NAMIC Wiki - User contributions [en]

File:Programming Week RS Slide6.JPG

2007-06-29T01:27:13Z

Rsierra:

Projects/Slicer3/2007 Project Week Display Optimization

2007-06-29T01:26:55Z

Rsierra:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|}

__NOTOC__
===Key Investigators===
* SPL: Raimundo Sierra, David Gobbi, Steve Pieper

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Improving the performance of slicer display

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Approach, Plan</h1>
# doing the resample to a 'native' size for the input volume and then upsampling to screen size still sounds best.
# using a vtkImageActor in the vtkSlicerSliceViewer (instead of the current vtkImageMapper and vtkActor2D) is likely to be faster, and can do the upsample needed in step (1),
# using a vtkImageActor for the slice model in the vtkSlicerViewer will bypass the power-of-2 resampling in vtkTexture that gives the artifacts I hate
# David thinks we should be able to use the existing functions of vtkImageReslice to get the background mask. He didn't thing having a two-output filter was a good idea based on his experience with the way the vtk pipeline executes.

</div>

<div style="width: 40%; float: left;">
<h1>Progress</h1>
# Implemented filter with aditional output, significantly faster rendering of slices
# Integrated building of alpha mask into one filter in form of a derived class from vtkReslice -> avoids multiple iterations through dataset
# TODO: integrate map to color and map to window level
[[Image:Programming_Week_RS_Slide4.JPG|thumb|240px|Previous rendering pipeline]]
[[Image:Programming_Week_RS_Slide6.JPG|thumb|240px|Now]]
</div>
<br style="clear: both;" />
</div>

===References===

==Additional Information==
[[Media:Slicer_Rendering.ppt | Slides with diagrams about the slicer rendering pipeline]]

Projects/Slicer3/2007 Project Week Display Optimization

2007-06-29T01:25:12Z

Rsierra:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|}

__NOTOC__
===Key Investigators===
* SPL: Raimundo Sierra, David Gobbi, Steve Pieper

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Improving the performance of slicer display

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Approach, Plan</h1>
# doing the resample to a 'native' size for the input volume and then upsampling to screen size still sounds best.
# using a vtkImageActor in the vtkSlicerSliceViewer (instead of the current vtkImageMapper and vtkActor2D) is likely to be faster, and can do the upsample needed in step (1),
# using a vtkImageActor for the slice model in the vtkSlicerViewer will bypass the power-of-2 resampling in vtkTexture that gives the artifacts I hate
# David thinks we should be able to use the existing functions of vtkImageReslice to get the background mask. He didn't thing having a two-output filter was a good idea based on his experience with the way the vtk pipeline executes.

</div>

<div style="width: 40%; float: left;">
<h1>Progress</h1>
# Implemented filter with aditional output, significantly faster rendering of slices
# Integrated building of alpha mask into one filter in form of a derived class from vtkReslice -> avoids multiple iterations through dataset
# TODO: integrate map to color and map to window level
[[Image:Programming_Week_RS_Slide4.JPG|thumb|320px]]
</div>
<br style="clear: both;" />
</div>

===References===

==Additional Information==
[[Media:Slicer_Rendering.ppt | Slides with diagrams about the slicer rendering pipeline]]

File:Programming Week RS Slide4.JPG

2007-06-29T01:24:30Z

Rsierra:

Projects/Slicer3/2007 Project Week Display Optimization

2007-06-29T01:21:25Z

Rsierra:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|}

__NOTOC__
===Key Investigators===
* SPL: Raimundo Sierra, David Gobbi, Steve Pieper

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Improving the performance of slicer display

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Approach, Plan</h1>
# doing the resample to a 'native' size for the input volume and then upsampling to screen size still sounds best.
# using a vtkImageActor in the vtkSlicerSliceViewer (instead of the current vtkImageMapper and vtkActor2D) is likely to be faster, and can do the upsample needed in step (1),
# using a vtkImageActor for the slice model in the vtkSlicerViewer will bypass the power-of-2 resampling in vtkTexture that gives the artifacts I hate
# David thinks we should be able to use the existing functions of vtkImageReslice to get the background mask. He didn't thing having a two-output filter was a good idea based on his experience with the way the vtk pipeline executes.

