NAMIC Wiki - User contributions [en]

Linear Mixed-effects shape model to explore Huntington's Disease Data

2013-06-21T14:00:05Z

Datar: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Ctrl01.png|fixed-effects slope for 7 control subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
Image:HD01.png|fixed-effects slope for 6 HD subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Dave Welch
* Utah: Manasi Datar, Josh Cates, Ross Whitaker

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

<h3>Objective</h3>
Make the linear mixed-effects shape model accessible for further exploration of Huntington's Disease Data

</div>

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

<h3>Approach, Plan</h3>
Meet with UIowa team to:
* give an overview of results from the linear mixed-effects shape model
* explain the ShapeWorks command line tools to optimize and analyze correspondences
* discuss next steps toward making these tools accessible to UIowa team

</div>

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

<h3>Progress</h3>
preliminary results look promising

[https://github.com/joshcates/ITKParticleShapeModeling ITKv4] module for mixed-effects model available on GitHub
* tested on Windows and Linux
* application to run mixed-effects model on single component shapes (90%)

To Do
* get working code for shape complexes (multiple structures per shape)
* example parameter file for preprocessing shapes, initializing correspondences and applying mixed-effects model
* extracting labels from input labelmap (various components in the shape) - clarify and possibly add a tool to the preprocessing stage

</div>
</div>

==References==
M Datar, P Muralidharan, A Kumar, S Gouttard, J Piven, G Gerig, RT Whitaker, PT Fletcher, [http://www.cs.utah.edu/~manasi/pubs/MixedEffectsSTIA2012.pdf Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy], STIA 2012

Linear Mixed-effects shape model to explore Huntington's Disease Data

2013-06-21T13:55:22Z

Datar: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Ctrl01.png|fixed-effects slope for 7 control subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
Image:HD01.png|fixed-effects slope for 6 HD subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Dave Welch
* Utah: Manasi Datar, Josh Cates, Ross Whitaker

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

<h3>Objective</h3>
Make the linear mixed-effects shape model accessible for further exploration of Huntington's Disease Data

</div>

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

<h3>Approach, Plan</h3>
Meet with UIowa team to:
* give an overview of results from the linear mixed-effects shape model
* explain the ShapeWorks command line tools to optimize and analyze correspondences
* discuss next steps toward making these tools accessible to UIowa team

</div>

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

<h3>Progress</h3>
preliminary results look promising

ITKv4 module for mixed-effects model available at: https://github.com/joshcates/ITKParticleShapeModeling
* tested on Windows and Linux
* application to run mixed-effects model on single component shapes (90%)

To Do
* get working code for shape complexes (multiple structures per shape)
* example parameter file for preprocessing shapes, initializing correspondences and applying mixed-effects model
* extracting labels from input labelmap (various components in the shape) - clarify and possibly add a tool to the preprocessing stage

</div>
</div>

==References==
M Datar, P Muralidharan, A Kumar, S Gouttard, J Piven, G Gerig, RT Whitaker, PT Fletcher, [http://www.cs.utah.edu/~manasi/pubs/MixedEffectsSTIA2012.pdf Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy], STIA 2012

Linear Mixed-effects shape model to explore Huntington's Disease Data

2013-06-21T12:20:27Z

Datar: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Ctrl01.png|fixed-effects slope for 7 control subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
Image:HD01.png|fixed-effects slope for 6 HD subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Dave Welch
* Utah: Manasi Datar, Josh Cates, Ross Whitaker

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

<h3>Objective</h3>
Make the linear mixed-effects shape model accessible for further exploration of Huntington's Disease Data

</div>

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

<h3>Approach, Plan</h3>
Meet with UIowa team to:
* give an overview of results from the linear mixed-effects shape model
* explain the ShapeWorks command line tools to optimize and analyze correspondences
* discuss next steps toward making these tools accessible to UIowa team

</div>

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

<h3>Progress</h3>
preliminary results look promising

ITKv4 module for mixed-effects model available
* tested on Windows and Linux
* application to run mixed-effects model on single component shapes (90%)

To Do
* get working code for shape complexes (multiple structures per shape)
* example parameter file for preprocessing shapes, initializing correspondences and applying mixed-effects model
* extracting labels from input labelmap (various components in the shape) - clarify and possibly add a tool to the preprocessing stage

</div>
</div>

==References==
M Datar, P Muralidharan, A Kumar, S Gouttard, J Piven, G Gerig, RT Whitaker, PT Fletcher, [http://www.cs.utah.edu/~manasi/pubs/MixedEffectsSTIA2012.pdf Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy], STIA 2012

Linear Mixed-effects shape model to explore Huntington's Disease Data

2013-06-20T18:09:48Z

Datar: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Ctrl01.png|fixed-effects slope for 7 control subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
Image:HD01.png|fixed-effects slope for 6 HD subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Dave Welch
* Utah: Manasi Datar, Josh Cates, Ross Whitaker

