NAMIC Wiki - User contributions [en]

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-25T15:17:56Z

Barabas:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:Tian_Cao_US_Volume.jpg|[http://sites.google.com/site/tiancaoshomepage/research/3dvr Volume rendering for 3D ultrasound]
Image:NCI-Volume-CT-Chest.jpg|Sample rendering using NCI volume renderer in Slicer
</gallery>

==Key Investigators==
* MIT Media Lab: Jim Barabas
* BWH: Noby Hata

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Review volume rendering support in slicer3.6.
* Test current capabilities and performance.
* Develop plan for extending rendering capabilities. (This work is towards longer-term goal of developing an image-based photorealistic volume renderer).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Examine code for current volume rendering support.
* Benchmark on available GPU architectures.
* Develop and test extensions to current volume shaders.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Read through code and shaders for the GPU-based volume renderers.

* Examined and found quick reproduction steps for bug in Apple/Nvidia shader compiler that prevents ITK volume renderer from working on recent Mac OS X releases.

* Possible fix identified: Concatenate sources (with redundant global variables removed) into single shader source file instead of linking several separate files.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

notes delivered to the NA-MIC Kit as a information on this wiki page.

==Findings==
Compared GPU shader architectures in Slicer 3.6:
* NCI renderer concatenates strings to assemble shader source, depending on settings chosen. This method is less fragile, but harder to debug/profile shader using external tools.
* VTK renderer links several individual shader sources, generated from .glsl files.
* NCI renderer supports multiple volumes rendered in a single pass
* NCI renderer contains a mode for adaptive transfer-function generation.
* NCI renderer pre-computes gradient volume in CPU, which can be slow initially, but may save time rendering.

Comments on current volume rendering capabilities:
* Could benefit from better defaults for renderer transfer functions. VirtualPlace renderer has row of clickable defaults that let users get nice appearance quickly.
* Transfer function editor is capable, could be easier to use if it was possible to translate whole function.

===Notes===

Other pages on volume rendering in Slicer
* [http://www.slicer.org/slicerWiki/index.php/Slicer3:Volume_Rendering_With_Cuda Unmaintained CUDA renderer for slicer ]
* [http://www.slicer.org/slicerWiki/index.php/Slicer3:Volume_Rendering Slicer3 Wiki]
* [http://www.slicer.org/slicerWiki/index.php/Slicer3:Volume_Rendering_Tutorials Slightly outdated tutorials]

We had a breakout session with demos of the Slicer renderers, as well as the VirtualPlace renderer, and the Microsoft Research client-server CUDA renderer.
[[2010 Summer Project Week Breakout Session: Volume Rendering]]

Traced shaders using 2010 Macbook Pro. Set breakpoints for gl*Shader* and gl*Program* functions using OpenGL Profiler and observed openGL state.

Tracing using OpenGL profiler:
get it to break on glCreateShaderObjectARB and glGetShaderInfoLog, glCreateProgramObjectARB

Attempts to use profiler cause slicer to balloon in memory (~11G and counting)
Spiraling in:
<pre>
1115 vtkRenderer::UpdateGeometry()
1115 vtkVolume::RenderVolumetricGeometry(vtkViewport*)
1115 vtkGPUVolumeRayCastMapper::Render(vtkRenderer*, vtkVolume*)
1115 vtkOpenGLGPUVolumeRayCastMapper::GPURender(vtkRenderer*, vtkVolume*)
1115 vtkOpenGLGPUVolumeRayCastMapper::PreRender(vtkRenderer*, vtkVolume*, double*, double*, int, unsigned int)
1115 vtkShaderProgram2::Use()
1115 vtkShaderProgram2::Build()
1115 glCreateProgram
1115 gloGetCGLDispatch
1115 0x139fee7b5
1115 _pthread_cond_wait
1115 __semwait_signal
</pre>

Using nvidia graphics, get:
<pre>
6/23/10 2:23:48 PM [0x0-0x65065].com.apple.ShaderBuilder[2220] (0) : fatal error C9999: Nested functions, aborting!
6/23/10 2:23:48 PM [0x0-0x65065].com.apple.ShaderBuilder[2220] Cg compiler terminated due to fatal error
6/23/10 2:23:48 PM com.apple.launchd.peruser.501[812] ([0x0-0x65065].com.apple.ShaderBuilder[2220]) Exited with exit code: 15
</pre>

Using intel graphics, get:
<pre>
6/23/10 2:46:45 PM com.apple.launchd.peruser.501[812] (com.apple.cvmsCompAgent_x86_64[2365]) Job appears to have crashed: Segmentation fault
6/23/10 2:46:45 PM com.apple.ReportCrash.Root[2369] 2010-06-23 14:46:45.366 ReportCrash[2369:2a03] Saved crash report for cvmsComp_x86_64[2365] version ??? (???) to /Library/Logs/DiagnosticReports/cvmsComp_x86_64_2010-06-23-144645_localhost.crash
</pre>

Possible location of failing source:
(located in Slicer3-lib/VTK/VolumeRendering/)

vtkGPUVolumeRayCastMapper_HeaderFS.glsl
vtkGPUVolumeRayCastMapper_ParallelProjectionFS.glsl
vtkGPUVolumeRayCastMapper_CompositeFS.glsl
vtkGPUVolumeRayCastMapper_CompositeNoCroppingFS.glsl
vtkGPUVolumeRayCastMapper_OneComponentFS.glsl
vtkGPUVolumeRayCastMapper_NoShadeFS.glsl

Bug appears to crash compiler when scalarFromValue() called inside trace(). Using intel graphics card causes recoverable crash. Nvidia crashes hard and kills ShaderBuilder.

So functions that implement scalarFromValue are:
vtkGPUVolumeRayCastMapper_FourComponentsFS.glsl
vtkGPUVolumeRayCastMapper_OneComponentFS.glsl

get called by:
vtkGPUVolumeRayCastMapper_CompositeFS.glsl
vtkGPUVolumeRayCastMapper_CompositeMaskFS.glsl

Looking to VTK docs (Looks like Slicer using vers 5.6.0

__________

Volume Rendering code overview:

VTK renderer lives in:
Slicer3-lib/VTK/VolumeRendering/*.glsl
Series of glsl fragment shaders are linked together to form single fragment program. Different .glsl files are linked depending on options chosen. This approach is nice and modular, but seems to expose a bug in the Apple/Nvidia shader compiler.

NCI renderer lives in:
Modules/VolumeRendering/VolumeRenderingReplacements/vtkSlicerGPURayCastVolumeMapper.cxx

==References==

</div>

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-25T15:00:11Z

Barabas:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:Tian_Cao_US_Volume.jpg|[http://sites.google.com/site/tiancaoshomepage/research/3dvr Volume rendering for 3D ultrasound]
Image:NCI-Volume-CT-Chest.jpg|Sample rendering using NCI volume renderer in Slicer
</gallery>

==Key Investigators==
* MIT Media Lab: Jim Barabas
* BWH: Noby Hata

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Review volume rendering support in slicer3.6.
* Test current capabilities and performance.
* Develop plan for extending rendering capabilities. (This work is towards longer-term goal of developing an image-based photorealistic volume renderer).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Examine code for current volume rendering support.
* Benchmark on available GPU architectures.
* Develop and test extensions to current volume shaders.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Read through code and shaders for the GPU-based volume renderers.

* Examined and found quick reproduction steps for bug in Apple/Nvidia shader compiler that prevents ITK volume renderer from working on recent Mac OS X releases.

* Possible fix identified: Concatenate sources (with redundant global variables removed) into single shader source file instead of linking several separate files.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

notes delivered to the NA-MIC Kit as a information on this wiki page.

==Findings==
Compared GPU shader architectures in Slicer 3.6:
* NCI renderer concatenates strings to assemble shader source, depending on settings chosen. This method is less fragile, but harder to debug/profile shader using external tools.
* VTK renderer links several individual shader sources, generated from .glsl files.
* NCI renderer supports multiple volumes rendered in a single pass
* NCI renderer contains a mode for adaptive transfer-function generation.
* NCI renderer pre-computes gradient volume in CPU, which can be slow initially, but may save time rendering.

Comments on current volume rendering capabilities:
* Could benefit from better defaults for renderer transfer functions. VirtualPlace renderer has row of clickable defaults that let users get nice appearance quickly.
* Transfer function editor is capable, could be easier to use if it was possible to translate whole function.