</div>

<div style="width: 40%; float: left;">
<h1>Progress</h1>
# Implemented filter with aditional output, significantly faster rendering of slices
# Integrated building of alpha mask into one filter in form of a derived class from vtkReslice -> avoids multiple iterations through dataset
# TODO: integrate map to color and map to window level
</div>
<br style="clear: both;" />
</div>

===References===

==Additional Information==
[[Media:Slicer_Rendering.ppt | Slides with diagrams about the slicer rendering pipeline]]

Projects/Slicer3/2007 Project Week Display Optimization

2007-05-30T16:34:42Z

Rsierra:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|}

__NOTOC__
===Key Investigators===
* SPL: Raimundo Sierra, David Gobbi, Steve Pieper

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Improving the performance of slicer display

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Approach, Plan</h1>
# doing the resample to a 'native' size for the input volume and then upsampling to screen size still sounds best.
# using a vtkImageActor in the vtkSlicerSliceViewer (instead of the current vtkImageMapper and vtkActor2D) is likely to be faster, and can do the upsample needed in step (1),
# using a vtkImageActor for the slice model in the vtkSlicerViewer will bypass the power-of-2 resampling in vtkTexture that gives the artifacts I hate
# David thinks we should be able to use the existing functions of vtkImageReslice to get the background mask. He didn't thing having a two-output filter was a good idea based on his experience with the way the vtk pipeline executes.

</div>

<div style="width: 40%; float: left;">
<h1>Progress</h1>
</div>
<br style="clear: both;" />
</div>

===References===

==Additional Information==
[[Media:Slicer_Rendering.ppt | Slides with diagrams about the slicer rendering pipeline]]

Projects/Slicer3/2007 Project Week Display Optimization

2007-05-30T16:33:42Z

Rsierra:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|}

__NOTOC__
===Key Investigators===
* SPL: Raimundo Sierra, David Gobbi, Steve Pieper

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Improving the performance of slicer display

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Approach, Plan</h1>
</div>

<div style="width: 40%; float: left;">
# doing the resample to a 'native' size for the input volume and then upsampling to screen size still sounds best.
# using a vtkImageActor in the vtkSlicerSliceViewer (instead of the current vtkImageMapper and vtkActor2D) is likely to be faster, and can do the upsample needed in step (1),
# using a vtkImageActor for the slice model in the vtkSlicerViewer will bypass the power-of-2 resampling in vtkTexture that gives the artifacts I hate
# David thinks we should be able to use the existing functions of vtkImageReslice to get the background mask. He didn't thing having a two-output filter was a good idea based on his experience with the way the vtk pipeline executes.

<h1>Progress</h1>
</div>
<br style="clear: both;" />
</div>

===References===

==Additional Information==
[[Media:Slicer_Rendering.ppt | Slides with diagrams about the slicer rendering pipeline]]

Projects/Slicer3/2007 Project Week Display Optimization

2007-05-30T16:32:10Z

Rsierra: /* Additional Information */

File:Slicer Rendering.ppt

2007-05-30T16:29:38Z

Rsierra: Slides for the 2007 Project Week; Display Optimization

Slides for the 2007 Project Week; Display Optimization

Projects/Slicer3/2007 Project Week Display Optimization

2007-05-30T16:26:26Z

Rsierra: importing template

2007 Programming/Project Week MIT

2007-05-22T15:12:49Z

Rsierra: /* NA-MIC Kit */

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007]]
== Logistics ==

'''Dates:''' June 25-29, 2007

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $200 (this will cover the cost of breakfast and lunch for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' There is no official hotel for the meeting. Here is some information about Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

This is a week of hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC calendar. A full week of hands on activities is held in the summer at MIT (typically the last week of June), and for half a week in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the NA-MIC Kit capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the NA-MIC Kit and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

=== Draft Agenda===
Please note that this agenda is a draft and will be finalized by June 15th.

* Monday June 25
** noon-1pm lunch
** 1-3:30pm Introduce Projects using templated wiki pages (all Project Leads)
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9-10am: NA-MIC Software Process (Bill Hoffman - TBC)
** 10-10:30am Slicer 3.0 Update(Jim Miller, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1-2pm: [[Special topic breakout: Non-Linear Registration]]
** 2-3pm: [[Special topic breakout: DWI/DTI]]
** 3-4pm: [[Special topic breakout: KWWidgets]]
** 4-5pm: [[Special topic breakout: Atlases]]
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** noon lunch
** 1-2pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
** 3:30-5pm Special topic breakout: TBD
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using the templated wiki pages
** noon lunch boxes and adjourn

