women's Hospital
* Tina Kapur, Ph.D., Brigham and Women's Hospital
* William M. Wells, Ph.D, Brigham and Women's Hospital
* Marianna Jakab, M.S., Brigham and Women's Hospital
* Debbie O'Shea Begley, Brigham and Women's Hospital, Workshop Coordinator
* Katie Mastrogiacomo, Brigham and Women's Hospital, Workshop Staff

== Agenda ==

The agenda for the meeting is available here as [[Media:2006_IGT_Workshop_Agenda.pdf|PDF]] and [[Media:2006_IGT_Workshop_Agenda.doc|MS WORD]] documents.

=== Thursday, October 19, 2006 ===
* 1:00-1:10pm: [[Media:Jolesz_IGT_Workshop_Oct_2006_Intro.ppt|Welcome]] (Ferenc Jolesz, Brigham and Women's Hospital) [[Media:Photo1.jpg|Photo]]
* 1:10-1:15pm: [[2006_IGT_Workshop_Presentation_Summary_Kikinis|2006 IGT Workshop Presentation Summary Kikinis]]
* 1:15-1:20pm: [[Media:Ellis_WorkshopGoals.ppt|Goals for the Workshop]] (Randy Ellis, Brigham and Women's Hospital)
*1:20-1:40pm: [[media:Cleary_system_design_IGT_workshop_Oct_2006.ppt|IGT System Design]] (Kevin Cleary, Georgetown University)
*1:40-2:00pm: [[media:Lorensen_IGS_WS.ppt|IGT Software Design and Process]] (Bill Lorensen, GE Research)
*2:00-2:20pm: [[media:Kazanzides-SystemEngineering.ppt|IGT System Engineering]] (Peter Kazanzides, Johns Hopkins University)
* 2:20-2:40pm: [[Media:Ellis_WorkshopHCI.ppt|IGT User Interfaces and Human-Computer Interactions]] (Randy Ellis, Brigham and Women's Hospital)
* 2:40-3:00pm: [[Media:Peters_IGS_WS_final.ppt|Evolution of a VR-Based IGT Environment]] (Terry Peters & David Gobbi, Robarts Research Institute, University of Western Ontario)
* 3:00-3:20pm: [[Media:Pizer_radoncseg.publ.ppt|System Challenges in Image-Analysis for Radiation Therapy]] (Steve Pizer, UNC)
* 3:20-3:40pm: [[Media:Galloway_Platform_Technology_for_Multiple_IGTapplications.ppt|Platform Technology for Multiple IGT applications]] (Bob Galloway, Vanderbilt)
* 3:40-4:00pm: Coffee Break
* 4:00-5:30pm: [[2006_IGT_Workshop_Panel_Discussion#Discussion|Panel Discussion I]] Chair: Jim Duncan, Yale.
* 5:30-6:30pm: Program Committee to capture the discussions and recommendations for the session

 

=== Friday, October 20, 2006 ===

* 8:00am: Continental Breakfast
* 8:55am: Welcome back
* 9:00-9:20am: [[Media:Fichtinger-IGT-Workshop-Oct19.ppt|Successes and Challenges in Therapy Delivery]] (Gabor Fichtinger, Johns Hopkins University)
* 9:20-9:40am: [[Media:Final_IGT_Workshop_HU_Lemke.ppt|IGT Challenges and Suggestions for Center]] (Heinz Lemke, Univerity of Southern California/CARS) (see also: [[Media:Lemke_11548_2006_Editorial_IJCARS_1_3_2006_LEMKE.pdf|The Operating Room and the need for an IT infrastructure and standards]])
* 9:40-10:00am:[[Media:Hata-ncigtws.ppt|Successes and Challenges in Effectors and Scanner Control]] (Noby Hata, Brigham and Women's Hospital)
* 10:00-10:15am: [[Media:Haller-IGT2006.ppt|NIBIB Perspective on IGT Research]] (John Haller, NIH)
* 10:15-10:30am: [[Media:Clarke_NCIGT_Oct_19th2006.ppt|NCI/NIST Perspective on IGT Research]] (Larry Clarke, NIH)
* 10:30-11:00am: Break
* 11:00-11:40am: [[2006_October_IGT_Workshop_Panel_Discussion_II|Panel Discussion II]], Chair: Keyvan Farahani, NIH
* 11:40-11:50pm: [[2006_October_IGT_Workshop_Breakout_Instructions|Instructions for Breakout Groups]]
* 11:50-1:00pm: Lunch
* 1:00-2:30pm: Breakout discussions
** Breakout Session 1: [[2006_IGT_Workshop_Workflow_Breakout|Workflows for IGT]] (Moderator: Stephen Aylward)
** Breakout Session 2: [[2006_IGT_Workshop_Validation_Breakout|Validation]] (Moderator: Kirby Vosburgh)
** Breakout Session 3: [[2006_IGT_Workshop_Robot_Breakout|Interfaces to Robots]] (Moderator: Peter Kazanzides)
** Breakout Session 4: [[2006_IGT_Workshop_Tracking_Breakout|Tracking]] (Moderators: Tina Kapur, Simon DiMaio)
** Breakout Session 5: [[2006_IGT_Workshop_Radiation_Therapy_Breakout|IGT Case Study: Radiation Therapy for Prostate]] (Moderator: Clare Tempany)
* 2:30pm-2:45pm: Coffee Break
* 2:45pm-3:30pm: Plenary Session (report back from each breakout session)
* 3:30pm: Adjourn (all except Program and Organizing Committees)

 

For Program and Organizing Committee:

* 3:30-4:30pm: Data gathering and documentation planning

 

== Community Links ==

[http://studierstube.icg.tu-graz.ac.at/opentracker/ OpenTracker]

* [http://www.ncigt.org/sign/documentation/splot.html SPLOT - OpenTracker Extension]

[http://isiswiki.georgetown.edu/zivy/casResearch.html Related links contributed by Ziv Yaniv]

 

== Contact ==

For further information about the program please contact: Tina Kapur (tkapur at bwh.harvard.edu)

For further information about the registration please contact : Debbie O'Shea Begley (djo at bwh.harvard.edu)

If you would like to be added to the mailing list for the workshop, please contact: Marianna Jakab (marianna at bwh.harvard.edu)

 

== Photos ==

Here are some photos from the IGT Workshop:

{|
|[[Image:IGT_break.JPG|thumb|102px]]
|[[Image:IGT_room_view.JPG|thumb|102px]]
|[[Image:IGT_room_view_2.JPG|thumb|102px]]
|[[Image:IGT_room_view_3.JPG|thumb|102px]]
|}

 

And here are a few from the Brigham dinner:

{|
|valign="top"|[[Image:Thai_sign.JPG|thumb|102px]]
|[[Image:Thai_dinner_1.JPG|thumb|102px]]
|[[Image:Thai_dinner_2.JPG|thumb|102px]]
|}

IGT:October 2006 IGT Workshop

2007-01-22T22:08:36Z

Simond: /* Thursday, October 19, 2006 */

==Summary==

This meeting was successfully concluded with over 75 registered attendees. A summary white paper will be made available here in February 2007.

== Registration and Attendee List ==

'''Registration Fee'''<nowiki>: US $250.00 payable onsite only by check payable to "BWPO Radiology" or cash. We can not accept credit cards, or payments before the meeting. </nowiki>

'''Registration'''<nowiki>: Registration for this workshop is quite simple. To register, please follow two steps: </nowiki>

# Create an account for yourself on this wiki by clicking here [[Special:Userlogin|Special:Userlogin]]
# After creating the account, go to the [[2006_IGT_Workshop_Attendee_List|2006 IGT Workshop Attendee List]] and add your name, Institution, an email address, and the name of the breakout session you will be attending on Friday.

== Goal ==

The goal of this workshop is to bring together researchers developing Image-Guided Therapy (IGT) systems for a 2-day workshop to share their recent advances and to identify synergies in future strategy. The intent of the workshop is to foster community-based development, to share best practices in engineering such systems, to identify gaps in the engineering infrastructure available to IGT researchers, and ultimately to facilitate the transfer of technology among NIH-sponsored research centers.

In this program, we define IGT systems as the integrated devices for therapy delivery that incorporate intra-operative medical imaging, navigation, or robotics. In the lectures and breakout groups of this two-day workshop, we plan to:

# discuss system architectures currently used in IGT systems
# identify challenges in the design and implementation of IGT systems
# identify gaps in the engineering infrastructure available to IGT researchers
# identify opportunities and mechanisms for sharing low-level components and high-level architectural design patterns, and
# identify opportunities for the National Center for Image Guided Therapy (NCIGT, http://www.ncigt.org) to help address these challenges and develop an open system architecture as part of its function as a biotechnology resource for the Image-Guided Therapy community.

The workshop will concentrate on the computer science and engineering aspects of such systems, as the clinical aspects have been covered in previous NIH-related workshops. The agenda will include plenary talks that will review technical aspects of IGT as well as breakout sessions in which the participants will concentrate on issues raised by the talks.

 '''Background on this workshop'''<nowiki>: The initial idea of this workshop was developed in ad-hoc meetings with collaborators across institutions including Georgetown, Johns Hopkins, UNC, NIH, GE Global Research, Kitware Inc., and Brigham and Women's Hospital. The Program Committee welcomed and encouraged suggestions from the IGT community on the content of this workshop until mid July, 2006, when the program was finalized. </nowiki>

== Sponsors ==

We would like to gratefully acknowledge our industry sponsors whose financial support is helping us keep the registration fee low.

* '''GE Healthcare'''
* '''Siemens Corporate Research (SCR)'''
* '''Northern Digital (NDI)'''
* '''Medtronic Navigation'''
* '''Brainlab'''
* '''Acoustic Med'''

If your company would like to sponsor the workshop, please send an email to tkapur at bwh.harvard.edu for additional information.