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

<h3>Objective</h3>
Make the linear mixed-effects shape model accessible for further exploration of Huntington's Disease Data

</div>

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

<h3>Approach, Plan</h3>
Meet with UIowa team to:
* give an overview of results from the linear mixed-effects shape model
* explain the ShapeWorks command line tools to optimze and analyze correspondences
* discuss next steps toward making these tools accessible to UIowa team

</div>

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

<h3>Progress</h3>
* preliminary results look promising
* ITKv4 module for mixed-effects model available
** ITKv4 module tested on Linux system
** Mixed-effects model for shapes from a single structure from the HD data (in progress). This should result in:
*** application (source code) to run mixed-effects shape model for HD data
*** an example parameter file
* To Do
** get working code for shape complexes (multiple structures per shape)
** extracting labels from input labelmap (various components in the shape) - clarify and possibly add a tool to the preprocessing stage

</div>
</div>

==References==
M Datar, P Muralidharan, A Kumar, S Gouttard, J Piven, G Gerig, RT Whitaker, PT Fletcher, [http://www.cs.utah.edu/~manasi/pubs/MixedEffectsSTIA2012.pdf Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy], STIA 2012

Linear Mixed-effects shape model to explore Huntington's Disease Data

2013-06-20T17:50:05Z

Datar: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Ctrl01.png|fixed-effects slope for 7 control subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
Image:HD01.png|fixed-effects slope for 6 HD subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Dave Welch
* Utah: Manasi Datar, Josh Cates, Ross Whitaker

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

<h3>Objective</h3>
Make the linear mixed-effects shape model accessible for further exploration of Huntington's Disease Data

</div>

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

<h3>Approach, Plan</h3>
Meet with UIowa team to:
* give an overview of results from the linear mixed-effects shape model
* explain the ShapeWorks command line tools to optimze and analyze correspondences
* discuss next steps toward making these tools accessible to UIowa team

</div>

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

<h3>Progress</h3>
* preliminary results look promising
* ITKv4 module for mixed-effects model available
** ITKv4 module tested on Linux system
** Mixed-effects model for shapes from a single structure from the HD data (in progress). This should result in:
*** application (source code) to run mixed-effects shape model for HD data
*** an example parameter file
* To Do
** get working code for shape complexes (multiple structures per shape)
** work on extracting labels from input labelmap (various components in the shape) - possibly add a tool to the preprocessing stage ?

</div>
</div>

==References==
M Datar, P Muralidharan, A Kumar, S Gouttard, J Piven, G Gerig, RT Whitaker, PT Fletcher, [http://www.cs.utah.edu/~manasi/pubs/MixedEffectsSTIA2012.pdf Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy], STIA 2012

Linear Mixed-effects shape model to explore Huntington's Disease Data

2013-06-20T17:49:24Z

Datar: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Ctrl01.png|fixed-effects slope for 7 control subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
Image:HD01.png|fixed-effects slope for 6 HD subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Dave Welch
* Utah: Manasi Datar, Josh Cates, Ross Whitaker

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

<h3>Objective</h3>
Make the linear mixed-effects shape model accessible for further exploration of Huntington's Disease Data

</div>

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

<h3>Approach, Plan</h3>
Meet with UIowa team to:
* give an overview of results from the linear mixed-effects shape model
* explain the ShapeWorks command line tools to optimze and analyze correspondences
* discuss next steps toward making these tools accessible to UIowa team

</div>

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

<h3>Progress</h3>
* preliminary results look promising
* ITKv4 module for mixed-effects model available
** ITKv4 module tested on Linux system
** Mixed-effects model for shapes from a single structure from the HD data (in progress). This should result in:
*** application (source code) to run mixed-effects shape model for HD data
*** an example parameter file
* To Do
** get working code for shape complexes (multiple structures per shape)
** work on extracting labels from input labelmap (various components in the shape)

</div>
</div>

==References==
M Datar, P Muralidharan, A Kumar, S Gouttard, J Piven, G Gerig, RT Whitaker, PT Fletcher, [http://www.cs.utah.edu/~manasi/pubs/MixedEffectsSTIA2012.pdf Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy], STIA 2012

Linear Mixed-effects shape model to explore Huntington's Disease Data

2013-06-20T15:09:42Z

Datar: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Ctrl01.png|fixed-effects slope for 7 control subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
Image:HD01.png|fixed-effects slope for 6 HD subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Dave Welch
* Utah: Manasi Datar, Josh Cates, Ross Whitaker

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

<h3>Objective</h3>
Make the linear mixed-effects shape model accessible for further exploration of Huntington's Disease Data

</div>

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

<h3>Approach, Plan</h3>
Meet with UIowa team to:
* give an overview of results from the linear mixed-effects shape model
* explain the ShapeWorks command line tools to optimze and analyze correspondences
* discuss next steps toward making these tools accessible to UIowa team