===Notes===
We had a breakout session with demos of the Slicer renderers, as well as the VirtualPlace renderer, and the Microsoft Research client-server CUDA renderer.
[[2010 Summer Project Week Breakout Session: Volume Rendering]]

Traced shaders using 2010 Macbook Pro. Set breakpoints for gl*Shader* and gl*Program* functions using OpenGL Profiler and observed openGL state.

Tracing using OpenGL profiler:
get it to break on glCreateShaderObjectARB and glGetShaderInfoLog, glCreateProgramObjectARB

Attempts to use profiler cause slicer to balloon in memory (~11G and counting)
Spiraling in:
<pre>
1115 vtkRenderer::UpdateGeometry()
1115 vtkVolume::RenderVolumetricGeometry(vtkViewport*)
1115 vtkGPUVolumeRayCastMapper::Render(vtkRenderer*, vtkVolume*)
1115 vtkOpenGLGPUVolumeRayCastMapper::GPURender(vtkRenderer*, vtkVolume*)
1115 vtkOpenGLGPUVolumeRayCastMapper::PreRender(vtkRenderer*, vtkVolume*, double*, double*, int, unsigned int)
1115 vtkShaderProgram2::Use()
1115 vtkShaderProgram2::Build()
1115 glCreateProgram
1115 gloGetCGLDispatch
1115 0x139fee7b5
1115 _pthread_cond_wait
1115 __semwait_signal
</pre>

Using nvidia graphics, get:
<pre>
6/23/10 2:23:48 PM [0x0-0x65065].com.apple.ShaderBuilder[2220] (0) : fatal error C9999: Nested functions, aborting!
6/23/10 2:23:48 PM [0x0-0x65065].com.apple.ShaderBuilder[2220] Cg compiler terminated due to fatal error
6/23/10 2:23:48 PM com.apple.launchd.peruser.501[812] ([0x0-0x65065].com.apple.ShaderBuilder[2220]) Exited with exit code: 15
</pre>

Using intel graphics, get:
<pre>
6/23/10 2:46:45 PM com.apple.launchd.peruser.501[812] (com.apple.cvmsCompAgent_x86_64[2365]) Job appears to have crashed: Segmentation fault
6/23/10 2:46:45 PM com.apple.ReportCrash.Root[2369] 2010-06-23 14:46:45.366 ReportCrash[2369:2a03] Saved crash report for cvmsComp_x86_64[2365] version ??? (???) to /Library/Logs/DiagnosticReports/cvmsComp_x86_64_2010-06-23-144645_localhost.crash
</pre>

Possible location of failing source:
(located in Slicer3-lib/VTK/VolumeRendering/)

vtkGPUVolumeRayCastMapper_HeaderFS.glsl
vtkGPUVolumeRayCastMapper_ParallelProjectionFS.glsl
vtkGPUVolumeRayCastMapper_CompositeFS.glsl
vtkGPUVolumeRayCastMapper_CompositeNoCroppingFS.glsl
vtkGPUVolumeRayCastMapper_OneComponentFS.glsl
vtkGPUVolumeRayCastMapper_NoShadeFS.glsl

Bug appears to crash compiler when scalarFromValue() called inside trace(). Using intel graphics card causes recoverable crash. Nvidia crashes hard and kills ShaderBuilder.

So functions that implement scalarFromValue are:
vtkGPUVolumeRayCastMapper_FourComponentsFS.glsl
vtkGPUVolumeRayCastMapper_OneComponentFS.glsl

get called by:
vtkGPUVolumeRayCastMapper_CompositeFS.glsl
vtkGPUVolumeRayCastMapper_CompositeMaskFS.glsl

Looking to VTK docs (Looks like Slicer using vers 5.6.0

__________

Volume Rendering code overview:

VTK renderer lives in:
Slicer3-lib/VTK/VolumeRendering/*.glsl
Series of glsl fragment shaders are linked together to form single fragment program. Different .glsl files are linked depending on options chosen. This approach is nice and modular, but seems to expose a bug in the Apple/Nvidia shader compiler.

NCI renderer lives in:
Modules/VolumeRendering/VolumeRenderingReplacements/vtkSlicerGPURayCastVolumeMapper.cxx

==References==

</div>

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-25T14:54:09Z

Barabas:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:Tian_Cao_US_Volume.jpg|[http://sites.google.com/site/tiancaoshomepage/research/3dvr Volume rendering for 3D ultrasound]
Image:NCI-Volume-CT-Chest.jpg|Sample rendering using NCI volume renderer in Slicer
</gallery>

==Key Investigators==
* MIT Media Lab: Jim Barabas
* BWH: Noby Hata

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Review volume rendering support in slicer3.6.
* Test current capabilities and performance.
* Develop plan for extending rendering capabilities. (This work is towards longer-term goal of developing an image-based photorealistic volume renderer).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Examine code for current volume rendering support.
* Benchmark on available GPU architectures.
* Develop and test extensions to current volume shaders.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Read through code and shaders for the GPU-based volume renderers.

* Examined and found quick reproduction steps for bug in Apple/Nvidia shader compiler that prevents ITK volume renderer from working on recent Mac OS X releases.

* Possible fix identified: Concatenate sources (with redundant global variables removed) into single shader source file instead of linking several separate files.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

notes delivered to the NA-MIC Kit as a information on this wiki page.

==Notes==
Compared GPU shader architectures in Slicer 3.6:
* NCI renderer concatenates strings to assemble shader source, depending on settings chosen. This method is less fragile, but harder to debug/profile shader using external tools.
* VTK renderer links several individual shader sources, generated from .glsl files.
* NCI renderer supports multiple volumes rendered in a single pass
* NCI renderer contains a mode for adaptive transfer-function generation.
* NCI renderer pre-computes gradient volume in CPU, which can be slow

Comments on current volume rendering capabilities:
* Could benefit from better defaults for renderer transfer functions. VirtualPlace renderer has row of clickable defaults that let users get nice appearance quickly.
* Transfer function editor is capable, could be easier to use if it was possible to translate whole function.

We had a breakout session with demos of the Slicer renderers, as well as the VirtualPlace renderer, and the Microsoft Research client-server CUDA renderer.
[[2010 Summer Project Week Breakout Session: Volume Rendering]]

Traced shaders using 2010 Macbook Pro. Set breakpoints for gl*Shader* and gl*Program* functions using OpenGL Profiler and observed openGL state.

Tracing using OpenGL profiler:
get it to break on glCreateShaderObjectARB and glGetShaderInfoLog, glCreateProgramObjectARB

Attempts to use profiler cause slicer to balloon in memory (~11G and counting)
Spiraling in:
<pre>
1115 vtkRenderer::UpdateGeometry()
1115 vtkVolume::RenderVolumetricGeometry(vtkViewport*)
1115 vtkGPUVolumeRayCastMapper::Render(vtkRenderer*, vtkVolume*)
1115 vtkOpenGLGPUVolumeRayCastMapper::GPURender(vtkRenderer*, vtkVolume*)
1115 vtkOpenGLGPUVolumeRayCastMapper::PreRender(vtkRenderer*, vtkVolume*, double*, double*, int, unsigned int)
1115 vtkShaderProgram2::Use()
1115 vtkShaderProgram2::Build()
1115 glCreateProgram
1115 gloGetCGLDispatch
1115 0x139fee7b5
1115 _pthread_cond_wait
1115 __semwait_signal
</pre>

Using nvidia graphics, get:
<pre>
6/23/10 2:23:48 PM [0x0-0x65065].com.apple.ShaderBuilder[2220] (0) : fatal error C9999: Nested functions, aborting!
6/23/10 2:23:48 PM [0x0-0x65065].com.apple.ShaderBuilder[2220] Cg compiler terminated due to fatal error
6/23/10 2:23:48 PM com.apple.launchd.peruser.501[812] ([0x0-0x65065].com.apple.ShaderBuilder[2220]) Exited with exit code: 15
</pre>

Using intel graphics, get:
<pre>
6/23/10 2:46:45 PM com.apple.launchd.peruser.501[812] (com.apple.cvmsCompAgent_x86_64[2365]) Job appears to have crashed: Segmentation fault
6/23/10 2:46:45 PM com.apple.ReportCrash.Root[2369] 2010-06-23 14:46:45.366 ReportCrash[2369:2a03] Saved crash report for cvmsComp_x86_64[2365] version ??? (???) to /Library/Logs/DiagnosticReports/cvmsComp_x86_64_2010-06-23-144645_localhost.crash
</pre>

Possible location of failing source:
(located in Slicer3-lib/VTK/VolumeRendering/)

vtkGPUVolumeRayCastMapper_HeaderFS.glsl
vtkGPUVolumeRayCastMapper_ParallelProjectionFS.glsl
vtkGPUVolumeRayCastMapper_CompositeFS.glsl
vtkGPUVolumeRayCastMapper_CompositeNoCroppingFS.glsl
vtkGPUVolumeRayCastMapper_OneComponentFS.glsl
vtkGPUVolumeRayCastMapper_NoShadeFS.glsl

Bug appears to crash compiler when scalarFromValue() called inside trace(). Using intel graphics card causes recoverable crash. Nvidia crashes hard and kills ShaderBuilder.