== Hotel Logistics ==

'''Date'''<nowiki>: October 19-20 (Thursday-Friday), 2006. </nowiki>

'''Location/Hotel'''<nowiki>: The </nowiki>[http://rockvillehotel.com/ Doubletree Hotel & Executive Meeting Center], 1750 Rockville Pike, Rockville, Maryland 20852. Phone number: +1 (301) 468-1100. Room rates for the meeting were US $166/night (+ applicable taxes) for reservations made prior to September 29, 2006 12am using the group code "BRI". After that date, rates revert to the regular ($300+/nt) and we are unable to get the hotel to release additional rooms at the lower rate.

Please note that the conference hotel only has rooms blocked for October 19th night. If you are need accommodation for additional nights, a conveniently located area hotel is the Ramada Inn, 1775 Rockville Pike, Rockville, MD 20852. Phone (301) 881-2300.

== Subway Information ==

[http://www.wmata.com/metrorail/systemmap.cfm Subway Map]

* Directions from Washington Reagan International Airport (DCA) to the Doubletree Hotel:
** Take the Yellow Line to Gallery Place 
** At Gallery Place, switch to the Red Line (going toward Shady Grove) 
** Get off at Twinbrook; the Doubletree is across the street 

== Program Committee ==

Ferenc Jolesz, M.D., Brigham and Women's Hospital, is the Workshop Chair. The program committee includes:

* Kevin Cleary, Ph.D., Georgetown
* Peter Kazanzides, Ph.D, Johns Hopkins
* Keyvan Farahani, Ph.D., NIH
* Bill Lorensen, M.S, GE Global Research
* Stephen Aylward, Ph.D., UNC, Kitware Inc.
* Randy Ellis, Ph.D., Brigham and Women's Hospital
* Ron Kikinis, M.D., Brigham and Women's Hospital
* Clare Tempany, M.D., Brigham and Women's Hospital

== Organizing Committee ==

* Simon DiMaio, Ph.D., Brigham and Women's Hospital
* Noby Hata, Ph.D., Brigham and Women's Hospital
* Dan Kacher, M.S., Brigham and Women's Hospital
* Eigil Samset, Ph.D., Brigham and Women's Hospital
* Tina Kapur, Ph.D., Brigham and Women's Hospital
* William M. Wells, Ph.D, Brigham and Women's Hospital
* Marianna Jakab, M.S., Brigham and Women's Hospital
* Debbie O'Shea Begley, Brigham and Women's Hospital, Workshop Coordinator
* Katie Mastrogiacomo, Brigham and Women's Hospital, Workshop Staff

== Agenda ==

The agenda for the meeting is available here as [[Media:2006_IGT_Workshop_Agenda.pdf|PDF]] and [[Media:2006_IGT_Workshop_Agenda.doc|MS WORD]] documents.

=== Thursday, October 19, 2006 ===
* 1:00-1:10pm: [[Media:Jolesz_IGT_Workshop_Oct_2006_Intro.ppt|Welcome]] (Ferenc Jolesz, Brigham and Women's Hospital) [[Media:Photo1.jpg|Photo]]
* 1:10-1:15pm: [[2006_IGT_Workshop_Presentation_Summary_Kikinis|2006 IGT Workshop Presentation Summary Kikinis]]
* 1:15-1:20pm: [[Media:Ellis_WorkshopGoals.ppt|Goals for the Workshop]] (Randy Ellis, Brigham and Women's Hospital)
*1:20-1:40pm: [[media:Cleary_system_design_IGT_workshop_Oct_2006.ppt|IGT System Design]] (Kevin Cleary, Georgetown University)
*1:40-2:00pm: [[media:Lorensen_IGS_WS.ppt|IGT Software Design and Process]] (Bill Lorensen, GE Research)
*2:00-2:20pm: [[media:Kazanzides-SystemEngineering.pdf|IGT System Engineering]] (Peter Kazanzides, Johns Hopkins University)
* 2:20-2:40pm: [[Media:Ellis_WorkshopHCI.ppt|IGT User Interfaces and Human-Computer Interactions]] (Randy Ellis, Brigham and Women's Hospital)
* 2:40-3:00pm: [[Media:Peters_IGS_WS_final.ppt|Evolution of a VR-Based IGT Environment]] (Terry Peters & David Gobbi, Robarts Research Institute, University of Western Ontario)
* 3:00-3:20pm: [[Media:Pizer_radoncseg.publ.ppt|System Challenges in Image-Analysis for Radiation Therapy]] (Steve Pizer, UNC)
* 3:20-3:40pm: [[Media:Galloway_Platform_Technology_for_Multiple_IGTapplications.ppt|Platform Technology for Multiple IGT applications]] (Bob Galloway, Vanderbilt)
* 3:40-4:00pm: Coffee Break
* 4:00-5:30pm: [[2006_IGT_Workshop_Panel_Discussion#Discussion|Panel Discussion I]] Chair: Jim Duncan, Yale.
* 5:30-6:30pm: Program Committee to capture the discussions and recommendations for the session

 

=== Friday, October 20, 2006 ===

* 8:00am: Continental Breakfast
* 8:55am: Welcome back
* 9:00-9:20am: [[Media:Fichtinger-IGT-Workshop-Oct19.ppt|Successes and Challenges in Therapy Delivery]] (Gabor Fichtinger, Johns Hopkins University)
* 9:20-9:40am: [[Media:Final_IGT_Workshop_HU_Lemke.ppt|IGT Challenges and Suggestions for Center]] (Heinz Lemke, Univerity of Southern California/CARS) (see also: [[Media:Lemke_11548_2006_Editorial_IJCARS_1_3_2006_LEMKE.pdf|The Operating Room and the need for an IT infrastructure and standards]])
* 9:40-10:00am:[[Media:Hata-ncigtws.ppt|Successes and Challenges in Effectors and Scanner Control]] (Noby Hata, Brigham and Women's Hospital)
* 10:00-10:15am: [[Media:Haller-IGT2006.ppt|NIBIB Perspective on IGT Research]] (John Haller, NIH)
* 10:15-10:30am: [[Media:Clarke_NCIGT_Oct_19th2006.ppt|NCI/NIST Perspective on IGT Research]] (Larry Clarke, NIH)
* 10:30-11:00am: Break
* 11:00-11:40am: [[2006_October_IGT_Workshop_Panel_Discussion_II|Panel Discussion II]], Chair: Keyvan Farahani, NIH
* 11:40-11:50pm: [[2006_October_IGT_Workshop_Breakout_Instructions|Instructions for Breakout Groups]]
* 11:50-1:00pm: Lunch
* 1:00-2:30pm: Breakout discussions
** Breakout Session 1: [[2006_IGT_Workshop_Workflow_Breakout|Workflows for IGT]] (Moderator: Stephen Aylward)
** Breakout Session 2: [[2006_IGT_Workshop_Validation_Breakout|Validation]] (Moderator: Kirby Vosburgh)
** Breakout Session 3: [[2006_IGT_Workshop_Robot_Breakout|Interfaces to Robots]] (Moderator: Peter Kazanzides)
** Breakout Session 4: [[2006_IGT_Workshop_Tracking_Breakout|Tracking]] (Moderators: Tina Kapur, Simon DiMaio)
** Breakout Session 5: [[2006_IGT_Workshop_Radiation_Therapy_Breakout|IGT Case Study: Radiation Therapy for Prostate]] (Moderator: Clare Tempany)
* 2:30pm-2:45pm: Coffee Break
* 2:45pm-3:30pm: Plenary Session (report back from each breakout session)
* 3:30pm: Adjourn (all except Program and Organizing Committees)

 

For Program and Organizing Committee:

* 3:30-4:30pm: Data gathering and documentation planning

 

== Community Links ==

[http://studierstube.icg.tu-graz.ac.at/opentracker/ OpenTracker]

* [http://www.ncigt.org/sign/documentation/splot.html SPLOT - OpenTracker Extension]

[http://isiswiki.georgetown.edu/zivy/casResearch.html Related links contributed by Ziv Yaniv]

 

== Contact ==

For further information about the program please contact: Tina Kapur (tkapur at bwh.harvard.edu)

For further information about the registration please contact : Debbie O'Shea Begley (djo at bwh.harvard.edu)

If you would like to be added to the mailing list for the workshop, please contact: Marianna Jakab (marianna at bwh.harvard.edu)

 

== Photos ==

Here are some photos from the IGT Workshop:

{|
|[[Image:IGT_break.JPG|thumb|102px]]
|[[Image:IGT_room_view.JPG|thumb|102px]]
|[[Image:IGT_room_view_2.JPG|thumb|102px]]
|[[Image:IGT_room_view_3.JPG|thumb|102px]]
|}

 

And here are a few from the Brigham dinner:

{|
|valign="top"|[[Image:Thai_sign.JPG|thumb|102px]]
|[[Image:Thai_dinner_1.JPG|thumb|102px]]
|[[Image:Thai_dinner_2.JPG|thumb|102px]]
|}

IGT:October 2006 IGT Workshop

2007-01-22T22:06:15Z

Simond: /* Thursday, October 19, 2006 */

==Summary==

This meeting was successfully concluded with over 75 registered attendees. A summary white paper will be made available here in February 2007.

== Registration and Attendee List ==

'''Registration Fee'''<nowiki>: US $250.00 payable onsite only by check payable to "BWPO Radiology" or cash. We can not accept credit cards, or payments before the meeting. </nowiki>

'''Registration'''<nowiki>: Registration for this workshop is quite simple. To register, please follow two steps: </nowiki>

# Create an account for yourself on this wiki by clicking here [[Special:Userlogin|Special:Userlogin]]
# After creating the account, go to the [[2006_IGT_Workshop_Attendee_List|2006 IGT Workshop Attendee List]] and add your name, Institution, an email address, and the name of the breakout session you will be attending on Friday.