</div>

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

<h3>Progress</h3>
* preliminary results look promising
* ITKv4 module for mixed-effects model available
** ITKv4 module tested on Linux system
** Mixed-effects model for shapes from a single structure from the HD data (in progress). This should result in:
*** application (source code) to run mixed-effects shape model for HD data
*** an example parameter file
** To Do: get working code for shape complexes (multiple structures per shape)

</div>
</div>

==References==
M Datar, P Muralidharan, A Kumar, S Gouttard, J Piven, G Gerig, RT Whitaker, PT Fletcher, [http://www.cs.utah.edu/~manasi/pubs/MixedEffectsSTIA2012.pdf Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy], STIA 2012

Linear Mixed-effects shape model to explore Huntington's Disease Data

2013-06-20T14:13:23Z

Datar: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Ctrl01.png|fixed-effects slope for 7 control subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
Image:HD01.png|fixed-effects slope for 6 HD subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Dave Welch
* Utah: Manasi Datar, Josh Cates, Ross Whitaker

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

<h3>Objective</h3>
Make the linear mixed-effects shape model accessible for further exploration of Huntington's Disease Data

</div>

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

<h3>Approach, Plan</h3>
Meet with UIowa team to:
* give an overview of results from the linear mixed-effects shape model
* explain the ShapeWorks command line tools to optimze and analyze correspondences
* discuss next steps toward making these tools accessible to UIowa team, to facilitate further exploration of the Huntington's disease Data

</div>

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

<h3>Progress</h3>
* preliminary results look promising
* ITKv4 module for mixed-effects model available
** ITKv4 module tested on Linux system
** Mixed-effects model for shapes from a single structure from the HD data (in progress). This should result in:
*** application (source code) to run mixed-effects shape model for HD data
*** an example parameter file
** To Do: get working code for shape complexes (multiple structures per shape)

</div>
</div>

==References==
M Datar, P Muralidharan, A Kumar, S Gouttard, J Piven, G Gerig, RT Whitaker, PT Fletcher, [http://www.cs.utah.edu/~manasi/pubs/MixedEffectsSTIA2012.pdf Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy], STIA 2012

Linear Mixed-effects shape model to explore Huntington's Disease Data

2013-06-20T14:12:55Z

Datar: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Ctrl01.png|fixed-effects slope for 7 control subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
Image:HD01.png|fixed-effects slope for 6 HD subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Dave Welch
* Utah: Manasi Datar, Josh Cates, Ross Whitaker

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

<h3>Objective</h3>
Make the linear mixed-effects shape model accessible for further exploration of Huntington's Disease Data

</div>

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

<h3>Approach, Plan</h3>
Meet with UIowa team to:
* give an overview of results from the linear mixed-effects shape model
* explain the ShapeWorks command line tools to optimze and analyze correspondences
* discuss next steps toward making these tools accessible to UIowa team, to facilitate further exploration of the Huntington's disease Data

</div>

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

<h3>Progress</h3>
* preliminary results look promising
* ITKv4 module for mixed-effects model available
** ITKv4 module tested on Linux system
** Mixed-effects model for shapes from a single structure from the HD data (in progress). This should result in:
*** application (source code) to run mixed-effects shape model for HD data
*** an example parameter file
** To Do: get working code for shape complex (multiple structures per shape)

</div>
</div>

==References==
M Datar, P Muralidharan, A Kumar, S Gouttard, J Piven, G Gerig, RT Whitaker, PT Fletcher, [http://www.cs.utah.edu/~manasi/pubs/MixedEffectsSTIA2012.pdf Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy], STIA 2012

Linear Mixed-effects shape model to explore Huntington's Disease Data

2013-06-20T14:06:12Z

Datar: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Ctrl01.png|fixed-effects slope for 7 control subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
Image:HD01.png|fixed-effects slope for 6 HD subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Dave Welch
* Utah: Manasi Datar, Josh Cates, Ross Whitaker

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

<h3>Objective</h3>
Make the linear mixed-effects shape model accessible for further exploration of Huntington's Disease Data

</div>

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

<h3>Approach, Plan</h3>
Meet with UIowa team to:
* give an overview of results from the linear mixed-effects shape model
* explain the ShapeWorks command line tools to optimze and analyze correspondences
* discuss next steps toward making these tools accessible to UIowa team, to facilitate further exploration of the Huntington's disease Data

</div>

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

<h3>Progress</h3>
* preliminary results look promising
* ITKv4 module for mixed-effects model (Josh) available for Manasi to test
** ITKv4 module tested on Linux system
** Mixed-effects model for shapes from a single structure from the HD data (in progress). This should result in:
*** application (source code) to run particle optimization for the HD data
*** an example parameter file
* Once tested, this module can be used by UIowa team on a larger cohort of cases

</div>
</div>

==References==
M Datar, P Muralidharan, A Kumar, S Gouttard, J Piven, G Gerig, RT Whitaker, PT Fletcher, [http://www.cs.utah.edu/~manasi/pubs/MixedEffectsSTIA2012.pdf Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy], STIA 2012