So functions that implement scalarFromValue are:
vtkGPUVolumeRayCastMapper_FourComponentsFS.glsl
vtkGPUVolumeRayCastMapper_OneComponentFS.glsl

get called by:
vtkGPUVolumeRayCastMapper_CompositeFS.glsl
vtkGPUVolumeRayCastMapper_CompositeMaskFS.glsl

Looking to VTK docs (Looks like Slicer using vers 5.6.0

__________

Volume Rendering code overview:

VTK renderer lives in:
Slicer3-lib/VTK/VolumeRendering/*.glsl
Series of glsl fragment shaders are linked together to form single fragment program. Different .glsl files are linked depending on options chosen. This approach is nice and modular, but seems to expose a bug in the Apple/Nvidia shader compiler.

NCI renderer lives in:
Modules/VolumeRendering/VolumeRenderingReplacements/vtkSlicerGPURayCastVolumeMapper.cxx

==References==

</div>

File:NCI-Volume-CT-Chest.jpg

2010-06-25T14:52:39Z

Barabas: Sample volume rendering using NCI volume renderer

Sample volume rendering using NCI volume renderer

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-25T14:33:27Z

Barabas:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:Tian_Cao_US_Volume.jpg|[http://sites.google.com/site/tiancaoshomepage/research/3dvr Volume rendering for 3D ultrasound]
</gallery>

==Key Investigators==
* MIT Media Lab: Jim Barabas
* BWH: Noby Hata

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Review volume rendering support in slicer3.6.
* Test current capabilities and performance.
* Develop plan for extending rendering capabilities. (This work is towards longer-term goal of developing an image-based photorealistic volume renderer).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Examine code for current volume rendering support.
* Benchmark on available GPU architectures.
* Develop and test extensions to current volume shaders.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Read through code and shaders for the GPU-based volume renderers.

* Examined and found quick reproduction steps for bug in Apple/Nvidia shader compiler that prevents ITK volume renderer from working on recent Mac OS X releases.

* Possible fix identified: Concatenate sources (with redundant global variables removed) into single shader source file instead of linking several separate files.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

notes delivered to the NA-MIC Kit as a information on this wiki page.

==Notes==
Compared GPU shader architectures in Slicer 3.6:
* NCI renderer concatenates strings to assemble shader source, depending on settings chosen. This method is less fragile, but harder to debug/profile shader using external tools.
* VTK renderer links several individual shader sources, generated from .glsl files.
* NCI renderer supports multiple volumes rendered in a single pass
* NCI renderer contains a mode for adaptive transfer-function generation.
* NCI renderer pre-computes gradient volume in CPU, which can be slow

Comments on current volume rendering capabilities:
* Could benefit from better defaults for renderer transfer functions. VirtualPlace renderer has row of clickable defaults that let users get nice appearance quickly.
* Transfer function editor is capable, could be easier to use if it was possible to translate whole function.

We had a breakout session with demos of the Slicer renderers, as well as the VirtualPlace renderer, and the Microsoft Research client-server CUDA renderer.
[[2010 Summer Project Week Breakout Session: Volume Rendering]]

Traced shaders using 2010 Macbook Pro. Set breakpoints for gl*Shader* and gl*Program* functions using OpenGL Profiler and observed openGL state.

Tracing using OpenGL profiler:
get it to break on glCreateShaderObjectARB and glGetShaderInfoLog, glCreateProgramObjectARB

Attempts to use profiler cause slicer to balloon in memory (~11G and counting)
Spiraling in:
<pre>
1115 vtkRenderer::UpdateGeometry()
1115 vtkVolume::RenderVolumetricGeometry(vtkViewport*)
1115 vtkGPUVolumeRayCastMapper::Render(vtkRenderer*, vtkVolume*)
1115 vtkOpenGLGPUVolumeRayCastMapper::GPURender(vtkRenderer*, vtkVolume*)
1115 vtkOpenGLGPUVolumeRayCastMapper::PreRender(vtkRenderer*, vtkVolume*, double*, double*, int, unsigned int)
1115 vtkShaderProgram2::Use()
1115 vtkShaderProgram2::Build()
1115 glCreateProgram
1115 gloGetCGLDispatch
1115 0x139fee7b5
1115 _pthread_cond_wait
1115 __semwait_signal
</pre>

Using nvidia graphics, get:
<pre>
6/23/10 2:23:48 PM [0x0-0x65065].com.apple.ShaderBuilder[2220] (0) : fatal error C9999: Nested functions, aborting!
6/23/10 2:23:48 PM [0x0-0x65065].com.apple.ShaderBuilder[2220] Cg compiler terminated due to fatal error
6/23/10 2:23:48 PM com.apple.launchd.peruser.501[812] ([0x0-0x65065].com.apple.ShaderBuilder[2220]) Exited with exit code: 15
</pre>

Using intel graphics, get:
<pre>
6/23/10 2:46:45 PM com.apple.launchd.peruser.501[812] (com.apple.cvmsCompAgent_x86_64[2365]) Job appears to have crashed: Segmentation fault
6/23/10 2:46:45 PM com.apple.ReportCrash.Root[2369] 2010-06-23 14:46:45.366 ReportCrash[2369:2a03] Saved crash report for cvmsComp_x86_64[2365] version ??? (???) to /Library/Logs/DiagnosticReports/cvmsComp_x86_64_2010-06-23-144645_localhost.crash
</pre>

Possible location of failing source:
(located in Slicer3-lib/VTK/VolumeRendering/)

vtkGPUVolumeRayCastMapper_HeaderFS.glsl
vtkGPUVolumeRayCastMapper_ParallelProjectionFS.glsl
vtkGPUVolumeRayCastMapper_CompositeFS.glsl
vtkGPUVolumeRayCastMapper_CompositeNoCroppingFS.glsl
vtkGPUVolumeRayCastMapper_OneComponentFS.glsl
vtkGPUVolumeRayCastMapper_NoShadeFS.glsl

Bug appears to crash compiler when scalarFromValue() called inside trace(). Using intel graphics card causes recoverable crash. Nvidia crashes hard and kills ShaderBuilder.

So functions that implement scalarFromValue are:
vtkGPUVolumeRayCastMapper_FourComponentsFS.glsl
vtkGPUVolumeRayCastMapper_OneComponentFS.glsl

get called by:
vtkGPUVolumeRayCastMapper_CompositeFS.glsl
vtkGPUVolumeRayCastMapper_CompositeMaskFS.glsl

Looking to VTK docs (Looks like Slicer using vers 5.6.0

__________

Volume Rendering code overview:

VTK renderer lives in:
Slicer3-lib/VTK/VolumeRendering/*.glsl
Series of glsl fragment shaders are linked together to form single fragment program. Different .glsl files are linked depending on options chosen. This approach is nice and modular, but seems to expose a bug in the Apple/Nvidia shader compiler.

NCI renderer lives in:
Modules/VolumeRendering/VolumeRenderingReplacements/vtkSlicerGPURayCastVolumeMapper.cxx

==References==

</div>

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-25T14:16:09Z

Barabas:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:Tian_Cao_US_Volume.jpg|[http://sites.google.com/site/tiancaoshomepage/research/3dvr Volume rendering for 3D ultrasound]
</gallery>

==Key Investigators==
* MIT Media Lab: Jim Barabas
* BWH: Noby Hata

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Review volume rendering support in slicer3.6.
* Test current capabilities and performance.
* Develop plan for extending rendering capabilities. (This work is towards longer-term goal of developing an image-based photorealistic volume renderer).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Examine code for current volume rendering support.
* Benchmark on available GPU architectures.
* Develop and test extensions to current volume shaders.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Read through code and shaders for the GPU-based volume renderers.

* Examined and found quick reproduction steps for bug in Apple/Nvidia shader compiler that prevents ITK volume renderer from working on recent Mac OS X releases.

* Possible fix identified: Concatenate sources (with redundant global variables removed) into single shader source file instead of linking several separate files.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

notes delivered to the NA-MIC Kit as a information on this wiki page.