== Goal ==

The goal of this workshop is to bring together researchers developing Image-Guided Therapy (IGT) systems for a 2-day workshop to share their recent advances and to identify synergies in future strategy. The intent of the workshop is to foster community-based development, to share best practices in engineering such systems, to identify gaps in the engineering infrastructure available to IGT researchers, and ultimately to facilitate the transfer of technology among NIH-sponsored research centers.

In this program, we define IGT systems as the integrated devices for therapy delivery that incorporate intra-operative medical imaging, navigation, or robotics. In the lectures and breakout groups of this two-day workshop, we plan to:

# discuss system architectures currently used in IGT systems
# identify challenges in the design and implementation of IGT systems
# identify gaps in the engineering infrastructure available to IGT researchers
# identify opportunities and mechanisms for sharing low-level components and high-level architectural design patterns, and
# identify opportunities for the National Center for Image Guided Therapy (NCIGT, http://www.ncigt.org) to help address these challenges and develop an open system architecture as part of its function as a biotechnology resource for the Image-Guided Therapy community.

The workshop will concentrate on the computer science and engineering aspects of such systems, as the clinical aspects have been covered in previous NIH-related workshops. The agenda will include plenary talks that will review technical aspects of IGT as well as breakout sessions in which the participants will concentrate on issues raised by the talks.

 '''Background on this workshop'''<nowiki>: The initial idea of this workshop was developed in ad-hoc meetings with collaborators across institutions including Georgetown, Johns Hopkins, UNC, NIH, GE Global Research, Kitware Inc., and Brigham and Women's Hospital. The Program Committee welcomed and encouraged suggestions from the IGT community on the content of this workshop until mid July, 2006, when the program was finalized. </nowiki>

== Sponsors ==

We would like to gratefully acknowledge our industry sponsors whose financial support is helping us keep the registration fee low.

* '''GE Healthcare'''
* '''Siemens Corporate Research (SCR)'''
* '''Northern Digital (NDI)'''
* '''Medtronic Navigation'''
* '''Brainlab'''
* '''Acoustic Med'''

If your company would like to sponsor the workshop, please send an email to tkapur at bwh.harvard.edu for additional information.

== Hotel Logistics ==

'''Date'''<nowiki>: October 19-20 (Thursday-Friday), 2006. </nowiki>

'''Location/Hotel'''<nowiki>: The </nowiki>[http://rockvillehotel.com/ Doubletree Hotel & Executive Meeting Center], 1750 Rockville Pike, Rockville, Maryland 20852. Phone number: +1 (301) 468-1100. Room rates for the meeting were US $166/night (+ applicable taxes) for reservations made prior to September 29, 2006 12am using the group code "BRI". After that date, rates revert to the regular ($300+/nt) and we are unable to get the hotel to release additional rooms at the lower rate.

Please note that the conference hotel only has rooms blocked for October 19th night. If you are need accommodation for additional nights, a conveniently located area hotel is the Ramada Inn, 1775 Rockville Pike, Rockville, MD 20852. Phone (301) 881-2300.

== Subway Information ==

[http://www.wmata.com/metrorail/systemmap.cfm Subway Map]

* Directions from Washington Reagan International Airport (DCA) to the Doubletree Hotel:
** Take the Yellow Line to Gallery Place 
** At Gallery Place, switch to the Red Line (going toward Shady Grove) 
** Get off at Twinbrook; the Doubletree is across the street 

== Program Committee ==

Ferenc Jolesz, M.D., Brigham and Women's Hospital, is the Workshop Chair. The program committee includes:

* Kevin Cleary, Ph.D., Georgetown
* Peter Kazanzides, Ph.D, Johns Hopkins
* Keyvan Farahani, Ph.D., NIH
* Bill Lorensen, M.S, GE Global Research
* Stephen Aylward, Ph.D., UNC, Kitware Inc.
* Randy Ellis, Ph.D., Brigham and Women's Hospital
* Ron Kikinis, M.D., Brigham and Women's Hospital
* Clare Tempany, M.D., Brigham and Women's Hospital

== Organizing Committee ==

* Simon DiMaio, Ph.D., Brigham and Women's Hospital
* Noby Hata, Ph.D., Brigham and Women's Hospital
* Dan Kacher, M.S., Brigham and Women's Hospital
* Eigil Samset, Ph.D., Brigham and Women's Hospital
* Tina Kapur, Ph.D., Brigham and Women's Hospital
* William M. Wells, Ph.D, Brigham and Women's Hospital
* Marianna Jakab, M.S., Brigham and Women's Hospital
* Debbie O'Shea Begley, Brigham and Women's Hospital, Workshop Coordinator
* Katie Mastrogiacomo, Brigham and Women's Hospital, Workshop Staff

== Agenda ==

The agenda for the meeting is available here as [[Media:2006_IGT_Workshop_Agenda.pdf|PDF]] and [[Media:2006_IGT_Workshop_Agenda.doc|MS WORD]] documents.

=== Thursday, October 19, 2006 ===

* 1:00-1:10pm: [[Media:Jolesz_IGT_Workshop_Oct_2006_Intro.ppt|Welcome]] (Ferenc Jolesz, Brigham and Women's Hospital) [[Media:Photo1.jpg|Photo]]
* 1:10-1:15pm: [[2006_IGT_Workshop_Presentation_Summary_Kikinis|2006 IGT Workshop Presentation Summary Kikinis]]
* 1:15-1:20pm: [[Media:Ellis_WorkshopGoals.ppt|Goals for the Workshop]] (Randy Ellis, Brigham and Women's Hospital)
*1:20-1:40pm: [[media:Cleary_system_design_IGT_workshop_Oct_2006.ppt|IGT System Design]] (Kevin Cleary, Georgetown University)
*1:40-2:00pm: [[media:Lorensen_IGS_WS.ppt|IGT Software Design and Process]] (Bill Lorensen, GE Research)
*2:00-2:20pm: [[media:Kazanzides-SystemEngineering.pdf‎|IGT System Engineering]] (Peter Kazanzides, Johns Hopkins University)
* 2:20-2:40pm: [[Media:Ellis_WorkshopHCI.ppt|IGT User Interfaces and Human-Computer Interactions]] (Randy Ellis, Brigham and Women's Hospital)
* 2:40-3:00pm: [[Media:Peters_IGS_WS_final.ppt|Evolution of a VR-Based IGT Environment]] (Terry Peters & David Gobbi, Robarts Research Institute, University of Western Ontario)
* 3:00-3:20pm: [[Media:Pizer_radoncseg.publ.ppt|System Challenges in Image-Analysis for Radiation Therapy]] (Steve Pizer, UNC)
* 3:20-3:40pm: [[Media:Galloway_Platform_Technology_for_Multiple_IGTapplications.ppt|Platform Technology for Multiple IGT applications]] (Bob Galloway, Vanderbilt)
* 3:40-4:00pm: Coffee Break
* 4:00-5:30pm: [[2006_IGT_Workshop_Panel_Discussion#Discussion|Panel Discussion I]] Chair: Jim Duncan, Yale.
* 5:30-6:30pm: Program Committee to capture the discussions and recommendations for the session

 

=== Friday, October 20, 2006 ===

* 8:00am: Continental Breakfast
* 8:55am: Welcome back
* 9:00-9:20am: [[Media:Fichtinger-IGT-Workshop-Oct19.ppt|Successes and Challenges in Therapy Delivery]] (Gabor Fichtinger, Johns Hopkins University)
* 9:20-9:40am: [[Media:Final_IGT_Workshop_HU_Lemke.ppt|IGT Challenges and Suggestions for Center]] (Heinz Lemke, Univerity of Southern California/CARS) (see also: [[Media:Lemke_11548_2006_Editorial_IJCARS_1_3_2006_LEMKE.pdf|The Operating Room and the need for an IT infrastructure and standards]])
* 9:40-10:00am:[[Media:Hata-ncigtws.ppt|Successes and Challenges in Effectors and Scanner Control]] (Noby Hata, Brigham and Women's Hospital)
* 10:00-10:15am: [[Media:Haller-IGT2006.ppt|NIBIB Perspective on IGT Research]] (John Haller, NIH)
* 10:15-10:30am: [[Media:Clarke_NCIGT_Oct_19th2006.ppt|NCI/NIST Perspective on IGT Research]] (Larry Clarke, NIH)
* 10:30-11:00am: Break
* 11:00-11:40am: [[2006_October_IGT_Workshop_Panel_Discussion_II|Panel Discussion II]], Chair: Keyvan Farahani, NIH
* 11:40-11:50pm: [[2006_October_IGT_Workshop_Breakout_Instructions|Instructions for Breakout Groups]]
* 11:50-1:00pm: Lunch
* 1:00-2:30pm: Breakout discussions
** Breakout Session 1: [[2006_IGT_Workshop_Workflow_Breakout|Workflows for IGT]] (Moderator: Stephen Aylward)
** Breakout Session 2: [[2006_IGT_Workshop_Validation_Breakout|Validation]] (Moderator: Kirby Vosburgh)
** Breakout Session 3: [[2006_IGT_Workshop_Robot_Breakout|Interfaces to Robots]] (Moderator: Peter Kazanzides)
** Breakout Session 4: [[2006_IGT_Workshop_Tracking_Breakout|Tracking]] (Moderators: Tina Kapur, Simon DiMaio)
** Breakout Session 5: [[2006_IGT_Workshop_Radiation_Therapy_Breakout|IGT Case Study: Radiation Therapy for Prostate]] (Moderator: Clare Tempany)
* 2:30pm-2:45pm: Coffee Break
* 2:45pm-3:30pm: Plenary Session (report back from each breakout session)
* 3:30pm: Adjourn (all except Program and Organizing Committees)

 

For Program and Organizing Committee:

* 3:30-4:30pm: Data gathering and documentation planning

 

== Community Links ==

[http://studierstube.icg.tu-graz.ac.at/opentracker/ OpenTracker]

* [http://www.ncigt.org/sign/documentation/splot.html SPLOT - OpenTracker Extension]

[http://isiswiki.georgetown.edu/zivy/casResearch.html Related links contributed by Ziv Yaniv]

 

== Contact ==

For further information about the program please contact: Tina Kapur (tkapur at bwh.harvard.edu)

For further information about the registration please contact : Debbie O'Shea Begley (djo at bwh.harvard.edu)

If you would like to be added to the mailing list for the workshop, please contact: Marianna Jakab (marianna at bwh.harvard.edu)

 

== Photos ==

Here are some photos from the IGT Workshop:

{|
|[[Image:IGT_break.JPG|thumb|102px]]
|[[Image:IGT_room_view.JPG|thumb|102px]]
|[[Image:IGT_room_view_2.JPG|thumb|102px]]
|[[Image:IGT_room_view_3.JPG|thumb|102px]]
|}

 

And here are a few from the Brigham dinner:

{|
|valign="top"|[[Image:Thai_sign.JPG|thumb|102px]]
|[[Image:Thai_dinner_1.JPG|thumb|102px]]
|[[Image:Thai_dinner_2.JPG|thumb|102px]]
|}

IGT:October 2006 IGT Workshop

2007-01-22T22:05:46Z

Simond: /* Thursday, October 19, 2006 */

==Summary==

This meeting was successfully concluded with over 75 registered attendees. A summary white paper will be made available here in February 2007.