Linear Mixed-effects shape model to explore Huntington's Disease Data

2013-06-20T14:04:30Z

Datar:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Ctrl01.png|fixed-effects slope for 7 control subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
Image:HD01.png|fixed-effects slope for 6 HD subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Dave Welch
* Utah: Manasi Datar, Josh Cates, Ross Whitaker

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

<h3>Objective</h3>
Make the linear mixed-effects shape model accessible for further exploration of Huntington's Disease Data

</div>

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

<h3>Approach, Plan</h3>
Meet with UIowa team to:
* give an overview of results from the linear mixed-effects shape model
* explain the ShapeWorks command line tools to optimze and analyze correspondences
* discuss next steps toward making these tools accessible to UIowa team, to facilitate further exploration of the Huntington's disease Data

</div>

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

<h3>Progress</h3>
* preliminary results look promising
* ITKv4 module for mixed-effects model (Josh) available for Manasi to test
** ITKv4 module tested on Linux system
** Mixed-effects model for shapes from a single structure from the HD data (in progress)
* Once tested, this module can be used by UIowa team on a larger cohort of cases

</div>
</div>

==References==
M Datar, P Muralidharan, A Kumar, S Gouttard, J Piven, G Gerig, RT Whitaker, PT Fletcher, [http://www.cs.utah.edu/~manasi/pubs/MixedEffectsSTIA2012.pdf Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy], STIA 2012

File:HD01.png

2013-06-20T14:02:39Z

Datar: visualization of the fixed-effects slope for 6 subjects with HD (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction

visualization of the fixed-effects slope for 6 subjects with HD (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction

File:Ctrl01.png

2013-06-20T14:00:17Z

Datar: visualization of the fixed-effects slope for 7 control subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction

visualization of the fixed-effects slope for 7 control subjects (10 sub-cortical structures, 3 time points each). blue => expansion, yellow => contraction

2013 Summer Project Week

2013-06-20T13:54:43Z

Datar: /* Huntington's Disease */

Back to [[Events]]
[[image:PW-MIT2013.png|300px]]

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT 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'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] (Steve Pieper) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans Johnson, Brad Lowekamp)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|
'''9:30-10:30am''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina Kapur)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
'''12pm''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[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"|[http://www.na-mic.org/Wiki/index.php/File:NamicToAmphi.png Lunch in Outdoor Amphitheather!]
|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)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-262]]
|
|<br>----------------------------------------<br>'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|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
|
|}

== '''Projects''' ==

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template this template] to create wiki pages for your project. Then link the page here with a list of key personnel.

==Some Stats==
73 Projects, 97 Attendees. First time attendees 25.

===Huntington's Disease===
* [[Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data]] (Hans, Demian)
* [[Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation]] (Hans)
* [[2013_Summer_Project_Week:SinglePrecisionRegistrationITK| Single Precision Registration]] (Hans, Brad Lowekamp, Dave, Ali Ghayoor)
* [[Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend]] (Dave)
* [[DWIConvert]] (Dave, Kent Williams)
* [[Enhance and update SPL atlas]] (Dave, Hans)
* [[Linear Mixed-effects shape model to explore Huntington's Disease Data]] (Manasi, Dave, Josh, Hans, Ross)


7 projects

===Traumatic Brain Injury===
* [[Visualization and quantification of peri-contusional white matter bundles in traumatic brain injury using diffusion tensor imaging]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[Clinically oriented assessment of local changes in the properties of white matter affected by intra-cranial hemorrhage]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[Exploring multi-modal registration for improved longitudinal modeling of patient-specific 4D DTI data]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[2013_Summer_Project_Week: A Portable Ultrasound Device for Intracranial Hemorrhage Detection|A Portable Ultrasound Device for Intracranial Hemorrhage Detection]] (Jason White, Vicki Noble, Kirby Vosburgh)


5 projects

===Atrial Fibrillation and Cardiac Image Analysis===
* [[2013_Summer_Project_Week:Fibrosis_analysis|Fibrosis distribution analysis]] (Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:SegmentationAidedRegistration|Segmentation Aided Registration]] (Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:CARMA_workflow_wizard|Cardiac MRI Toolkit LA segmentation and enhancement quantification workflow wizard]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Documentataion|Cardiac MRI Toolkit Documentation Project]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Visualization|LA model visualization]] (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_AutoLASeg|Cardiac MRI Toolkit: Automatic LA Segmentation with Graph Cuts Module]] (Salma Bengali, Alan Morris, Josh Cates, Gopal, Ross Whitaker, Rob MacLeod)
* [[2013_Summer_Project_Week:Sobolev_Segmenter|Medical Volume Segmentation Using Sobolev Active Contours]] (Arie Nakhmani, Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:Left_Ventricle_Motion_Analysis_using_Tagged_MRI|Left Ventricle Motion Analysis using Tagged MRI]] (Yang Yu, Shaoting Zhang, Dimitris Metaxas)