==Notes==
We had a breakout session with demos of the Slicer renderers, as well as the VirtualPlace renderer, and the Microsoft Research client-server CUDA renderer.
[[2010 Summer Project Week Breakout Session: Volume Rendering]]

Traced shaders using 2010 Macbook Pro. Set breakpoints for gl*Shader* and gl*Program* functions using OpenGL Profiler and observed openGL state.

Tracing using OpenGL profiler:
get it to break on glCreateShaderObjectARB and glGetShaderInfoLog, glCreateProgramObjectARB

Attempts to use profiler cause slicer to balloon in memory (~11G and counting)
Spiraling in:
<pre>
1115 vtkRenderer::UpdateGeometry()
1115 vtkVolume::RenderVolumetricGeometry(vtkViewport*)
1115 vtkGPUVolumeRayCastMapper::Render(vtkRenderer*, vtkVolume*)
1115 vtkOpenGLGPUVolumeRayCastMapper::GPURender(vtkRenderer*, vtkVolume*)
1115 vtkOpenGLGPUVolumeRayCastMapper::PreRender(vtkRenderer*, vtkVolume*, double*, double*, int, unsigned int)
1115 vtkShaderProgram2::Use()
1115 vtkShaderProgram2::Build()
1115 glCreateProgram
1115 gloGetCGLDispatch
1115 0x139fee7b5
1115 _pthread_cond_wait
1115 __semwait_signal
</pre>

Using nvidia graphics, get:
<pre>
6/23/10 2:23:48 PM [0x0-0x65065].com.apple.ShaderBuilder[2220] (0) : fatal error C9999: Nested functions, aborting!
6/23/10 2:23:48 PM [0x0-0x65065].com.apple.ShaderBuilder[2220] Cg compiler terminated due to fatal error
6/23/10 2:23:48 PM com.apple.launchd.peruser.501[812] ([0x0-0x65065].com.apple.ShaderBuilder[2220]) Exited with exit code: 15
</pre>

Using intel graphics, get:
<pre>
6/23/10 2:46:45 PM com.apple.launchd.peruser.501[812] (com.apple.cvmsCompAgent_x86_64[2365]) Job appears to have crashed: Segmentation fault
6/23/10 2:46:45 PM com.apple.ReportCrash.Root[2369] 2010-06-23 14:46:45.366 ReportCrash[2369:2a03] Saved crash report for cvmsComp_x86_64[2365] version ??? (???) to /Library/Logs/DiagnosticReports/cvmsComp_x86_64_2010-06-23-144645_localhost.crash
</pre>

Possible location of failing source:
(located in Slicer3-lib/VTK/VolumeRendering/)

vtkGPUVolumeRayCastMapper_HeaderFS.glsl
vtkGPUVolumeRayCastMapper_ParallelProjectionFS.glsl
vtkGPUVolumeRayCastMapper_CompositeFS.glsl
vtkGPUVolumeRayCastMapper_CompositeNoCroppingFS.glsl
vtkGPUVolumeRayCastMapper_OneComponentFS.glsl
vtkGPUVolumeRayCastMapper_NoShadeFS.glsl

Bug appears to crash compiler when scalarFromValue() called inside trace(). Using intel graphics card causes recoverable crash. Nvidia crashes hard and kills ShaderBuilder.

So functions that implement scalarFromValue are:
vtkGPUVolumeRayCastMapper_FourComponentsFS.glsl
vtkGPUVolumeRayCastMapper_OneComponentFS.glsl

get called by:
vtkGPUVolumeRayCastMapper_CompositeFS.glsl
vtkGPUVolumeRayCastMapper_CompositeMaskFS.glsl

Looking to VTK docs (Looks like Slicer using vers 5.6.0

__________

Volume Rendering code overview:

VTK renderer lives in:
Slicer3-lib/VTK/VolumeRendering/*.glsl
Series of glsl fragment shaders are linked together to form single fragment program. Different .glsl files are linked depending on options chosen. This approach is nice and modular, but seems to expose a bug in the Apple/Nvidia shader compiler.

NCI renderer lives in:
Modules/VolumeRendering/VolumeRenderingReplacements/vtkSlicerGPURayCastVolumeMapper.cxx

==References==

</div>

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-25T14:12:22Z

Barabas:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:Tian_Cao_US_Volume.jpg|[http://sites.google.com/site/tiancaoshomepage/research/3dvr Volume rendering for 3D ultrasound]
</gallery>

==Key Investigators==
* MIT Media Lab: Jim Barabas
* BWH: Noby Hata

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Review volume rendering support in slicer3.6. Test current capabilities and performance. Develop plan for extending rendering capabilities. (This work is towards longer-term goal of developing an image-based photorealistic volume renderer).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Examine code for current volume rendering support. Benchmark on available GPU architectures. Develop and test extensions to current volume shaders.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
Read through code and shaders for the GPU-based volume renderers.

Examined and found quick reproduction steps for bug in Apple/Nvidia shader compiler that prevents ITK volume renderer from working on recent Mac OS X releases.

Possible fix identified: Concatenate sources (with redundant global variables removed) into single shader source file instead of linking several separate files.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a information on this wiki page.

==Notes==
We had a breakout session with demos of the Slicer renderers, as well as the VirtualPlace renderer, and the Microsoft Research client-server CUDA renderer.
[[2010 Summer Project Week Breakout Session: Volume Rendering]]

Spent time tracing shaders using 2010 Macbook Pro. Set breakpoints for gl*Shader* and gl*Program* functions using OpenGL Profiler and observed openGL state.

Tracing using OpenGL profiler:
get it to break on glCreateShaderObjectARB and glGetShaderInfoLog, glCreateProgramObjectARB

Attempts to use profiler cause slicer to balloon in memory (~11G and counting)
Spiraling in:
<pre>
1115 vtkRenderer::UpdateGeometry()
1115 vtkVolume::RenderVolumetricGeometry(vtkViewport*)
1115 vtkGPUVolumeRayCastMapper::Render(vtkRenderer*, vtkVolume*)
1115 vtkOpenGLGPUVolumeRayCastMapper::GPURender(vtkRenderer*, vtkVolume*)
1115 vtkOpenGLGPUVolumeRayCastMapper::PreRender(vtkRenderer*, vtkVolume*, double*, double*, int, unsigned int)
1115 vtkShaderProgram2::Use()
1115 vtkShaderProgram2::Build()
1115 glCreateProgram
1115 gloGetCGLDispatch
1115 0x139fee7b5
1115 _pthread_cond_wait
1115 __semwait_signal
</pre>

Using nvidia graphics, get:
<pre>
6/23/10 2:23:48 PM [0x0-0x65065].com.apple.ShaderBuilder[2220] (0) : fatal error C9999: Nested functions, aborting!
6/23/10 2:23:48 PM [0x0-0x65065].com.apple.ShaderBuilder[2220] Cg compiler terminated due to fatal error
6/23/10 2:23:48 PM com.apple.launchd.peruser.501[812] ([0x0-0x65065].com.apple.ShaderBuilder[2220]) Exited with exit code: 15
</pre>

Using intel graphics, get:
<pre>
6/23/10 2:46:45 PM com.apple.launchd.peruser.501[812] (com.apple.cvmsCompAgent_x86_64[2365]) Job appears to have crashed: Segmentation fault
6/23/10 2:46:45 PM com.apple.ReportCrash.Root[2369] 2010-06-23 14:46:45.366 ReportCrash[2369:2a03] Saved crash report for cvmsComp_x86_64[2365] version ??? (???) to /Library/Logs/DiagnosticReports/cvmsComp_x86_64_2010-06-23-144645_localhost.crash
</pre>

Possible location of failing source:
(located in Slicer3-lib/VTK/VolumeRendering/)

vtkGPUVolumeRayCastMapper_HeaderFS.glsl
vtkGPUVolumeRayCastMapper_ParallelProjectionFS.glsl
vtkGPUVolumeRayCastMapper_CompositeFS.glsl
vtkGPUVolumeRayCastMapper_CompositeNoCroppingFS.glsl
vtkGPUVolumeRayCastMapper_OneComponentFS.glsl
vtkGPUVolumeRayCastMapper_NoShadeFS.glsl

Bug appears to crash compiler when scalarFromValue() called inside trace(). Using intel graphics card causes recoverable crash. Nvidia crashes hard and kills ShaderBuilder.