== Registration and Attendee List ==

'''Registration Fee'''<nowiki>: US $250.00 payable onsite only by check payable to "BWPO Radiology" or cash. We can not accept credit cards, or payments before the meeting. </nowiki>

'''Registration'''<nowiki>: Registration for this workshop is quite simple. To register, please follow two steps: </nowiki>

# Create an account for yourself on this wiki by clicking here [[Special:Userlogin|Special:Userlogin]]
# After creating the account, go to the [[2006_IGT_Workshop_Attendee_List|2006 IGT Workshop Attendee List]] and add your name, Institution, an email address, and the name of the breakout session you will be attending on Friday.

== Goal ==

The goal of this workshop is to bring together researchers developing Image-Guided Therapy (IGT) systems for a 2-day workshop to share their recent advances and to identify synergies in future strategy. The intent of the workshop is to foster community-based development, to share best practices in engineering such systems, to identify gaps in the engineering infrastructure available to IGT researchers, and ultimately to facilitate the transfer of technology among NIH-sponsored research centers.

In this program, we define IGT systems as the integrated devices for therapy delivery that incorporate intra-operative medical imaging, navigation, or robotics. In the lectures and breakout groups of this two-day workshop, we plan to:

# discuss system architectures currently used in IGT systems
# identify challenges in the design and implementation of IGT systems
# identify gaps in the engineering infrastructure available to IGT researchers
# identify opportunities and mechanisms for sharing low-level components and high-level architectural design patterns, and
# identify opportunities for the National Center for Image Guided Therapy (NCIGT, http://www.ncigt.org) to help address these challenges and develop an open system architecture as part of its function as a biotechnology resource for the Image-Guided Therapy community.

The workshop will concentrate on the computer science and engineering aspects of such systems, as the clinical aspects have been covered in previous NIH-related workshops. The agenda will include plenary talks that will review technical aspects of IGT as well as breakout sessions in which the participants will concentrate on issues raised by the talks.

 '''Background on this workshop'''<nowiki>: The initial idea of this workshop was developed in ad-hoc meetings with collaborators across institutions including Georgetown, Johns Hopkins, UNC, NIH, GE Global Research, Kitware Inc., and Brigham and Women's Hospital. The Program Committee welcomed and encouraged suggestions from the IGT community on the content of this workshop until mid July, 2006, when the program was finalized. </nowiki>

== Sponsors ==

We would like to gratefully acknowledge our industry sponsors whose financial support is helping us keep the registration fee low.

* '''GE Healthcare'''
* '''Siemens Corporate Research (SCR)'''
* '''Northern Digital (NDI)'''
* '''Medtronic Navigation'''
* '''Brainlab'''
* '''Acoustic Med'''

If your company would like to sponsor the workshop, please send an email to tkapur at bwh.harvard.edu for additional information.

== Hotel Logistics ==

'''Date'''<nowiki>: October 19-20 (Thursday-Friday), 2006. </nowiki>

'''Location/Hotel'''<nowiki>: The </nowiki>[http://rockvillehotel.com/ Doubletree Hotel & Executive Meeting Center], 1750 Rockville Pike, Rockville, Maryland 20852. Phone number: +1 (301) 468-1100. Room rates for the meeting were US $166/night (+ applicable taxes) for reservations made prior to September 29, 2006 12am using the group code "BRI". After that date, rates revert to the regular ($300+/nt) and we are unable to get the hotel to release additional rooms at the lower rate.

Please note that the conference hotel only has rooms blocked for October 19th night. If you are need accommodation for additional nights, a conveniently located area hotel is the Ramada Inn, 1775 Rockville Pike, Rockville, MD 20852. Phone (301) 881-2300.

== Subway Information ==

[http://www.wmata.com/metrorail/systemmap.cfm Subway Map]

* Directions from Washington Reagan International Airport (DCA) to the Doubletree Hotel:
** Take the Yellow Line to Gallery Place 
** At Gallery Place, switch to the Red Line (going toward Shady Grove) 
** Get off at Twinbrook; the Doubletree is across the street 

== Program Committee ==

Ferenc Jolesz, M.D., Brigham and Women's Hospital, is the Workshop Chair. The program committee includes:

* Kevin Cleary, Ph.D., Georgetown
* Peter Kazanzides, Ph.D, Johns Hopkins
* Keyvan Farahani, Ph.D., NIH
* Bill Lorensen, M.S, GE Global Research
* Stephen Aylward, Ph.D., UNC, Kitware Inc.
* Randy Ellis, Ph.D., Brigham and Women's Hospital
* Ron Kikinis, M.D., Brigham and Women's Hospital
* Clare Tempany, M.D., Brigham and Women's Hospital

== Organizing Committee ==

* Simon DiMaio, Ph.D., Brigham and Women's Hospital
* Noby Hata, Ph.D., Brigham and Women's Hospital
* Dan Kacher, M.S., Brigham and Women's Hospital
* Eigil Samset, Ph.D., Brigham and Women's Hospital
* Tina Kapur, Ph.D., Brigham and Women's Hospital
* William M. Wells, Ph.D, Brigham and Women's Hospital
* Marianna Jakab, M.S., Brigham and Women's Hospital
* Debbie O'Shea Begley, Brigham and Women's Hospital, Workshop Coordinator
* Katie Mastrogiacomo, Brigham and Women's Hospital, Workshop Staff

== Agenda ==

The agenda for the meeting is available here as [[Media:2006_IGT_Workshop_Agenda.pdf|PDF]] and [[Media:2006_IGT_Workshop_Agenda.doc|MS WORD]] documents.

=== Thursday, October 19, 2006 ===

* 1:00-1:10pm: [[Media:Jolesz_IGT_Workshop_Oct_2006_Intro.ppt|Welcome]] (Ferenc Jolesz, Brigham and Women's Hospital) [[Media:Photo1.jpg|Photo]]
* 1:10-1:15pm: [[2006_IGT_Workshop_Presentation_Summary_Kikinis|2006 IGT Workshop Presentation Summary Kikinis]]
* 1:15-1:20pm: [[Media:Ellis_WorkshopGoals.ppt|Goals for the Workshop]] (Randy Ellis, Brigham and Women's Hospital)
*1:20-1:40pm: [[media:Cleary_system_design_IGT_workshop_Oct_2006.ppt|IGT System Design]] (Kevin Cleary, Georgetown University)
*1:40-2:00pm: [[media:Lorensen_IGS_WS.ppt|IGT Software Design and Process]] (Bill Lorensen, GE Research)
*2:00-2:20pm: [[image:Kazanzides-SystemEngineering.pdf‎|IGT System Engineering]] (Peter Kazanzides, Johns Hopkins University)
* 2:20-2:40pm: [[Media:Ellis_WorkshopHCI.ppt|IGT User Interfaces and Human-Computer Interactions]] (Randy Ellis, Brigham and Women's Hospital)
* 2:40-3:00pm: [[Media:Peters_IGS_WS_final.ppt|Evolution of a VR-Based IGT Environment]] (Terry Peters & David Gobbi, Robarts Research Institute, University of Western Ontario)
* 3:00-3:20pm: [[Media:Pizer_radoncseg.publ.ppt|System Challenges in Image-Analysis for Radiation Therapy]] (Steve Pizer, UNC)
* 3:20-3:40pm: [[Media:Galloway_Platform_Technology_for_Multiple_IGTapplications.ppt|Platform Technology for Multiple IGT applications]] (Bob Galloway, Vanderbilt)
* 3:40-4:00pm: Coffee Break
* 4:00-5:30pm: [[2006_IGT_Workshop_Panel_Discussion#Discussion|Panel Discussion I]] Chair: Jim Duncan, Yale.
* 5:30-6:30pm: Program Committee to capture the discussions and recommendations for the session

 