8 projects

===Radiation Therapy===
* [[2013_Summer_Project_Week:Landmark_Registration| Landmark Registration]] (Steve, Nadya, Greg, Paolo, Erol)
* [[2013_Summer_Project_Week:Slicer_RT:_DICOM-RT_Export | SlicerRT: Dicom-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]] (Greg Sharp, Kevin Wang, Maxime Desplanques)
* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, Kevin Wang, Andrey Fedorov)
* [[2013_Summer_Project_Week:Deformable_transforms | Deformable transform handling in Transforms module]] (Csaba Pinter, Alex Yarmarkovich, Andras Lasso)
* [[2013_Summer_Project_Week:Brachy_HDR_Ultrasound | Creating DICOM series from ultrasound for prostate HDR brachytherapy]] (Adam Rankin)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Christian Wachinger, Karl Fritscher, Greg Sharp, Matthew Brennan)
* [[2013_Summer_Project_Week:Prostate_radiotherapy_DICOM_communication|DICOM communication between Slicer and Oncentra Prostate radiation therapy planning system]] (Andrey Fedorov, Csaba Pinter, Emily Neubauer-Sugar, Alireza Mehrtash)


8 projects

===IGT and Device Integration with Slicer===
* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering for Neurosurgery]] (Lauren O'Donnell)
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Stephen Aylward, Isaiah Norton, Tamas Ungi)
* [[2013_Summer_Project_Week:Ultrasound_Needle_Detection| Ultrasound Needle Detection]] (Alireza Mehrtash, Daniel Kostro, Matthew Toews, Tamas Ungi, William Wells, Tina Kapur)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:LabelMapStatistics| Label map statistics]] (Laurent Chauvin, Csaba Pinter)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
* [[2013_Summer_Project_Week:3D_prostate_segmentation_of_Ultrasound_image| Segmentation of Prostate Gland from 3D US for Prostate Interventions]] (Xu Li, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:3D_prostate_registration_of_Ultrasound_image_using_MRI| Registration of an MRI delineated image of the Prostate Gland ot a 3D US for Prostate Interventions]] (Demian Wassermann, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:ProstateBRP| MRI-guided robotic prostate interventinos]] (Junichi Tokuda, Greg Fischer, Nirav Patel, Nobuhiko Hata, Clare Tempnay)


12 projects

===Chronic Obstructive Pulmonary Disease===
* [[2013_Summer_Project_Week:Airway_Inspector_Porting | Porting Airway Inspector to Slicer 4]] (Raul San Jose, Demian Wassermann, Rola Harmouche)
* [[2013_Summer_Project_Week:MRML_Infrastructure_Airway_Inspector | Airway Inspector: Slicer Extension and MRML Infrastructure]] (Demian Wassermann, Raul San Jose, Rola Harmouche)
* [[2013_Summer_Project_Week:Nipype_CLI_Integration | Integration of Nipype with CLI modules in the Chest Imaging Platform Library ]] (Rola Harmouche,Demian Wassermann, Raul San Jose)


3 projects

=== '''Additional Collaborations'''===
* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ivan Kolesov, Allen Tannenbaum, Ron Kikinis)
* [[2013_Summer_Project_Week:XNAT 3D Viewer| XNAT 3D Viewer]] (Amanda Hartung, Steve Pieper, Daniel Haehn)
* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpenIGTLink]] (Sebastian Tauscher, Thomas Neff, Junichi Tokuda, Nobuhiko Hata)
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
* [[2013_Summer_Project_Week: Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease| Individualized Neuroimaging Content Analysis using 3D Slicer]] (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
* [[2013_Summer_Project_Week:CMFReg | Cranio-Maxillofacial Registration]] (Vinicius Boen)
* [[2013_Summer_Project_Week:DTIPipelineExtensions | DTI Analysis Pipeline as Slicer4 Extensions]] (Francois Budin)
*[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Lilla Zollei, Nathaniel Reynolds, Daniel Haehn, Nicolas Rannou, Steve Pieper, Rudolph Pienaar)
* [[2013_Summer_Project_Week:Biomedical_Image_Computing_Teaching_Modules|3D Slicer based Biomedical image computing teaching modules]] (A. Vilchis, J-C. Avila-Vilchis, S. Pujol)
* [[2013_Summer_Project_Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer|Analyzing Breast Tumor Heterogeneity Using 3D Slicer]] (Sneha Durgapal, Jayender Jagadeesan, Tobias Penzkofer, Vivek Narayan)
* [[2013_Summer_Project_Week:WMH Segmentation for Stroke|WMH Segmentation for Stroke]] (Adrian Dalca, Ramesh Sridharan, Kayhan Batmanghelich, Polina Golland)
* [[2013_Summer_Project_Week:WMQL Integration in Slicer|White Matter Query Language (WMQL) Integration in Slicer]] (Demian Wassermann, Carl-Fredrik Westin)
* [[2013_Summer_Project_Week:Documentation for Slicer 4.2 Data Loading and 3D Visualization|Documentation for Slicer 4.2 Data Loading and 3D Visualization]] (Parth Amin WIT, Matt Flynn WIT, Dr. Pujol HMS)
* [[2013_Summer_Project_Week:WM Geometry Tools|Integration in Slicer of white matter geometry tools]] (Peter Savadjiev, Carl-Fredrik Westin)