So functions that implement scalarFromValue are:
vtkGPUVolumeRayCastMapper_FourComponentsFS.glsl
vtkGPUVolumeRayCastMapper_OneComponentFS.glsl

get called by:
vtkGPUVolumeRayCastMapper_CompositeFS.glsl
vtkGPUVolumeRayCastMapper_CompositeMaskFS.glsl

Looking to VTK docs (Looks like Slicer using vers 5.6.0

__________

Volume Rendering code overview:

VTK renderer lives in:
Slicer3-lib/VTK/VolumeRendering/*.glsl
Series of glsl fragment shaders are linked together to form single fragment program. Different .glsl files are linked depending on options chosen. This approach is nice and modular, but seems to expose a bug in the Apple/Nvidia shader compiler.

NCI renderer lives in:
Modules/VolumeRendering/VolumeRenderingReplacements/vtkSlicerGPURayCastVolumeMapper.cxx

==References==

</div>

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-25T13:59:46Z

Barabas:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:Tian_Cao_US_Volume.jpg|[http://sites.google.com/site/tiancaoshomepage/research/3dvr Volume rendering for 3D ultrasound]
</gallery>

==Key Investigators==
* MIT Media Lab: Jim Barabas
* BWH: Noby Hata

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Review volume rendering support in slicer3.6. Test current capabilities and performance. Develop plan for extending rendering capabilities. (This work is towards longer-term goal of developing an image-based photorealistic volume renderer).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Examine code for current volume rendering support. Benchmark on available GPU architectures. Develop and test extensions to current volume shaders.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
Read through code and shaders for the GPU-based volume renderers.

Examined and found quick reproduction steps for bug in Apple/Nvidia shader compiler that prevents ITK volume renderer from working on recent Mac OS X releases.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a information on this wiki page.

==Notes==
We had a breakout session with demos of the Slicer renderers, as well as the VirtualPlace renderer, and the Microsoft Research client-server CUDA renderer.
[[2010 Summer Project Week Breakout Session: Volume Rendering]]

Spent time tracing shaders using 2010 Macbook Pro. Set breakpoints for gl*Shader* and gl*Program* functions using OpenGL Profiler and observed openGL state.

Tracing using OpenGL profiler:
get it to break on glCreateShaderObjectARB and glGetShaderInfoLog, glCreateProgramObjectARB

Attempts to use profiler cause slicer to balloon in memory (~11G and counting)
Spiraling in:
<pre>
1115 vtkRenderer::UpdateGeometry()
1115 vtkVolume::RenderVolumetricGeometry(vtkViewport*)
1115 vtkGPUVolumeRayCastMapper::Render(vtkRenderer*, vtkVolume*)
1115 vtkOpenGLGPUVolumeRayCastMapper::GPURender(vtkRenderer*, vtkVolume*)
1115 vtkOpenGLGPUVolumeRayCastMapper::PreRender(vtkRenderer*, vtkVolume*, double*, double*, int, unsigned int)
1115 vtkShaderProgram2::Use()
1115 vtkShaderProgram2::Build()
1115 glCreateProgram
1115 gloGetCGLDispatch
1115 0x139fee7b5
1115 _pthread_cond_wait
1115 __semwait_signal
</pre>

Using nvidia graphics, get:
<pre>
6/23/10 2:23:48 PM [0x0-0x65065].com.apple.ShaderBuilder[2220] (0) : fatal error C9999: Nested functions, aborting!
6/23/10 2:23:48 PM [0x0-0x65065].com.apple.ShaderBuilder[2220] Cg compiler terminated due to fatal error
6/23/10 2:23:48 PM com.apple.launchd.peruser.501[812] ([0x0-0x65065].com.apple.ShaderBuilder[2220]) Exited with exit code: 15
</pre>

Using intel graphics, get:
<pre>
6/23/10 2:46:45 PM com.apple.launchd.peruser.501[812] (com.apple.cvmsCompAgent_x86_64[2365]) Job appears to have crashed: Segmentation fault
6/23/10 2:46:45 PM com.apple.ReportCrash.Root[2369] 2010-06-23 14:46:45.366 ReportCrash[2369:2a03] Saved crash report for cvmsComp_x86_64[2365] version ??? (???) to /Library/Logs/DiagnosticReports/cvmsComp_x86_64_2010-06-23-144645_localhost.crash
</pre>

Possible location of failing source:
(located in Slicer3-lib/VTK/VolumeRendering/)

vtkGPUVolumeRayCastMapper_HeaderFS.glsl
vtkGPUVolumeRayCastMapper_ParallelProjectionFS.glsl
vtkGPUVolumeRayCastMapper_CompositeFS.glsl
vtkGPUVolumeRayCastMapper_CompositeNoCroppingFS.glsl
vtkGPUVolumeRayCastMapper_OneComponentFS.glsl
vtkGPUVolumeRayCastMapper_NoShadeFS.glsl

Bug appears to crash compiler when scalarFromValue() called inside trace(). Using intel graphics card causes recoverable crash. Nvidia crashes hard and kills ShaderBuilder.

So functions that implement scalarFromValue are:
vtkGPUVolumeRayCastMapper_FourComponentsFS.glsl
vtkGPUVolumeRayCastMapper_OneComponentFS.glsl

get called by:
vtkGPUVolumeRayCastMapper_CompositeFS.glsl
vtkGPUVolumeRayCastMapper_CompositeMaskFS.glsl

Looking to VTK docs (Looks like Slicer using vers 5.6.0

__________

Volume Rendering code overview:

VTK renderer lives in:
Slicer3-lib/VTK/VolumeRendering/*.glsl
Series of glsl fragment shaders are linked together to form single fragment program. Different .glsl files are linked depending on options chosen. This approach is nice and modular, but seems to expose a bug in the Apple/Nvidia shader compiler.

NCI renderer lives in:
Modules/VolumeRendering/VolumeRenderingReplacements/vtkSlicerGPURayCastVolumeMapper.cxx

==References==

</div>

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-25T13:47:57Z

Barabas:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:Tian_Cao_US_Volume.jpg|[http://sites.google.com/site/tiancaoshomepage/research/3dvr Volume rendering for 3D ultrasound]
</gallery>

==Key Investigators==
* MIT Media Lab: Jim Barabas
* BWH: Noby Hata

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Review volume rendering support in slicer3.6. Test current capabilities and performance. Develop plan for extending rendering capabilities. (This work is towards longer-term goal of developing an image-based photorealistic volume renderer).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Examine code for current volume rendering support. Benchmark on available GPU architectures. Develop and test extensions to current volume shaders.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
Read through code and shaders for the GPU-based volume renderers.

Examined and found quick reproduction steps for bug in Apple/Nvidia shader compiler that prevents ITK volume renderer from working on recent Mac OS X releases.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a information on this wiki page.

==Notes==
We had a breakout session with demos of the Slicer renderers, as well as the VirtualPlace renderer, and the Microsoft Research client-server CUDA renderer.
[[2010 Summer Project Week Breakout Session: Volume Rendering]]

==References==

</div>

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-21T17:56:26Z

Barabas:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:Tian_Cao_US_Volume.jpg|[http://sites.google.com/site/tiancaoshomepage/research/3dvr Volume rendering for 3D ultrasound]
</gallery>

==Key Investigators==
* MIT Media Lab: Jim Barabas
* BWH: Noby Hata

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Review volume rendering support in slicer3.6. Test current capabilities and performance. Develop plan for extending rendering capabilities. (This work is towards longer-term goal of developing an image-based photorealistic volume renderer).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Examine code for current volume rendering support. Benchmark on available GPU architectures. Develop and test extensions to current volume shaders.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a information on this wiki page.

==References==

</div>

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-21T17:37:13Z

Barabas:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:Tian_Cao_US_Volume.jpg|[http://sites.google.com/site/tiancaoshomepage/research/3dvr Volume rendering for 3D ultrasound]
</gallery>

==Key Investigators==
* Jim Barabas
* Noby Hata

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Review volume rendering support in slicer3.6. Test current capabilities and performance. Develop plan for extending rendering capabilities. (This work is towards longer-term goal of developing an image-based photorealistic volume renderer).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Examine code for current volume rendering support. Benchmark on available GPU architectures. Develop and test extensions to current volume shaders.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a information on this wiki page.

==References==

</div>

File:Tian Cao US Volume.jpg

2010-06-21T17:33:02Z

Barabas: Sample Ultrasound volume rendering from http://sites.google.com/site/tiancaoshomepage/

Sample Ultrasound volume rendering from http://sites.google.com/site/tiancaoshomepage/

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-21T17:28:45Z

Barabas:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Jim Barabas
* Noby Hata

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Review volume rendering support in slicer3.6. Test current capabilities and performance. Develop plan for extending rendering capabilities. (This work is towards longer-term goal of developing an image-based photorealistic volume renderer).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Examine code for current volume rendering support. Benchmark on available GPU architectures. Develop and test extensions to current volume shaders.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a information on this wiki page.