=== Friday, October 20, 2006 ===

* 8:00am: Continental Breakfast
* 8:55am: Welcome back
* 9:00-9:20am: [[Media:Fichtinger-IGT-Workshop-Oct19.ppt|Successes and Challenges in Therapy Delivery]] (Gabor Fichtinger, Johns Hopkins University)
* 9:20-9:40am: [[Media:Final_IGT_Workshop_HU_Lemke.ppt|IGT Challenges and Suggestions for Center]] (Heinz Lemke, Univerity of Southern California/CARS) (see also: [[Media:Lemke_11548_2006_Editorial_IJCARS_1_3_2006_LEMKE.pdf|The Operating Room and the need for an IT infrastructure and standards]])
* 9:40-10:00am:[[Media:Hata-ncigtws.ppt|Successes and Challenges in Effectors and Scanner Control]] (Noby Hata, Brigham and Women's Hospital)
* 10:00-10:15am: [[Media:Haller-IGT2006.ppt|NIBIB Perspective on IGT Research]] (John Haller, NIH)
* 10:15-10:30am: [[Media:Clarke_NCIGT_Oct_19th2006.ppt|NCI/NIST Perspective on IGT Research]] (Larry Clarke, NIH)
* 10:30-11:00am: Break
* 11:00-11:40am: [[2006_October_IGT_Workshop_Panel_Discussion_II|Panel Discussion II]], Chair: Keyvan Farahani, NIH
* 11:40-11:50pm: [[2006_October_IGT_Workshop_Breakout_Instructions|Instructions for Breakout Groups]]
* 11:50-1:00pm: Lunch
* 1:00-2:30pm: Breakout discussions
** Breakout Session 1: [[2006_IGT_Workshop_Workflow_Breakout|Workflows for IGT]] (Moderator: Stephen Aylward)
** Breakout Session 2: [[2006_IGT_Workshop_Validation_Breakout|Validation]] (Moderator: Kirby Vosburgh)
** Breakout Session 3: [[2006_IGT_Workshop_Robot_Breakout|Interfaces to Robots]] (Moderator: Peter Kazanzides)
** Breakout Session 4: [[2006_IGT_Workshop_Tracking_Breakout|Tracking]] (Moderators: Tina Kapur, Simon DiMaio)
** Breakout Session 5: [[2006_IGT_Workshop_Radiation_Therapy_Breakout|IGT Case Study: Radiation Therapy for Prostate]] (Moderator: Clare Tempany)
* 2:30pm-2:45pm: Coffee Break
* 2:45pm-3:30pm: Plenary Session (report back from each breakout session)
* 3:30pm: Adjourn (all except Program and Organizing Committees)

 

For Program and Organizing Committee:

* 3:30-4:30pm: Data gathering and documentation planning

 

== Community Links ==

[http://studierstube.icg.tu-graz.ac.at/opentracker/ OpenTracker]

* [http://www.ncigt.org/sign/documentation/splot.html SPLOT - OpenTracker Extension]

[http://isiswiki.georgetown.edu/zivy/casResearch.html Related links contributed by Ziv Yaniv]

 

== Contact ==

For further information about the program please contact: Tina Kapur (tkapur at bwh.harvard.edu)

For further information about the registration please contact : Debbie O'Shea Begley (djo at bwh.harvard.edu)

If you would like to be added to the mailing list for the workshop, please contact: Marianna Jakab (marianna at bwh.harvard.edu)

 

== Photos ==

Here are some photos from the IGT Workshop:

{|
|[[Image:IGT_break.JPG|thumb|102px]]
|[[Image:IGT_room_view.JPG|thumb|102px]]
|[[Image:IGT_room_view_2.JPG|thumb|102px]]
|[[Image:IGT_room_view_3.JPG|thumb|102px]]
|}

 

And here are a few from the Brigham dinner:

{|
|valign="top"|[[Image:Thai_sign.JPG|thumb|102px]]
|[[Image:Thai_dinner_1.JPG|thumb|102px]]
|[[Image:Thai_dinner_2.JPG|thumb|102px]]
|}

IGT:October 2006 IGT Workshop

2007-01-22T21:59:15Z

Simond: /* Thursday, October 19, 2006 */

==Summary==

This meeting was successfully concluded with over 75 registered attendees. A summary white paper will be made available here in February 2007.

== Registration and Attendee List ==

'''Registration Fee'''<nowiki>: US $250.00 payable onsite only by check payable to "BWPO Radiology" or cash. We can not accept credit cards, or payments before the meeting. </nowiki>

'''Registration'''<nowiki>: Registration for this workshop is quite simple. To register, please follow two steps: </nowiki>

# Create an account for yourself on this wiki by clicking here [[Special:Userlogin|Special:Userlogin]]
# After creating the account, go to the [[2006_IGT_Workshop_Attendee_List|2006 IGT Workshop Attendee List]] and add your name, Institution, an email address, and the name of the breakout session you will be attending on Friday.

== Goal ==

The goal of this workshop is to bring together researchers developing Image-Guided Therapy (IGT) systems for a 2-day workshop to share their recent advances and to identify synergies in future strategy. The intent of the workshop is to foster community-based development, to share best practices in engineering such systems, to identify gaps in the engineering infrastructure available to IGT researchers, and ultimately to facilitate the transfer of technology among NIH-sponsored research centers.

In this program, we define IGT systems as the integrated devices for therapy delivery that incorporate intra-operative medical imaging, navigation, or robotics. In the lectures and breakout groups of this two-day workshop, we plan to:

# discuss system architectures currently used in IGT systems
# identify challenges in the design and implementation of IGT systems
# identify gaps in the engineering infrastructure available to IGT researchers
# identify opportunities and mechanisms for sharing low-level components and high-level architectural design patterns, and
# identify opportunities for the National Center for Image Guided Therapy (NCIGT, http://www.ncigt.org) to help address these challenges and develop an open system architecture as part of its function as a biotechnology resource for the Image-Guided Therapy community.

The workshop will concentrate on the computer science and engineering aspects of such systems, as the clinical aspects have been covered in previous NIH-related workshops. The agenda will include plenary talks that will review technical aspects of IGT as well as breakout sessions in which the participants will concentrate on issues raised by the talks.

 '''Background on this workshop'''<nowiki>: The initial idea of this workshop was developed in ad-hoc meetings with collaborators across institutions including Georgetown, Johns Hopkins, UNC, NIH, GE Global Research, Kitware Inc., and Brigham and Women's Hospital. The Program Committee welcomed and encouraged suggestions from the IGT community on the content of this workshop until mid July, 2006, when the program was finalized. </nowiki>

== Sponsors ==

We would like to gratefully acknowledge our industry sponsors whose financial support is helping us keep the registration fee low.

* '''GE Healthcare'''
* '''Siemens Corporate Research (SCR)'''
* '''Northern Digital (NDI)'''
* '''Medtronic Navigation'''
* '''Brainlab'''
* '''Acoustic Med'''

If your company would like to sponsor the workshop, please send an email to tkapur at bwh.harvard.edu for additional information.

== Hotel Logistics ==

'''Date'''<nowiki>: October 19-20 (Thursday-Friday), 2006. </nowiki>

'''Location/Hotel'''<nowiki>: The </nowiki>[http://rockvillehotel.com/ Doubletree Hotel & Executive Meeting Center], 1750 Rockville Pike, Rockville, Maryland 20852. Phone number: +1 (301) 468-1100. Room rates for the meeting were US $166/night (+ applicable taxes) for reservations made prior to September 29, 2006 12am using the group code "BRI". After that date, rates revert to the regular ($300+/nt) and we are unable to get the hotel to release additional rooms at the lower rate.

Please note that the conference hotel only has rooms blocked for October 19th night. If you are need accommodation for additional nights, a conveniently located area hotel is the Ramada Inn, 1775 Rockville Pike, Rockville, MD 20852. Phone (301) 881-2300.

== Subway Information ==

[http://www.wmata.com/metrorail/systemmap.cfm Subway Map]

* Directions from Washington Reagan International Airport (DCA) to the Doubletree Hotel:
** Take the Yellow Line to Gallery Place 
** At Gallery Place, switch to the Red Line (going toward Shady Grove) 
** Get off at Twinbrook; the Doubletree is across the street 

== Program Committee ==

Ferenc Jolesz, M.D., Brigham and Women's Hospital, is the Workshop Chair. The program committee includes:

* Kevin Cleary, Ph.D., Georgetown
* Peter Kazanzides, Ph.D, Johns Hopkins
* Keyvan Farahani, Ph.D., NIH
* Bill Lorensen, M.S, GE Global Research
* Stephen Aylward, Ph.D., UNC, Kitware Inc.
* Randy Ellis, Ph.D., Brigham and Women's Hospital
* Ron Kikinis, M.D., Brigham and Women's Hospital
* Clare Tempany, M.D., Brigham and Women's Hospital

== Organizing Committee ==

* Simon DiMaio, Ph.D., Brigham and Women's Hospital
* Noby Hata, Ph.D., Brigham and Women's Hospital
* Dan Kacher, M.S., Brigham and Women's Hospital
* Eigil Samset, Ph.D., Brigham and Women's Hospital
* Tina Kapur, Ph.D., Brigham and Women's Hospital
* William M. Wells, Ph.D, Brigham and Women's Hospital
* Marianna Jakab, M.S., Brigham and Women's Hospital
* Debbie O'Shea Begley, Brigham and Women's Hospital, Workshop Coordinator
* Katie Mastrogiacomo, Brigham and Women's Hospital, Workshop Staff

== Agenda ==

The agenda for the meeting is available here as [[Media:2006_IGT_Workshop_Agenda.pdf|PDF]] and [[Media:2006_IGT_Workshop_Agenda.doc|MS WORD]] documents.