=== Preparation ===

# 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_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: 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)
# By 3pm ET on June 21, 2007: Complete the templated wiki page for your project. THe final version of this template will be circulated by May 25th.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
*[[DBP2:MIND | Longitudinal Classification of White Matter Lesions in Lupus]] (MIND/UNM)
*[[DBP2:JHU | Segmentation and Registration Tools for Robotic Prostate Interventions]] (JHU/Queen's)
*[[DBP2:UNC |Longitudinal MRI study of early brain development in neuropsychiatric disorder: UNC Autism Study]] (UNC)
*[[DBP2:Harvard|Velocardiofacial Syndrome (VCFS) as a genetic model for schizophrenia]] (Harvard)

===Structural Analysis===
*EMSegmentation Validation (Brad Davis, Sylvain Bouix)
*vtkITK wrapper for rule based segmentation (John Melonakos, Brad Davis, Marek Kubicki)
** Application of the Slicer2 module on DBP data
** Conversion to Slicer3

===Diffusion Image Analysis===
* [[Algorithm:UNC:DTI#Population_Analysis | DTI population analysis]] (Casey Goodlett)
* Slicer3 Whole brain Seeding platform: data representation and pipeline execution (Raul San Jose, Lauren O'Donnell, Alex Y.)
* Slicer3 Tractography editor (Lauren O'Donnell, Raul San Jose, Alex Y.)

===NA-MIC Kit===
* Slicer3
** [[2007_Project_Week_MIT_QDEC_Slicer3_Integration | QDEC integration into Slicer3]] (Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
** [[2007_Project_Week_MIT_Display_Optimization | Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
** [[2007_Project_Week_MIT_MRML_Scenes_for_the_Execution_Model]], including transforms (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
** Support for Unstructured Grids (Steve, Nicole, Alex, Curt)
** Python support in Slicer3 (Luca, Steve, depends on Dan's availability)
** CPack, Ctest infrastructure improvements (Andy, Katie, Steve)
** Drafting Human Interface and Slicer Style Guidelines (Wendy)
** Slicer Matlab Pipeline for scalars and tensors (Katharina, Sylvain, Steve)
* Slicer2

===External Collaborations===
* Meshing
** Adding VTK interactive wwidgets to Slicer3 (Will, Vince, Kiran, Curt)
** Migrate Iowa Neural Net code to pure ITK (Vince, Stephen)
*IGT
** [[Tracker Integration]] (Noby, Haiying, Katie Hayes BWH)
** [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
** [[Collaboration/JHU/Brachytherapy needle positioning robot integration|Brachytherapy needle positioning robot integration]] (Csaba Csoma, Peter Kazanzides JHU, David Gobbi Queen's, Katie Hayes BWH)
** [[Collaboration/BWH/RadVision and Tracker Integration|RadVision and Tracker Integration]] (Jack Blevins, Noby)
* Registration
** [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
** [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe)
** [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
* [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek(GE))
* [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
* [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
* [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)

===Non-Medical Collaborations===
* AstroMed (Michael Halle, Douglas Alan)

==Attendee List==
#Kilian Pohl, BWH, Core 1
#John Melonakos, Georgia Tech, Core 1, (Hotel at MIT request)
#Tauseef Rehman, Georgia Tech, Core 1
#Casey Goodlett, UNC, Core 1, (Hotel at MIT request)
#W. Bryan Smith, UCSD/NCMIR, Core 2 (Tentative)
#Jim Miller, GE Core 2, Booked at the Hotel At MIT
#Steve Pieper, Isomics, Core 2
#Katie Hayes, BWH, Core 2
#Dan Blezek, GE Core 2, Booked at the Hotel At MIT
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
#Peter Kazanzides, JHU, Collaborator
#Wendy Plesniak, BWH, Collaborator
#Luca Antiga, Mario Negri Institute, Collaborator
#Sylvain Bouix, BWH, Core 3
#Marek Kubicki, BWH, Core 3
#Chris Wyatt, Virginia Tech, Collaborator
#Nicole Aucoin, BWH, Core 2
#Will Schroeder, Kitware, Core 2
#Yumin Yuan, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Stephen Aylward, Kitware, Collaborator
#Luis Ibanez, Kitware, Core 2
#Raimundo Sierra, BWH, Core 2
#Clare Tempany, BWH Collaborator (Tuesday, June 26th only)
#Noby Hata, BWH Collaborator (Monday, June 25th only)
#Haiying Liu, BWH Collaborator
#Alex Yarmarkovich, Isomics, Core 2
#Vincent Magnotta, University of Iowa, Collaborator (Hotel at MIT request)
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Rhiannon Carlson, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Skip Talbot, Northwestern University, Collaborator
#Alex Kogan, Northwestern University, Collaborator
#Vladimir Kleper, Northwestern University, Collaborator
#Pat Mongkolwat, Northwestern University, Collaborator
#Csaba Csoma, Johns Hopkins University, Collaborator (Hotel at MIT request)
#David Gobbi, Queen's University, Collaborator (Hotel at MIT request)
#Kai Ding, University of Iowa, Gary's student
#H. Jeremy Bockholt, The MIND Institute, DBP2:MIND PI
#Mark Scully, The MIND Institute, DBP2:MIND software engineer
#Sumner Williams, The MIND Institute, Magnotta/Johnson/Bockholt BRAINS grant software engineer
#Greg Sharp, MGH, Collaborator
#Lauren O'Donnell, BWH
#Raul San Jose, BWH
#Katharina Quintus, BWH, Core 3
#Marc Niethammer, BWH. Core 3
#Kevin Teich, MGH
#Michael Halle, BWH/IIC
#James Ross, GE
#Kiran Shivanna, University of Iowa, Collaborator (Hotel at MIT request)
#Douglas Alan, Harvard IIC
#Heather Cody Hazlett, UNC Core 3 (only part of week) (Hotel @ MIT request)
#Clement Vachet, UNC Core 3 (CS programmer) - full week (Hotel @ MIT request)
#Rachel G. Smith, UNC Core 3 (image lab manager) - tentative (may not be full week) (Hotel @ MIT request)