16 projects

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin, Ron Kikinis)
* [[2013_Summer_Project_Week:Patient_hierarchy | Patient hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Andras Lasso, Csaba Pinter, Jc, Steve, Jim)
* [[2013_Summer_Project_Week:CLI_Matlab | CLI module implementation in Matlab]] (Andras Lasso, Jc, Steve, Jim)
* [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
* [[ITK -VTK wrapper]] (Paolo Zaffino, Greg Sharp, Steve Pieper)
* [[2013_Summer_Project_Week:Optimizing start time of slicer| Optimizing start time of slicer]] (Jc, Steve)
* [[Common resampling and conversion utility functions in Slicer]] (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)
* [[2013_Summer_Project_Week:SimpleITK_GUI| Common Usage GUI for SimpleITK]] (Brad Lowekamp, Hans Johnson, Dave Welch)
* [[2013_Summer_Project_Week:Extension_dependencies| Extension dependencies]] (Jc, Adam Rankin)
* [[2013_Summer_Project_Week:Parameter_heirarchy| Parameter (time) Hierarchy]] (Adam Rankin)
* [[2013_Summer_Project_Week:ITK_Shared_IO_Libraries| ITK Shared I/O Libraries]] (Brad Lowekamp)
* [[2013_Summer_Project_Week:Python_Embedding| Python Embedding Library]] (Rui, Jim, Jc, Steve)

14 projects

== '''Background''' ==

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy 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. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 25th 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 40-50 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], [http://www.cimit.org CIMIT], and OCAIRO. 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 17-21, 2013.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' http://www.regonline.com/namic2013summerprojweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list before May 27th. See [[2013_Summer_Project_Week/RoomSharing|here]]

== '''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 projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. 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 Thursday May 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, all project leads to complete [[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 13: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## 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.)
## Where possible, 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. (Matt)
# 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.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1233699 Please click here to register.])

#Parth Amin, WIT, aminp@wit.edu
#Charles Anderson, BWH, canderson26@partners.org
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
#Juan Carlos Avila Vilchis, Univ del Estado de Mexico, jc.avila.vilchis@hotmail.com
#Kayhan Batmanghelich, MIT, kayhan@csail.mit.edu
#Salma Bengali, Univ UT, salma.bengali@carma.utah.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Taylor Braun-Jones, GE Healthcare, taylor.braun-jones@ge.com
#Matthew Brennan, MIT, brennanm@mit.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Ivan Buzurovic, BWH/HMS, ibuzurovic@lroc.harvard.edu
#Josh Cates, Univ UT, cates@sci.utah.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Laurent Chauvin, BWH - SPL, lchauvin@bwh.harvard.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Adrian Dalca, MIT, adalca@MIT.EDU
#Matthew D'Artista, BWH - SPL, mdartista7@gmail.com
#Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
#Sneha Durgapal, BWH, durgapalsneha@gmail.com
#Luping Fang, Zhejiang Univ of Technology (China), flp@zjut.edu.cn
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Gregory Fischer, WPI, gfischer@wpi.edu
#Barton Fiske, zSpace Inc, bfiske@zspace.com
#Matthew Flynn, WIT, flynnm3@wit.edu
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Maria Gonzalez-Puente, WIT, gonzalezpuentem@wit.edu
#Dan Groszmann, GE Healthcare, daniel.groszmann@ge.com
#Daniel Haehn, Boston Childrens Hospital, daniel.haehn@childrens.harvard.edu
#Michael Halle, BWH-SPL, mhalle@bwh.harvard.edu
#Rola Harmouche, BWH, rharmo@bwh.harvard.edu
#Amanda Hartung, Rochester Inst of Tech, amh1646@rit.edu
#Nobuhiko Hata, BWH, hata@bwh.harvard.edu
#Nicholas Herlambang, AZE Technology Inc, nicholas.herlambang@azetech.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Andrei Irimia, UCLA, andrei.irimia@loni.ucla.edu
#Jayender Jagadeesan, BWH-SPL, jayender@bwh.harvard.edu
#Sylvain Jaume, WIT, jaumes@wit.edu
#Daniel Jimenez, daniel.jimenez@gmail.com
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Alex Kikinis, BWH, alexkikinis@gmail.com
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Nils Klarlund, IEEE, klarlund@ieee.org
#Daniel Kostro, BWH, dkostro@bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
#Rui Li, GE Global Research, li.rui@ge.com
#Xu Li, BWH, lixu0103@gmail.com
#Lichen Liang, MGH, lichenl@nmr.mgh.harvard.edu
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
#Nikos Makris, MGH, nikos@nmr.mgh.harvard.edu
#Katie Mastrogiacomo, BWH - SPL, kmast@bwh.harvard.edu
#Alireza Mehrtash, BWH - SPL, mehrtash@bwh.harvard.edu
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Isaiah Norton, BWH, inorton@bwh.harvard.edu
#Lauren O'Donnell, BWH, odonnell@bwh.harvard.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Jian Pan, Zhejiang Univ of Technology (China), pj@zjut.edu.cn
#George Papadimitriou, MGH, georgep@nmr.mgh.harvard.edu
#Nirav Patel, WPI, napatel@wpi.edu
#Tobias Penzkofer, BWH - SPL, pt@bwh.harvard.edu
#Rudolph Pienaar, Boston Childrens Hospital, Rudolph.Pienaar@childrens.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#William Plishker, IGI Technologies, will@igitechnologies.com
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
#Nathaniel Reynolds, MGH, reynolds@nmr.mgh.harvard.edu
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
#Peter Savadjiev, BWH, petersv@bwh.harvard.edu
#Tobias Schroeder, GE Healthcare, tobias.schroeder@ge.com
#Anuja Sharma, Univ UT-SCI Institute, anuja@cs.utah.edu
#Greg Sharp, MGH, gcsharp@partners.org
#Nadya Shusharina, MGH, nshusharina@partners.org
#Sebastian Tauscher, Leibniz Univ Hannover (Germany), sebastian.tauscher@imes.uni-hannover.de
#Clare Tempany, BWH, ctempanyafdhal@partners.org
#Cyrill von Tiesenhausen, KUKA Laboratories (Germany), cyrill.tiesenhausen@kuka.com
#Gaurie Tilak, BWH, gaurie_tilak@hms.harvard.edu
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Junichi Tokuda, BWH, tokuda@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
#Kirby Vosburgh, BWH, kirby@bwh.harvard.edu
#Christian Wachinger, MIT, wachinge@mit.edu
#Bo Wang, Univ UT-SCI Institute, bowang@sci.utah.edu
#Demian Wassermann, BWH, demian@bwh.harvard.edu
#David Welch, Univ Iowa, david-welch@uiowa.edu
#William Wells, BWH/HMS, sw@bwh.harvard.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Alex Yarmarkovich, Isomics Inc, alexy@bwh.harvard.edu
#Kitaro Yoshimitsu, BWH, kitarof1@bwh.harvard.edu
#Yang Yu, Rutgers Univ, yyu@cs.rutgers.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
#Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu

Linear Mixed-effects shape model to explore Huntington's Disease Data

2013-06-20T13:54:18Z

Datar: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:fixedEffects01.png|fixed-effects (slope) [blue denotes expansion, yellow denotes contraction]
Image:fixedEffects02.png|fixed-effects (slope) [blue denotes expansion, yellow denotes contraction]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Dave Welch
* Utah: Manasi Datar, Josh Cates, Ross Whitaker

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

<h3>Objective</h3>
Make the linear mixed-effects shape model accessible for further exploration of Huntington's Disease Data

</div>

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

<h3>Approach, Plan</h3>
Meet with UIowa team to:
* give an overview of results from the linear mixed-effects shape model
* explain the ShapeWorks command line tools to optimze and analyze correspondences
* discuss next steps toward making these tools accessible to UIowa team, to facilitate further exploration of the Huntington's disease Data

</div>

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

<h3>Progress</h3>
* preliminary results look promising
* ITKv4 module for mixed-effects model (Josh) available for Manasi to test
** ITKv4 module tested on Linux system
** Mixed-effects model for shapes from a single structure from the HD data (in progress)
* Once tested, this module can be used by UIowa team on a larger cohort of cases

</div>
</div>

==References==
M Datar, P Muralidharan, A Kumar, S Gouttard, J Piven, G Gerig, RT Whitaker, PT Fletcher, [http://www.cs.utah.edu/~manasi/pubs/MixedEffectsSTIA2012.pdf Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy], STIA 2012

Linear Mixed-effects shape model to explore Huntington's Disease Data

2013-06-20T13:45:58Z

Datar: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:fixedEffects01.png|fixed-effects (slope) [blue denotes expansion, yellow denotes contraction]
Image:fixedEffects02.png|fixed-effects (slope) [blue denotes expansion, yellow denotes contraction]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Dave Welch
* Utah: Manasi Datar, Ross Whitaker

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

<h3>Objective</h3>
Make the linear mixed-effects shape model accessible for further exploration of Huntington's Disease Data

</div>

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

<h3>Approach, Plan</h3>
Meet with UIowa team to:
* give an overview of results from the linear mixed-effects shape model
* explain the ShapeWorks command line tools to optimze and analyze correspondences
* discuss next steps toward making these tools accessible to UIowa team, to facilitate further exploration of the Huntington's disease Data

</div>

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

<h3>Progress</h3>
* preliminary results look promising
* ITKv4 module for mixed-effects model (Josh) available for Manasi to test
** ITKv4 module tested on Linux system
** Mixed-effects model for single component HD shapes (in progress)
* Once tested, this module can be used by UIowa team on a larger cohort of cases