=== Thursday, October 19, 2006 ===

* 1:00-1:10pm: [[Media:Jolesz_IGT_Workshop_Oct_2006_Intro.ppt|Welcome]] (Ferenc Jolesz, Brigham and Women's Hospital) [[Media:Photo1.jpg|Photo]]
* 1:10-1:15pm: [[2006_IGT_Workshop_Presentation_Summary_Kikinis|2006 IGT Workshop Presentation Summary Kikinis]]
* 1:15-1:20pm: [[Media:Ellis_WorkshopGoals.ppt|Goals for the Workshop]] (Randy Ellis, Brigham and Women's Hospital)
*1:20-1:40pm: [[media:Cleary_system_design_IGT_workshop_Oct_2006.ppt|IGT System Design]] (Kevin Cleary, Georgetown University)
*1:40-2:00pm: [[media:Lorensen_IGS_WS.ppt|IGT Software Design and Process]] (Bill Lorensen, GE Research)
*2:00-2:20pm: [[image:Kazanzides-SystemEngineering.ppt‎|IGT System Engineering]] (Peter Kazanzides, Johns Hopkins University)
* 2:20-2:40pm: [[Media:Ellis_WorkshopHCI.ppt|IGT User Interfaces and Human-Computer Interactions]] (Randy Ellis, Brigham and Women's Hospital)
* 2:40-3:00pm: [[Media:Peters_IGS_WS_final.ppt|Evolution of a VR-Based IGT Environment]] (Terry Peters & David Gobbi, Robarts Research Institute, University of Western Ontario)
* 3:00-3:20pm: [[Media:Pizer_radoncseg.publ.ppt|System Challenges in Image-Analysis for Radiation Therapy]] (Steve Pizer, UNC)
* 3:20-3:40pm: [[Media:Galloway_Platform_Technology_for_Multiple_IGTapplications.ppt|Platform Technology for Multiple IGT applications]] (Bob Galloway, Vanderbilt)
* 3:40-4:00pm: Coffee Break
* 4:00-5:30pm: [[2006_IGT_Workshop_Panel_Discussion#Discussion|Panel Discussion I]] Chair: Jim Duncan, Yale.
* 5:30-6:30pm: Program Committee to capture the discussions and recommendations for the session

 

=== Friday, October 20, 2006 ===

* 8:00am: Continental Breakfast
* 8:55am: Welcome back
* 9:00-9:20am: [[Media:Fichtinger-IGT-Workshop-Oct19.ppt|Successes and Challenges in Therapy Delivery]] (Gabor Fichtinger, Johns Hopkins University)
* 9:20-9:40am: [[Media:Final_IGT_Workshop_HU_Lemke.ppt|IGT Challenges and Suggestions for Center]] (Heinz Lemke, Univerity of Southern California/CARS) (see also: [[Media:Lemke_11548_2006_Editorial_IJCARS_1_3_2006_LEMKE.pdf|The Operating Room and the need for an IT infrastructure and standards]])
* 9:40-10:00am:[[Media:Hata-ncigtws.ppt|Successes and Challenges in Effectors and Scanner Control]] (Noby Hata, Brigham and Women's Hospital)
* 10:00-10:15am: [[Media:Haller-IGT2006.ppt|NIBIB Perspective on IGT Research]] (John Haller, NIH)
* 10:15-10:30am: [[Media:Clarke_NCIGT_Oct_19th2006.ppt|NCI/NIST Perspective on IGT Research]] (Larry Clarke, NIH)
* 10:30-11:00am: Break
* 11:00-11:40am: [[2006_October_IGT_Workshop_Panel_Discussion_II|Panel Discussion II]], Chair: Keyvan Farahani, NIH
* 11:40-11:50pm: [[2006_October_IGT_Workshop_Breakout_Instructions|Instructions for Breakout Groups]]
* 11:50-1:00pm: Lunch
* 1:00-2:30pm: Breakout discussions
** Breakout Session 1: [[2006_IGT_Workshop_Workflow_Breakout|Workflows for IGT]] (Moderator: Stephen Aylward)
** Breakout Session 2: [[2006_IGT_Workshop_Validation_Breakout|Validation]] (Moderator: Kirby Vosburgh)
** Breakout Session 3: [[2006_IGT_Workshop_Robot_Breakout|Interfaces to Robots]] (Moderator: Peter Kazanzides)
** Breakout Session 4: [[2006_IGT_Workshop_Tracking_Breakout|Tracking]] (Moderators: Tina Kapur, Simon DiMaio)
** Breakout Session 5: [[2006_IGT_Workshop_Radiation_Therapy_Breakout|IGT Case Study: Radiation Therapy for Prostate]] (Moderator: Clare Tempany)
* 2:30pm-2:45pm: Coffee Break
* 2:45pm-3:30pm: Plenary Session (report back from each breakout session)
* 3:30pm: Adjourn (all except Program and Organizing Committees)

 

For Program and Organizing Committee:

* 3:30-4:30pm: Data gathering and documentation planning

 

== Community Links ==

[http://studierstube.icg.tu-graz.ac.at/opentracker/ OpenTracker]

* [http://www.ncigt.org/sign/documentation/splot.html SPLOT - OpenTracker Extension]

[http://isiswiki.georgetown.edu/zivy/casResearch.html Related links contributed by Ziv Yaniv]

 

== Contact ==

For further information about the program please contact: Tina Kapur (tkapur at bwh.harvard.edu)

For further information about the registration please contact : Debbie O'Shea Begley (djo at bwh.harvard.edu)

If you would like to be added to the mailing list for the workshop, please contact: Marianna Jakab (marianna at bwh.harvard.edu)

 

== Photos ==

Here are some photos from the IGT Workshop:

{|
|[[Image:IGT_break.JPG|thumb|102px]]
|[[Image:IGT_room_view.JPG|thumb|102px]]
|[[Image:IGT_room_view_2.JPG|thumb|102px]]
|[[Image:IGT_room_view_3.JPG|thumb|102px]]
|}

 

And here are a few from the Brigham dinner:

{|
|valign="top"|[[Image:Thai_sign.JPG|thumb|102px]]
|[[Image:Thai_dinner_1.JPG|thumb|102px]]
|[[Image:Thai_dinner_2.JPG|thumb|102px]]
|}

IGT:October 2006 IGT Workshop

2007-01-22T21:58:35Z

Simond: /* Thursday, October 19, 2006 */

==Summary==

This meeting was successfully concluded with over 75 registered attendees. A summary white paper will be made available here in February 2007.

== Registration and Attendee List ==

'''Registration Fee'''<nowiki>: US $250.00 payable onsite only by check payable to "BWPO Radiology" or cash. We can not accept credit cards, or payments before the meeting. </nowiki>

'''Registration'''<nowiki>: Registration for this workshop is quite simple. To register, please follow two steps: </nowiki>

# Create an account for yourself on this wiki by clicking here [[Special:Userlogin|Special:Userlogin]]
# After creating the account, go to the [[2006_IGT_Workshop_Attendee_List|2006 IGT Workshop Attendee List]] and add your name, Institution, an email address, and the name of the breakout session you will be attending on Friday.

== Goal ==

The goal of this workshop is to bring together researchers developing Image-Guided Therapy (IGT) systems for a 2-day workshop to share their recent advances and to identify synergies in future strategy. The intent of the workshop is to foster community-based development, to share best practices in engineering such systems, to identify gaps in the engineering infrastructure available to IGT researchers, and ultimately to facilitate the transfer of technology among NIH-sponsored research centers.

In this program, we define IGT systems as the integrated devices for therapy delivery that incorporate intra-operative medical imaging, navigation, or robotics. In the lectures and breakout groups of this two-day workshop, we plan to:

# discuss system architectures currently used in IGT systems
# identify challenges in the design and implementation of IGT systems
# identify gaps in the engineering infrastructure available to IGT researchers
# identify opportunities and mechanisms for sharing low-level components and high-level architectural design patterns, and
# identify opportunities for the National Center for Image Guided Therapy (NCIGT, http://www.ncigt.org) to help address these challenges and develop an open system architecture as part of its function as a biotechnology resource for the Image-Guided Therapy community.

The workshop will concentrate on the computer science and engineering aspects of such systems, as the clinical aspects have been covered in previous NIH-related workshops. The agenda will include plenary talks that will review technical aspects of IGT as well as breakout sessions in which the participants will concentrate on issues raised by the talks.

 '''Background on this workshop'''<nowiki>: The initial idea of this workshop was developed in ad-hoc meetings with collaborators across institutions including Georgetown, Johns Hopkins, UNC, NIH, GE Global Research, Kitware Inc., and Brigham and Women's Hospital. The Program Committee welcomed and encouraged suggestions from the IGT community on the content of this workshop until mid July, 2006, when the program was finalized. </nowiki>

== Sponsors ==

We would like to gratefully acknowledge our industry sponsors whose financial support is helping us keep the registration fee low.

* '''GE Healthcare'''
* '''Siemens Corporate Research (SCR)'''
* '''Northern Digital (NDI)'''
* '''Medtronic Navigation'''
* '''Brainlab'''
* '''Acoustic Med'''

If your company would like to sponsor the workshop, please send an email to tkapur at bwh.harvard.edu for additional information.

== Hotel Logistics ==

'''Date'''<nowiki>: October 19-20 (Thursday-Friday), 2006. </nowiki>

'''Location/Hotel'''<nowiki>: The </nowiki>[http://rockvillehotel.com/ Doubletree Hotel & Executive Meeting Center], 1750 Rockville Pike, Rockville, Maryland 20852. Phone number: +1 (301) 468-1100. Room rates for the meeting were US $166/night (+ applicable taxes) for reservations made prior to September 29, 2006 12am using the group code "BRI". After that date, rates revert to the regular ($300+/nt) and we are unable to get the hotel to release additional rooms at the lower rate.

Please note that the conference hotel only has rooms blocked for October 19th night. If you are need accommodation for additional nights, a conveniently located area hotel is the Ramada Inn, 1775 Rockville Pike, Rockville, MD 20852. Phone (301) 881-2300.