2007 Programming/Project Week MIT

2007-05-03T20:31:50Z

Rsierra: /* Attendee List */

Back to [[Engineering:Programming_Events|Programming/Project Events]]

June 25-29, 2007, MIT

==Please Note==

Programming/Project week is one of the major events in the NA-MIC calendar. This will be our third annual Summer Programmming/Project Week.

* Core 1 - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* Core 2 - bring your code for infrastructure and applications to extend the NA-MIC Kit capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* Core 3 - bring your data to work on with the NA-MIC Kit and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* 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.

* 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.

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

== Projects ==

===Structural Analysis===
*EMSegmentation Validation (Brad Davis, Sylvain Bouix)
*vtkITK wrapper for rule based segmentation (Brad Davis, John Melonakis, Marek Kubiki)
** Application of the Slicer2 module on DBP data
** Conversion to Slicer3

===Diffusion Image Analysis===

===NA-MIC Kit===
* Slicer3
** [[2007_Project_Week_MIT_QDEC_Slicer3_Integration | QDEC integration into Slicer3]] (Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
** Display Optimization (Raimundo Sierra, David Gobbi, Steve Pieper)
** MRML Scenes for the Execution Model, including transforms (Jim Miller, Brad Davis, Nicole Aucoin, Steve Pieper)
** Support for Unstructured Grids (Steve, Nicole, Alex, Curt)
** Python support in Slicer3 (depends on Dan's availability)
** CPack, Ctest infrastructure improvements (Andy, Katie, Steve)
* Slicer2

===External Collaborations===
* Meshing
** Adding VTK interactive wwidgets to Slicer3 (Will, Vince, Kiran, Curt)
** Migrate Iowa Neural Net code to pure ITK (Vince, Stephen)
*IGT Projects
** Tracker Integration (Noby and ...)

===Non-Medical Collaborations===

== Logistics ==

'''Dates:''' June 25-29, 2007
'''Registration Fee:''' Registration fee is TBD. It will be payable by check onsite.

== 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.
* 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_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: 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)
# By 3pm ET on June 14, 2007: Complete the top half of [[media:NA-MIC_Latest_4-Block_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# [[Engineering:TCON_2007#2005-06-14|June 14, 2007: TCON#3 Review of 4-Blocks (Structural, DTI, Collaboration, Other)]]
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Review of 4-Blocks (NA-MIC Kit)]]
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

==Attendee List==
#Kilian Pohl, BWH, Core 1
#John Melonakos, Georgia Tech, Core 1
#W. Bryan Smith, UCSD/NCMIR, Core 2 (Tentative)
#Jim Miller, GE Core 2
#Steve Pieper, Isomics, Core 2
#Katie Hayes, BWH, Core 2
#Dan Blezek, GE Core 2 (Tentative)
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
#Peter Kazanzides, JHU, Collaborator
#Wendy Plesniak, BWH, Collaborator
#Luca Antiga, Mario Negri Institute, Collaborator
#Sylvain Bouix, BWH, Core 3
#Chris Wyatt, Virginia Tech, Collaborator
#Nicole Aucoin, BWH, Core 2
#Will Schroeder, Kitware, Core 2
#Sebastien Barre, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Stephen Aylward, Kitware, Core 2
#Raimundo Sierra, BWH, Core 2