==References==

</div>

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-21T17:28:11Z

Barabas:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
[[File:http://6626272284770066605-a-1802744773732722657-s-sites.googlegroups.com/site/tiancaoshomepage/research/4.jpg?attachauth=ANoY7cpJVerynmTIwvxEI6J4_cGafrjVI2SkJpDKQWMFiPD3yGmloLTePLqSdR-RuFl308Hqui5YuD0kis0Hy2J9j1V3hspEVfA9G_hl8YHKnogm5gVJpQGqm_ZuBAquu1QswZVFg9HORVAPgmtRvCAJ2Ch01kVv7eYV91rnL89rCy3zNw_ToD6-7kx-IufmV_FyRtDcAPYCdEF5r3lKI7os4g7bm0mBcw%3D%3D&attredirects=0]]
</gallery>

==Key Investigators==
* Jim Barabas
* Noby Hata

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Review volume rendering support in slicer3.6. Test current capabilities and performance. Develop plan for extending rendering capabilities. (This work is towards longer-term goal of developing an image-based photorealistic volume renderer).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Examine code for current volume rendering support. Benchmark on available GPU architectures. Develop and test extensions to current volume shaders.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a information on this wiki page.

==References==

</div>

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-21T17:11:53Z

Barabas: /* Key Investigators */

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-21T04:27:07Z

Barabas:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Jim Barabas
* Noby Hata

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Review volume rendering support in slicer3.6. Test current capabilities and performance. Develop plan for extending rendering capabilities.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Examine code for current volume rendering support. Benchmark on available GPU architectures. Develop and test extensions to current volume shaders.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a information on this wiki page.

==References==

</div>

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-21T01:54:10Z

Barabas: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Jim Barabas

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Review volume rendering support in slicer3.6. Test current capabilities and performance. Develop plan for extending rendering capabilities.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Examine code for current volume rendering support. Benchmark on available GPU architectures. Develop and test extensions to current volume shaders.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a information on this wiki page.

==References==

</div>

2010 Summer Project Week

2010-06-21T01:53:45Z

Barabas: /* NA-MIC Kit Internals */

Back to [[Project Events]], [[Events]]

[[Image:PW-MIT2010.png|500px|right]]

__TOC__
==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="250px"|Monday, June 21
!width="250px"|Tuesday, June 22
!width="250px"|Wednesday, June 23
!width="250px"|Thursday, June 24
!width="250px"|Friday, June 25
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am:''' NA-MIC Kit Update (Jim Miller)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''9:45am:''' [[Media:2010_Project_Week_Slicer.ppt|3D Slicer Update]] (Steve Pieper)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10:30-11am:''' OpenIGTLink Update (Junichi Tokuda)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''11am-12pm:''' Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room A]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
|'''9am-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:30pm: Tutorial:''' [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)
<br>[[MIT_Project_Week_Rooms#32-155|32-155 (Stata Lecture Hall)]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> QT/Slicer (Steve, JC, J2)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm: <font color="#4020ff">Breakout Session:'''</font>
<br> [[2010 Summer Project Week Breakout Session: Data Management |Data Management]] (Dan Marcus, Stephen Aylward)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
<br>----------------------------------------<br>
'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)
<br>----------------------------------------<br>
'''3-5pm: <font color="#4020ff">Breakout Session:'''</font><br>
[[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widgets]] (Nicole, Kilian, JC)
|'''1-2pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)
<br>----------------------------------------<br>
'''2-3pm:''' Build Instructions: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>
[[2010 Summer Project Week Breakout Session: Volume Rendering|Volume Rendering Demos and Discussion]] (Yin Wu, Steve Pieper)
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

Please note:
*We need to empty room by 1:30pm on Friday. You are welcome to use wireless in Stata.
*Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
*Next Project Week [[AHM_2011| January 3-7, 2011, Salt Lake City, Utah]]

==Projects==

=== Segmentation ===
#[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
#[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
#[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
#[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
#[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)
#[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
#[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)

=== Registration ===
#[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
#[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
#[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
#[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
#[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward, Andriy Fedorov)
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Sylvain Bouix, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== Shape Analysis ===
#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
# [[2010_Summer_Project_Week_Shape_Analysis_UNC|Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
# [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

=== Diffusion ===
#[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
#[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
#[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)
#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)

=== IGT ===
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
#[[2010_Summer_Project_Week_Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound|Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)
#[[2010_Summer_Project_Week_Prostate_Intervention|Prostate Intervention(Junichi, Sam Song, Tamas Ungi)]]
#[[2010_Summer_Project_Week_Liver_Ablation|Liver Ablation (Haiying Liu, Noby Hata)]]
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
# [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)
#[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)
#[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)
#[[2010_Summer_Project_Week_Tracking_Neuroendoscope_Using_EM_Tracker_and_OpenIGTLink|Tracking Neuroendoscope Using EM Tracker and OpenIGTLink]] (Laurent Chauvin, Junichi Tokuda, Noby Hata)
#[[2010_Summer_Project_Week_Implementing_OpenCV_to_Slicer3_for_Neuroendoscopic_Surgery|Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery]] (Atsushi Yamada, Junichi Tokuda, Noby Hata)

=== Radiotherapy ===
#[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
#[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)
#[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )

=== Analysis ===
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_Summer_Project_Week_Mouse_Brain_Cortical_Thickness_Analysis|Mouse brain cortical thickness analysis]] (Joohwi Lee, Ipek Oguz, Martin Styner)
#[[2010_Summer_Project_Week_Primate image analysis using the standard Slicer pipeline|Primate image analysis using the standard Slicer pipeline]] (Yundi Shi, Martin Styner, Andriy Fedorov)
#[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl Fritscher, Vince Magnotta, Peter Karasev, Curt Lisle, Ron Kikinis)
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)

===[[Microscopy Image Analysis]] ===
# [[ 2010 Project Week DICOM supplement 145 | DICOM supplement 145 ]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
# [[ 2010 Summer Project Week Microscopy extensions for ITK | Microscopy Extensions for ITK ]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
# [[Import/Export Farsight-GoFigure results]] ( Arnaud Gelas, Lydie Souhait, Raghav Padmanabhan, Sean Megason, Badri Roysam)
# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Kishore Mosaliganti, Arnaud Gelas, Sean Megason, Raghu Machiraju)
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Arnaud Gelas, Stever Pieper)
# [[Seedings results comparison]] (Antonin Perrot-Audet, Raghav Padmanabhan, Kishore Mosaliganti, Badri Roysam, Sean Megason)
# [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
# [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)

=== NA-MIC Kit Internals ===
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)
#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andriy Fedorov, Yanling Liu, Alex Yarmarkovich, Jim Barabas)
#[[2010 NAMIC Project week:Inventory of Volume Rendering Functionality|Inventory of Volume Rendering Functionality]] (Jim Barabas, Noby Hata)
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis, Alexander Zaitsev)
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]](David Partyka, Steve Pieper, Katie Hayes)
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)
#[[2010 NAMIC Project week: Volume Rendering for Virtual Colonoscopy|Volume Rendering for Virtual Colonoscopy]] (Hiro Yoshida, Yin Wu, Steve Piper, Ron Kikinis)

=== Workflows and Integration ===
# [[Summer_project_week_2010_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>