== Subway Information ==

[http://www.wmata.com/metrorail/systemmap.cfm Subway Map]

* Directions from Washington Reagan International Airport (DCA) to the Doubletree Hotel:
** Take the Yellow Line to Gallery Place 
** At Gallery Place, switch to the Red Line (going toward Shady Grove) 
** Get off at Twinbrook; the Doubletree is across the street 

== Program Committee ==

Ferenc Jolesz, M.D., Brigham and Women's Hospital, is the Workshop Chair. The program committee includes:

* Kevin Cleary, Ph.D., Georgetown
* Peter Kazanzides, Ph.D, Johns Hopkins
* Keyvan Farahani, Ph.D., NIH
* Bill Lorensen, M.S, GE Global Research
* Stephen Aylward, Ph.D., UNC, Kitware Inc.
* Randy Ellis, Ph.D., Brigham and Women's Hospital
* Ron Kikinis, M.D., Brigham and Women's Hospital
* Clare Tempany, M.D., Brigham and Women's Hospital

== Organizing Committee ==

* Simon DiMaio, Ph.D., Brigham and Women's Hospital
* Noby Hata, Ph.D., Brigham and Women's Hospital
* Dan Kacher, M.S., Brigham and Women's Hospital
* Eigil Samset, Ph.D., Brigham and Women's Hospital
* Tina Kapur, Ph.D., Brigham and Women's Hospital
* William M. Wells, Ph.D, Brigham and Women's Hospital
* Marianna Jakab, M.S., Brigham and Women's Hospital
* Debbie O'Shea Begley, Brigham and Women's Hospital, Workshop Coordinator
* Katie Mastrogiacomo, Brigham and Women's Hospital, Workshop Staff

== Agenda ==

The agenda for the meeting is available here as [[Media:2006_IGT_Workshop_Agenda.pdf|PDF]] and [[Media:2006_IGT_Workshop_Agenda.doc|MS WORD]] documents.

=== Thursday, October 19, 2006 ===

* 1:00-1:10pm: [[Media:Jolesz_IGT_Workshop_Oct_2006_Intro.ppt|Welcome]] (Ferenc Jolesz, Brigham and Women's Hospital) [[Media:Photo1.jpg|Photo]]
* 1:10-1:15pm: [[2006_IGT_Workshop_Presentation_Summary_Kikinis|2006 IGT Workshop Presentation Summary Kikinis]]
* 1:15-1:20pm: [[Media:Ellis_WorkshopGoals.ppt|Goals for the Workshop]] (Randy Ellis, Brigham and Women's Hospital)
*1:20-1:40pm: [[media:Cleary_system_design_IGT_workshop_Oct_2006.ppt|IGT System Design]] (Kevin Cleary, Georgetown University)
*1:40-2:00pm: [[media:Lorensen_IGS_WS.ppt|IGT Software Design and Process]] (Bill Lorensen, GE Research)
*2:00-2:20pm: [[media:Kazanzides_SystemEngineering.ppt‎|IGT System Engineering]] (Peter Kazanzides, Johns Hopkins University)
* 2:20-2:40pm: [[Media:Ellis_WorkshopHCI.ppt|IGT User Interfaces and Human-Computer Interactions]] (Randy Ellis, Brigham and Women's Hospital)
* 2:40-3:00pm: [[Media:Peters_IGS_WS_final.ppt|Evolution of a VR-Based IGT Environment]] (Terry Peters & David Gobbi, Robarts Research Institute, University of Western Ontario)
* 3:00-3:20pm: [[Media:Pizer_radoncseg.publ.ppt|System Challenges in Image-Analysis for Radiation Therapy]] (Steve Pizer, UNC)
* 3:20-3:40pm: [[Media:Galloway_Platform_Technology_for_Multiple_IGTapplications.ppt|Platform Technology for Multiple IGT applications]] (Bob Galloway, Vanderbilt)
* 3:40-4:00pm: Coffee Break
* 4:00-5:30pm: [[2006_IGT_Workshop_Panel_Discussion#Discussion|Panel Discussion I]] Chair: Jim Duncan, Yale.
* 5:30-6:30pm: Program Committee to capture the discussions and recommendations for the session

 

=== Friday, October 20, 2006 ===

* 8:00am: Continental Breakfast
* 8:55am: Welcome back
* 9:00-9:20am: [[Media:Fichtinger-IGT-Workshop-Oct19.ppt|Successes and Challenges in Therapy Delivery]] (Gabor Fichtinger, Johns Hopkins University)
* 9:20-9:40am: [[Media:Final_IGT_Workshop_HU_Lemke.ppt|IGT Challenges and Suggestions for Center]] (Heinz Lemke, Univerity of Southern California/CARS) (see also: [[Media:Lemke_11548_2006_Editorial_IJCARS_1_3_2006_LEMKE.pdf|The Operating Room and the need for an IT infrastructure and standards]])
* 9:40-10:00am:[[Media:Hata-ncigtws.ppt|Successes and Challenges in Effectors and Scanner Control]] (Noby Hata, Brigham and Women's Hospital)
* 10:00-10:15am: [[Media:Haller-IGT2006.ppt|NIBIB Perspective on IGT Research]] (John Haller, NIH)
* 10:15-10:30am: [[Media:Clarke_NCIGT_Oct_19th2006.ppt|NCI/NIST Perspective on IGT Research]] (Larry Clarke, NIH)
* 10:30-11:00am: Break
* 11:00-11:40am: [[2006_October_IGT_Workshop_Panel_Discussion_II|Panel Discussion II]], Chair: Keyvan Farahani, NIH
* 11:40-11:50pm: [[2006_October_IGT_Workshop_Breakout_Instructions|Instructions for Breakout Groups]]
* 11:50-1:00pm: Lunch
* 1:00-2:30pm: Breakout discussions
** Breakout Session 1: [[2006_IGT_Workshop_Workflow_Breakout|Workflows for IGT]] (Moderator: Stephen Aylward)
** Breakout Session 2: [[2006_IGT_Workshop_Validation_Breakout|Validation]] (Moderator: Kirby Vosburgh)
** Breakout Session 3: [[2006_IGT_Workshop_Robot_Breakout|Interfaces to Robots]] (Moderator: Peter Kazanzides)
** Breakout Session 4: [[2006_IGT_Workshop_Tracking_Breakout|Tracking]] (Moderators: Tina Kapur, Simon DiMaio)
** Breakout Session 5: [[2006_IGT_Workshop_Radiation_Therapy_Breakout|IGT Case Study: Radiation Therapy for Prostate]] (Moderator: Clare Tempany)
* 2:30pm-2:45pm: Coffee Break
* 2:45pm-3:30pm: Plenary Session (report back from each breakout session)
* 3:30pm: Adjourn (all except Program and Organizing Committees)

 

For Program and Organizing Committee:

* 3:30-4:30pm: Data gathering and documentation planning

 

== Community Links ==

[http://studierstube.icg.tu-graz.ac.at/opentracker/ OpenTracker]

* [http://www.ncigt.org/sign/documentation/splot.html SPLOT - OpenTracker Extension]

[http://isiswiki.georgetown.edu/zivy/casResearch.html Related links contributed by Ziv Yaniv]

 

== Contact ==

For further information about the program please contact: Tina Kapur (tkapur at bwh.harvard.edu)

For further information about the registration please contact : Debbie O'Shea Begley (djo at bwh.harvard.edu)

If you would like to be added to the mailing list for the workshop, please contact: Marianna Jakab (marianna at bwh.harvard.edu)

 

== Photos ==

Here are some photos from the IGT Workshop:

{|
|[[Image:IGT_break.JPG|thumb|102px]]
|[[Image:IGT_room_view.JPG|thumb|102px]]
|[[Image:IGT_room_view_2.JPG|thumb|102px]]
|[[Image:IGT_room_view_3.JPG|thumb|102px]]
|}

 

And here are a few from the Brigham dinner:

{|
|valign="top"|[[Image:Thai_sign.JPG|thumb|102px]]
|[[Image:Thai_dinner_1.JPG|thumb|102px]]
|[[Image:Thai_dinner_2.JPG|thumb|102px]]
|}

File:2007 Project Half Week InterventionalImaging.ppt

2007-01-10T07:18:36Z

Simond:

2007 Project Half Week

2007-01-10T07:17:33Z

Simond: /* External Collaborations */

Back to [[AHM_2007|AHM_2007]]

== Results ==
Results of this event will be summarized here after it is completed.

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# Scripts to run and visualize [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
# Data assimilation for NAMIC (Stephen) [[Media:2007_Project_Half_Week_MIDAS.ppt | 4 block PPT Jan 2007]]
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration (Stephen, Jim, Ross)]] [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
## Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration.ppt| 4-block PPT Jan 2007]]
#Genus Zero Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]
#Thickness Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]
#Shape Analysis of Caudate paper (Jim, Martin, Marc, Sylvain, Martha), [[Media:2007_Project_Half_Week_Caudate_Paper.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]
#ITK Probabilistic/Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT)

===NA-MIC Kit===
#Slicer3 Infrastructure Projects
##'''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) [[Media:2007 Programming Half Week SlicerArch.ppt | 4-block ppt]]
##'''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4-block ppt]]
##'''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
##'''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
###See [[Slicer3:UIEngineering|Slicer3:UIEngineering]]
##'''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
###[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI]
###[[Slicer3:DTMRI|Tractography]] '''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
###[[Slicer3:Editor|Editor]] '''Steve''' [[Media:2007_Programming_Half_Week_Editor.ppt | 4-block ppt]]
###[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''
###[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]] '''Haiying'''
###[[Slicer3:Slicer_Daemon|Slicer Daemon Interface (for unu, matlab)]] '''Steve Pieper''' (merged with Katharina Quintus's project using Slicer Daemon)
##'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)
##Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[media:2007 AHM Programming Half Week Slicer3 Launch.ppt | 4-block PPT]]
##'''[[Slicer3:Pipeline_Integration|Pipeline Integration]]''' ('''Jags''')
##'''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Neil''', Bill, Jim) [[Image:2007_Project_Half_Week_GridExecution.ppt]]
##'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')
#Malab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]
#Model Hierarchies (Alex, Lauren, Kilian, Brad, Ron) -- generalize concepts from DTI and EM group nodes to support atlas hierachies like in slicer2, [[Media:2007_Programming_Half_Week_HierModel.ppt| 4-block PPT Jan 2007]]

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT Jan 2007]]
#Developing IGT workflow for Slicer3 (Simon DiMaio, Haiying Liu, Noby Hata, Stephen Aylward) [[IGT|IGT Project page in NA-MIC wiki]] ([[Media:2007_Project_Half_Week_InterventionalImaging.ppt|4 block PPT, Interventional Imaging]])
#Radiology Workstation Module for Slicer3 (Pat, Steve)
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]]
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]]
##Voxel meshing as an execuation module in Slicer3 [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Mesh Quality Visualization Development [[Media:Mesh_Quality_Visualization.ppt|Mapped Quality 4 block PPT Jan 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Bounding Box Projection Meshing [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
##Tetrahedral Mesh Generation Tools in VTK [[Media:Tetmesh_VTK_Tools.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure)[[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | Alcohol Exposure 4 block PPT Jan 2007]] (Kilian Pohl, Chris Wyatt)

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

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

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# 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]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## 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. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# 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]].