# Yousef Al-Kofahi , CompuCyte Corporation
# Peter Anderson , retired
# Nicole Aucoin , BWH
# Michel Audette , Kitware
# Stephen Aylward , Kitware, Inc
# Alexis Boucharin , UNC Neuro Image Research and Analysis Laboratories
# Sylvain Bouix , BWH
# Michael Bowers , Johns Hopkins University
# Francois Budin , UNC
# Everette Burdette , Acoustic MedSystems, Inc.
# Laurent CHAUVIN , Brigham and Women's Hospital
# Min Chen , Johns Hopkins University
# Jason Crane , UCSF
# Manasi Datar , SCI Institute
# Liya Ding , The Ohio State University
# Ryan Eckbo , BWH
# Ilker Ersoy , University of Missouri Columbia
# Andriy Fedorov , Surgical Planning Lab
# Jean-Christophe Fillion-Robin , Kitware Inc.
# Julien Finet , Kitware Inc
# James Fishbaugh , SCI Institute
# Karl Fritscher , UMIT
# Yi Gao , Gerogia Tech
# Arnaud GELAS , Harvard Medical School
# Randy Gollub , MGH
# Chris Gorgolewski , SPL
# alexandre gouaillard , CoSMo Software
# Sylvain Gouttard , SCI Institute
# Kedar Grama , Rensselaer Polytechnic Institute
# Daniel Haehn , University of Pennsylvania
# Adel Hafiane , ENSI-Bourges
# Nathan Hageman ,
# Dieter Hahn , University Erlangen
# Michael Halle , BWH/SPL
# Corentin Hamel , UNC Chapel Hill
# Nobuhiko Hata , Brigham and Women's Hospital
# Kathryn Hayes , Brigham and Women's Hospital
# Nicholas Herlambang , AZE, Ltd.
# Leslie Holton , Medtronic Navigation
# Luis Ibanez , KITWARE Inc.
# Jayender Jagadeesan , SPL
# Hans Johnson , University of Iowa
# Tina Kapur , Brigham and Women's Hospital
# Ron Kikinis , Brigham and Women's Hospital
# Minjeong Kim , UNC-Chapel Hill
# Ivan Kolesov , Georgia Institute of Technology
# Garrett Larson , UNC-CH
# Joohwi Lee , UNC Chapel Hill
# Rui Li , MGH
# Stefan Lienhard , LMI
# Curtis Lisle , KnowledgeVis, LLC
# Haiying Liu , Brigham and Women's Hospital
# Felix Liu , Beth Israel Deaconess Medical Center
# Yanling Liu , SAIC-Frederick, Inc.
# Bradley Lowekamp , Lockheed Martin
# raghu machiraju , The Ohio State University
# Vincent Magnotta , The University of Iowa
# mathieu malaterre , CoSMo Software
# Daniel Marcus , Washington University
# William Marks , Focused Ultrasound Lab, BWH, HMS
# Katie Mastrogiacomo , Brigham and Women's Hospital
# Joy Matsui , University
# Sean Megason , Harvard Medical School
# Dominik Meier , BWH, Boston MA
# bjoern menze , CSAIL MIT
# Mikhail Milchenko , WUSTL
# James Miller , GE Research
# Kishore Mosaliganti , Harvard Medical School
# Marc Niethammer , UNC Chapel Hill
# Isaiah Norton , BWH Neurosurgery
# Beck Olson , UCSF
# John Onofrey , Yale University
# Raghav Padmanabhan , RPI
# Kannappan Palaniappan , university of Missouri
# Beatriz Paniagua , University of North Caolina at Chapel Hill
# Xenophon Papademetris , Yale University
# Eun-Joo Park , Brigham & Women's Hospital
# David Partyka , Kitware Inc
# Pratik Patel ,
# Sudhir Pathak , Univeristy Of Pittsburgh
# Thierry PECOT , Ohio State University
# Marta Peroni , Politecnico di Milano
# Antonin Perrot-Audet , Harvard Medical School
# Steve Pieper , Isomics, Inc.
# Wendy Plesniak , BWH
# Kilian Pohl , IBM
# Sonia Pujol , Brigham and Women's Hospital
# Nicolas Rannou , Harvard Medical School
# Tammy Riklin Raviv , MIT, CSAIL
# Marco Ruiz , UCSD
# Johannes Schick , SPL
# William Schroeder , Kitware
# Mark Scully , The Mind Research Network
# Greg Sharp , MGH
# Yundi Shi , UNC Chapel Hill
# Nadya Shusharina , MGH
# Shantanu Singh , The Ohio State University
# Gareth Smith , Wolfson Medical Imaging Centre (WMIC)
# Lydie Souhait , Harvard Medical School
# Dominik Spinczyk , Silesian University of Technology
# Padmapriya Srinivasan ,
# Xiaodong Tao , GE Research
# Matthew Toews , Brigham and Women's Hospital, Harvard Medical School
# Junichi Tokuda , Brigham and Women's Hospital
# Tamas Ungi , Queen's University
# Clement Vachet , UNC Chapel Hill
# Veda Vadyar , Brigham and Women's Hospital
# Gopalkrishna Veni , SCI Institute
# Stuart Wallace , Massachusetts General Hospital
# Demian Wassermann , SPL/LMI/PNL
# Adam Weinrich , Nokia
# Sandy Wells , BWH
# Phillip White , BWH/HMS
# Guorong Wu , University of North Carolina at Chapel Hill
# Yin Wu , Mass General Hospital
# Atsushi Yamada , Nagoya Institute of Technology
# Alexander Yarmarkovich , ISOMICS
# Alexander Zaitsev , Brigham and Womens Hospital

2010 Summer Project Week Breakout Session: Volume Rendering

2010-06-17T19:41:38Z

Barabas: /* Participants */

[[2010_Summer_Project_Week|Back to Project Week 2010]]

= Breakout session on Volume Rendering =
Goal of this session is to compare and contrast various volume rendering approaches in the context of clinical application scenarios. This will mainly be done through hands-on demos and group discussion.

* When: 3pm Thursday June 24
* Where: at a projector in the project week room.

Systems to examine:
* VTK GPU Raycasting in slicer 3.6 (GLSL)
* NCI GPU Raycasting in slicer 3.6 (GLSL)
* Microsoft research volume rendering demo (CUDA, closed source)
* Others?

Scenarios:
* Virtual Colonoscopy
* PET-CT
* Microscopy

== Preparation ==
Earlier in the project week we will work on getting the same datasets loaded on the various systems.

== Participants ==
Please add your name to the list if you are interested in participating in this session
# Steve Pieper, Isomics, Inc.
# Julien Finet, Kitware Inc.
# Alex Yarmarkovich, Isomics, Inc.
# Yanling Liu, SAIC-Frederick/NCI-Frederick.
# Jim Barabas, MIT Media Lab.

2010 NAMIC Project week:Inventory of Volume Rendering Functionality

2010-06-17T18:51:58Z

Barabas: Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|Projects List </gallery> ==Key Investigators== * Jim Barabas <div style="margin: 20px;"> <div sty…'

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Jim Barabas

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Review volume rendering support in slicer3.6. Test current capabilities and performance. Develop plan for extending rendering capabilities.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Examine code for current volume rendering support. Benchmark on available GPU architectures. Develop and test extensions to current volume shaders.
</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

Complete success of this project is near!

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a information on this wiki page.

==References==

</div>

2010 Summer Project Week

2010-06-17T18:46:04Z

Barabas:

Back to [[Project Events]], [[Events]]

[[Image:PW-MIT2010.png|500px|right]]

__TOC__
==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="250px"|Monday, June 21
!width="250px"|Tuesday, June 22
!width="250px"|Wednesday, June 23
!width="250px"|Thursday, June 24
!width="250px"|Friday, June 25
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|8:30am
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|9am-12pm
|
|'''9am:''' NA-MIC Kit Update (Jim Miller)<br>----------------------------------------<br>'''9:45am:''' 3D Slicer Update (Steve Pieper)<br>----------------------------------------<br>'''10:30-11am:''' OpenIGTLink Update (Junichi Tokuda)<br>----------------------------------------<br>'''11am-12pm:''' Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
|'''9am-12pm: Breakout Session:''' [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
|'''9am-5pm: Breakout Session:''' [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
|-
|12pm-1pm
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes<br>Adjourn by 1:30pm
|-
|1pm-5:30pm
|'''1-1:05pm:''' <font color="#0000cc">Ron Kikinis: Welcome</font><br>----------------------------------------<br>'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br>----------------------------------------<br>'''3:30-5:30pm: Tutorial:''' [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)
|'''1-3pm: Breakout Session:''' QT/Slicer (Steve, JC, J2)<br>----------------------------------------<br>'''3-4pm:''' [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]<br>----------------------------------------<br>'''4-5pm: Breakout Session:''' [[2010 Summer Project Week Breakout Session: Data Management |Data Management]] (Dan Marcus, Stephen Aylward)
|'''12:45-1pm:''' [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]<br>----------------------------------------<br>'''1-3pm: Breakout Session:''' [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)<br>----------------------------------------<br>'''3-5pm: Breakout Session:''' [[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)<br>----------------------------------------<br>'''3-4pm: Breakout Session:''' [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widgets]] (Nicole, Kilian, JC)
|'''1-2pm: Breakout Session:''' [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)<br>----------------------------------------<br>'''2-3pm:''' Build Instructions: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)<br>----------------------------------------<br>'''3-4pm: Breakout Session:''' [[2010 Summer Project Week Breakout Session: Volume Rendering|Volume Rendering Demos and Discussion]] (Yin Wu, Steve Pieper)
|
|-
|5:30pm
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|}