2007 Project Half Week

2007-01-10T06:47:02Z

Simond: /* External Collaborations */

Back to [[AHM_2007|AHM_2007]]

== Results ==
Results of this event will be summarized here after it is completed.

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# Scripts to run and visualize [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
# Data assimilation for NAMIC (Stephen) [[Media:2007_Project_Half_Week_MIDAS.ppt | 4 block PPT Jan 2007]]
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration (Stephen, Jim, Ross)]] [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
## Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration.ppt| 4-block PPT Jan 2007]]
#Genus Zero Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]
#Thickness Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]
#Shape Analysis of Caudate paper (Jim, Martin, Marc, Sylvain, Martha), [[Media:2007_Project_Half_Week_Caudate_Paper.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]
#ITK Probabilistic/Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT)

===NA-MIC Kit===
#Slicer3 Infrastructure Projects
##'''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) [[Media:2007 Programming Half Week SlicerArch.ppt | 4-block ppt]]
##'''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4-block ppt]]
##'''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
##'''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
###See [[Slicer3:UIEngineering|Slicer3:UIEngineering]]
##'''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
###[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI]
###[[Slicer3:DTMRI|Tractography]] '''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
###[[Slicer3:Editor|Editor]] '''Steve''' [[Media:2007_Programming_Half_Week_Editor.ppt | 4-block ppt]]
###[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''
###[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]] '''Haiying'''
###[[Slicer3:Slicer_Daemon|Slicer Daemon Interface (for unu, matlab)]] '''Steve Pieper''' (merged with Katharina Quintus's project using Slicer Daemon)
##'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)
##Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[media:2007 AHM Programming Half Week Slicer3 Launch.ppt | 4-block PPT]]
##'''[[Slicer3:Pipeline_Integration|Pipeline Integration]]''' ('''Jags''')
##'''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Neil''', Bill, Jim) [[Image:2007_Project_Half_Week_GridExecution.ppt]]
##'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')
#Malab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]
#Model Hierarchies (Alex, Lauren, Kilian, Brad, Ron) -- generalize concepts from DTI and EM group nodes to support atlas hierachies like in slicer2.

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT Jan 2007]]
#Developing IGT workflow for Slicer3 (Simon DiMaio, Haiying Liu, Noby Hata, Stephen Aylward) [[IGT|IGT Project page in NA-MIC wiki]] ([[Media:2007_Project_Half_Week_RealTimeImageStreaming.ppt|4 block PPT, Sierra and DiMaio]])
#Radiology Workstation Module for Slicer3 (Pat, Steve)
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]]
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]]
##Voxel meshing as an execuation module in Slicer3 [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Mesh Quality Visualization Development [[Media:Mesh_Quality_Visualization.ppt|Mapped Quality 4 block PPT Jan 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Bounding Box Projection Meshing [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
##Tetrahedral Mesh Generation Tools in VTK [[Media:Tetmesh_VTK_Tools.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure)[[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | Alcohol Exposure 4 block PPT Jan 2007]] (Kilian Pohl, Chris Wyatt)

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

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

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# 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]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## 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. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# 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]].

IGT-AHM2007-DiMaio-Sierra

2007-01-09T01:50:56Z

Simond:

== Objectives ==

* Gain understanding of Slicer3 architecture.
* Develop a simple demonstration module for Interventional Image Streaming (IIS).
 

== Interventional Image Streaming ==

* Communication between IIS module and Opentracker source
** opentracker and SPLOT built
** Slicer3 with Opentracker 2.0 to be built
* Create "coder" and "decoder" SPLOT transforms for spatio-temporal image compression of a sequence of image frames
* Update image frames in Slicer window. Demonstrate image stream from OT File Source.
* Move IIS module to IGT library? (maybe after AHM)

IGT-Tutorials

2007-01-09T01:41:35Z

Simond:

[[Image:Slicer3-IGT-Architecture.png|300px|thumb]]

'''This page contains materials for IGT application development and tutorial.'''

* [[Media:Igt-tutorial-updated.ppt| Plastic Skull Tutorial]]
* [[Media:Slicer-IGT.zip| Slicer-IGT]] (including Slicer2.6 for IGT, SPLOT server and skull CT scan)
* [[Install Fedora Core 6 on Dell Laptop Inspiron 1501 | Install Fedora Core 6 on Dell Laptop Inspiron 1501]]
* [[Build Slicer3 on Dell Laptop Inspiron 1501 (Fedora Core 6) | Build Slicer3 on Dell Laptop Inspiron 1501 (Fedora Core 6)]]
* [[Build and Run SPLOT on Dell Laptop Inspiron 1501 (Fedora Core 6) | Build and Run SPLOT on Dell Laptop Inspiron 1501 (Fedora Core 6)]]

*[[AHM 2007 Logistics|AHM_2007_Logistics]]
* AHM 2007 Projects
The objective of our attending AHM 2007 is to present our work with Slicer 3 and solicit support and contribution from the developer community. Each one of us present example project based on Haying's preliminary implementation.
** [[IGT-AHM2007-DiMaio-Sierra]]
** [[IGT-AHM2007-Liu]]
** [[IGT-AHM2007-Hata]]

AHM 2007:Slicer3 Developer Feedback

2007-01-06T05:32:19Z

Simond: /* Feedback */

Back to [[AHM_2007#Wednesday.2C_Jan_10_2007:Project_Activities]]

=Topics for this session:=

* Information to the developer community about how these projects have approached developing their code for slicer3 (what's the architecture of their modules)
* Feedback to the base developers about what was easy or hard in the code writing
* What would they like to see in the slicer3 base and/or in VTK, ITK, KKWidgets, etc to make the module development more effective

=DTI=
==DTI Module: Raul San Jose==

==Tractography Module: [http://www.na-mic.org/Wiki/index.php/User:Lauren Lauren O'Donnell]==

===Module Architecture ===
* Tractography is represented as a vtkMRMLFiberBundleNode. Display parameters are stored in a vtkMRMLFiberBundleDisplayNode, and storage (load/save) handled by vtkMRMLFiberBundleStorageNode. Basic operations of adding new fiber bundles, etc. are in vtkMRMLFiberBundleLogic.
* vtkMRMLFiberBundleDisplayLogic is needed to create "hidden" slicer models that will be rendered in the MRML scene. Otherwise base classes would have to be heavily edited to handle tractography display using the display node.
* There will be several slicer module units to handle tractography. The division will be by Load/Save/Display, Editing (to manually add, select, delete, or to use ROI selection), Seeding, etc.
* Initial work is on the Load/Save/Display and the entire MRML infrastructure.

===Feedback on Slicer3 ===
* When adding a new module and a new datatype, it is difficult to find the places in Base code that must be edited.
* It is also difficult to understand how the MRML callback happens, and how to set a new one up. It would be great to have a simple overview on the observers somewhere (or even the SVN web for easier code navigation).
* If a vtkMRMLNode inherits from another one used in slicer (for example mine inherits from the modelNode currently) then the subclass will show up on all of the superclass menus. This is because the vtk "IsA" function is used rather than a direct match. I believe this is feature that is not desired.

===What I would like in Slicer3 base...===
* More documentation, comments, etc.

=EM=

=IGT=

Noby Hata, Haying Liu, Simon DiMaio, Raimundo Sierra
==Hisotory of our involvement==
*Summer 2006: Haying Liu joined the core development team and implmented '''MRAblation module''' from the Slicer 2.6. There he
**learned the architecture of Slicer 3.
**get familiar with KWWidgits

*Fall 2006: Haying Liu implemented IGTDemo* classes. There he
** contributed vtkIGTDemoLogic and vtkIGTDemoGui in the Base.
** Modiy CMake to enable link external library opentracker

**December 2006
**Two additional members joined IGT-Slier3 task force
***Simon DiMaio representing prostate robot project [[http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=7070178&p_grant_num=1R01CA111288-01A1&p_query=&ticket=29242393&p_audit_session_id=195929678&p_keywords=| PI Tempany1R01CA111288]]
***Raimundo Sierra representing Neuroendoscope project [[http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=7126732&p_grant_num=5U41RR019703-02&p_query=&ticket=29242406&p_audit_session_id=195929678&p_keywords=| PI Jolesz 5U41RR019703]]

**January 4th, 2007, at 1249 Boylston
Implementation strategy for IGT-Slicer is discussed and preliminary design proposed (by Hata and Liu)
[[Image:Slicer3-IGT-Architecture.png|200px|thumb]]

==Our timeline==
**IGT tutorial demo on alpha (done)
**IGT tutorial demo on beta (during AHM week by Liu)
**Neurosurgical navigation with GE Nav (spring to summer)
**Building with IGSTK (during AHM week, by Hata)
**Neurosurgical navigationi with JHU robot (by March)
**Integration to MR/T (fall)

==Feedback==
*genutiltest.tcl is great!
*Request to create account for SVN has not been returned from Kitware. Cannot contribute codes to SVN tree.
*Guideline for creating library and modules would be helpful for those joining Slicer community. Template (blank) code may be helpful.
*Don't understand what "NA-MIC sandbox" means...
*Application-specific customization and streamlining of the GUI will be important for IGT applications. To what extent is this possible?
*Performance bounds are important to understand for IGT applications. Can we talk about determinism and performance as Slicer scales?