Please note:
*We need to empty room by 1:30pm on Friday. You are welcome to use wireless in Stata.
*Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
*Next Project Week [[AHM_2011|in Utah]]

==Projects==

=== Segmentation ===
#[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
#[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
#[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
#[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
#[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
#[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
#[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)

=== Registration ===
#[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
#[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
#[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
#[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
#[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Sylvain Bouix, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
#[[2010_Summer_Project_Week_Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound|Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)
#[[2010_Summer_Project_Week_Prostate_Intervention|Prostate Intervention(Junichi, Sam Song, Tamas Ungi)]]
#[[2010_Summer_Project_Week_Liver_Ablation|Liver Ablation (Haiying Liu, Noby Hata)]]
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
#[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
# [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)
#[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)
#[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)
#[[2010_Summer_Project_Week_Tracking_Neuroendoscope_Using_EM_Tracker_and_OpenIGTLink|Tracking Neuroendoscope Using EM Tracker and OpenIGTLink]] (Lauren Chauvin, Junichi Tokuda, Noby Hata)
#[[2010_Summer_Project_Week_Implementing_OpenCV_to_Slicer3_for_Neuroendoscopic_Surgery|Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery]] (Atsushi Yamada, Junichi Tokuda, Noby Hata)

=== Radiotherapy ===
#[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
#[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)
#[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )

=== Analysis ===
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl Fritscher, Vince Magnota, Peter Karasev, Curt Lisle, Ron Kikinis)
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_Summer_Project_Week_Mouse_Brain_Cortical_Thickness_Analysis|Mouse brain cortical thickness analysis]] (Joohwi Lee, Ipek Oguz, Martin Styner)
#[[2010_Summer_Project_Week_Primate image analysis using the standard Slicer pipeline|Primate image analysis using the standard Slicer pipeline]] (Yundi Shi, Martin Styner)
#[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)

===[[Microscopy Image Analysis]] ===
# [[ 2010 Project Week DICOM supplement 145 | DICOM supplement 145 ]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
# [[ 2010 Summer Project Week Microscopy extensions for ITK | Microscopy Extensions for ITK ]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
# [[ 2010 Summer Project Week Flow Cytometry | Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)
# [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
# [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
# [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)
# [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
# [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)

=== Shape Analysis ===
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
# [[2010_Summer_Project_Week_Shape_Analysis_UNC|Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
# [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)
#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)

=== Diffusion ===
#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)
#[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
#[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)
#[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)

=== NA-MIC Kit Internals ===
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)
#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich, Jim Barabas)
#[[2010 NAMIC Project week:Inventory of Volume Rendering Functionality|Inventory of Volume Rendering Functionality]] (Jim Barabas)
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis, Alexander Zaitsev)
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]](David Partyka, Steve Pieper, Katie Hayes)
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

=== Workflows and Integration ===
# [[Summer_project_week_2010_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesnyak, Charles Guttmann, Ron Kikinis)

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>

# Yousef Al-Kofahi , CompuCyte Corporation
# Peter Anderson , retired
# Nicole Aucoin , BWH
# Michel Audette , Kitware
# Stephen Aylward , Kitware, Inc
# Alexis Boucharin , UNC Neuro Image Research and Analysis Laboratories
# Sylvain Bouix , BWH
# Michael Bowers , Johns Hopkins University
# Francois Budin , UNC
# Everette Burdette , Acoustic MedSystems, Inc.
# Laurent CHAUVIN , Brigham and Women's Hospital
# Min Chen , Johns Hopkins University
# Jason Crane , UCSF
# Manasi Datar , SCI Institute
# Liya Ding , The Ohio State University
# Ryan Eckbo , BWH
# Ilker Ersoy , University of Missouri Columbia
# Andriy Fedorov , Surgical Planning Lab
# Jean-Christophe Fillion-Robin , Kitware Inc.
# Julien Finet , Kitware Inc
# James Fishbaugh , SCI Institute
# Karl Fritscher , UMIT
# Yi Gao , Gerogia Tech
# Arnaud GELAS , Harvard Medical School
# Randy Gollub , MGH
# Chris Gorgolewski , SPL
# alexandre gouaillard , CoSMo Software
# Sylvain Gouttard , SCI Institute
# Kedar Grama , Rensselaer Polytechnic Institute
# Daniel Haehn , University of Pennsylvania
# Adel Hafiane , ENSI-Bourges
# Nathan Hageman ,
# Dieter Hahn , University Erlangen
# Michael Halle , BWH/SPL
# Corentin Hamel , UNC Chapel Hill
# Nobuhiko Hata , Brigham and Women's Hospital
# Kathryn Hayes , Brigham and Women's Hospital
# Nicholas Herlambang , AZE, Ltd.
# Leslie Holton , Medtronic Navigation
# Luis Ibanez , KITWARE Inc.
# Jayender Jagadeesan , SPL
# Hans Johnson , University of Iowa
# Tina Kapur , Brigham and Women's Hospital
# Ron Kikinis , Brigham and Women's Hospital
# Minjeong Kim , UNC-Chapel Hill
# Ivan Kolesov , Georgia Institute of Technology
# Garrett Larson , UNC-CH
# Joohwi Lee , UNC Chapel Hill
# Rui Li , MGH
# Stefan Lienhard , LMI
# Curtis Lisle , KnowledgeVis, LLC
# Haiying Liu , Brigham and Women's Hospital
# Felix Liu , Beth Israel Deaconess Medical Center
# Yanling Liu , SAIC-Frederick, Inc.
# Bradley Lowekamp , Lockheed Martin
# raghu machiraju , The Ohio State University
# Vincent Magnotta , The University of Iowa
# mathieu malaterre , CoSMo Software
# Daniel Marcus , Washington University
# William Marks , Focused Ultrasound Lab, BWH, HMS
# Katie Mastrogiacomo , Brigham and Women's Hospital
# Joy Matsui , University
# Sean Megason , Harvard Medical School
# Dominik Meier , BWH, Boston MA
# bjoern menze , CSAIL MIT
# Mikhail Milchenko , WUSTL
# James Miller , GE Research
# Kishore Mosaliganti , Harvard Medical School
# Marc Niethammer , UNC Chapel Hill
# Isaiah Norton , BWH Neurosurgery
# Beck Olson , UCSF
# John Onofrey , Yale University
# Raghav Padmanabhan , RPI
# Kannappan Palaniappan , university of Missouri
# Beatriz Paniagua , University of North Caolina at Chapel Hill
# Xenophon Papademetris , Yale University
# Eun-Joo Park , Brigham & Women's Hospital
# David Partyka , Kitware Inc
# Pratik Patel ,
# Sudhir Pathak , Univeristy Of Pittsburgh
# Thierry PECOT , Ohio State University
# Marta Peroni , Politecnico di Milano
# Antonin Perrot-Audet , Harvard Medical School
# Steve Pieper , Isomics, Inc.
# Wendy Plesniak , BWH
# Kilian Pohl , IBM
# Sonia Pujol , Brigham and Women's Hospital
# Nicolas Rannou , Harvard Medical School
# Tammy Riklin Raviv , MIT, CSAIL
# Marco Ruiz , UCSD
# Johannes Schick , SPL
# William Schroeder , Kitware
# Mark Scully , The Mind Research Network
# Greg Sharp , MGH
# Yundi Shi , UNC Chapel Hill
# Nadya Shusharina , MGH
# Shantanu Singh , The Ohio State University
# Gareth Smith , Wolfson Medical Imaging Centre (WMIC)
# Lydie Souhait , Harvard Medical School
# Dominik Spinczyk , Silesian University of Technology
# Padmapriya Srinivasan ,
# Xiaodong Tao , GE Research
# Matthew Toews , Brigham and Women's Hospital, Harvard Medical School
# Junichi Tokuda , Brigham and Women's Hospital
# Tamas Ungi , Queen's University
# Clement Vachet , UNC Chapel Hill
# Veda Vadyar , Brigham and Women's Hospital
# Gopalkrishna Veni , SCI Institute
# Stuart Wallace , Massachusetts General Hospital
# Demian Wassermann , SPL/LMI/PNL
# Adam Weinrich , Nokia
# Sandy Wells , BWH
# Phillip White , BWH/HMS
# Guorong Wu , University of North Carolina at Chapel Hill
# Yin Wu , Mass General Hospital
# Atsushi Yamada , Nagoya Institute of Technology
# Alexander Yarmarkovich , ISOMICS
# Alexander Zaitsev , Brigham and Womens Hospital