</div>
</div>

==References==
M Datar, P Muralidharan, A Kumar, S Gouttard, J Piven, G Gerig, RT Whitaker, PT Fletcher, [http://www.cs.utah.edu/~manasi/pubs/MixedEffectsSTIA2012.pdf Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy], STIA 2012

Linear Mixed-effects shape model to explore Huntington's Disease Data

2013-06-19T19:20:52Z

Datar: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:fixedEffects01.png|fixed-effects (slope) [blue denotes expansion, yellow denotes contraction]
Image:fixedEffects02.png|fixed-effects (slope) [blue denotes expansion, yellow denotes contraction]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Dave Welch
* Utah: Manasi Datar, Ross Whitaker

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

<h3>Objective</h3>
Make the linear mixed-effects shape model accessible for further exploration of Huntington's Disease Data

</div>

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

<h3>Approach, Plan</h3>
Meet with UIowa team to:
* give an overview of results from the linear mixed-effects shape model
* explain the ShapeWorks command line tools to optimze and analyze correspondences
* discuss next steps toward making these tools accessible to UIowa team, to facilitate further exploration of the Huntington's disease Data

</div>

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

<h3>Progress</h3>
* preliminary results look promising
* ITKv4 module for mixed-effects model (Josh) available for Manasi to test
* Once tested, this module can be used by UIowa team on a larger cohort of cases

</div>
</div>

==References==
M Datar, P Muralidharan, A Kumar, S Gouttard, J Piven, G Gerig, RT Whitaker, PT Fletcher, [http://www.cs.utah.edu/~manasi/pubs/MixedEffectsSTIA2012.pdf Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy], STIA 2012

2013 Summer Project Week

2013-06-16T20:25:28Z

Datar: /* Huntington's Disease */

Back to [[Events]]
[[image:PW-MIT2013.png|300px]]

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT 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'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] (Steve Pieper) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans Johnson, Brad Lowekamp)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina Kapur)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[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)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|<br>----------------------------------------<br>'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|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
|
|}

== '''Projects''' ==

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template this template] to create wiki pages for your project. Then link the page here with a list of key personnel.

===Huntington's Disease===
* [[Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend]] (Dave)
* [[DWIConvert]] (Dave, Kent Williams)
* [[Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data]] (Hans, Demian)
* [[Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation]] (Hans)
* [[Enhance and update SPL atlas]] (Dave, Hans)
* [[Linear Mixed-effects shape model to explore Huntington's Disease Data]] (Dave, Manasi, Hans, Ross)
* [[2013_Summer_Project_Week:SinglePrecisionRegistrationITK| Single Precision Registration]] (Hans, Brad Lowekamp, Dave, Ali Ghayoor)

===Traumatic Brain Injury===
* [[Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[Visualization and quantification of peri-contusional white matter bundles in traumatic brain injury using diffusion tensor imaging]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[Clinically oriented assessment of local changes in the properties of white matter affected by intra-cranial hemorrhage]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[2013_Summer_Project_Week: A Portable Ultrasound Device for Intracranial Hemorrhage Detection|A Portable Ultrasound Device for Intracranial Hemorrhage Detection]] (Jason White, Vicki Noble, Kirby Vosburgh)
* [[Exploring multi-modal registration for improved longitudinal modeling of patient-specific 4D DTI data]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)

===Atrial Fibrillation and Cardiac Image Analysis===
* [[2013_Summer_Project_Week:Fibrosis_analysis|Fibrosis distribution analysis]] (Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:CARMA_workflow_wizard|Cardiac MRI Toolkit LA segmentation and enhancement quantification workflow wizard]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Documentataion|Cardiac MRI Toolkit Documentation Project]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Visualization|LA model visualization]] (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_AutoLASeg|Cardiac MRI Toolkit: Automatic LA Segmentation with Graph Cuts Module]] (Salma Bengali, Alan Morris, Josh Cates, Gopal, Ross Whitaker, Rob MacLeod)
* [[2013_Summer_Project_Week:Sobolev_Segmenter|Medical Volume Segmentation Using Sobolev Active Contours]] (Arie Nakhmani, Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:Left_Ventricle_Motion_Analysis_using_Tagged_MRI|Left Ventricle Motion Analysis using Tagged MRI]] (Yang Yu, Shaoting Zhang, Dimitris Metaxas)

===Radiation Therapy===
* [[2013_Summer_Project_Week:Landmark_Registration| Landmark Registration]] (Steve, Nadya, Greg, Paolo, Erol)
* [[2013_Summer_Project_Week:Slicer_RT:_DICOM-RT_Export | SlicerRT: Dicom-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]] (Greg Sharp, Kevin Wang, Maxime Desplanques)
* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, Kevin Wang, Andrey Fedorov, anyone else?)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Christian Wachinger, Karl Fritscher, Greg Sharp, Matthew Brennan)
* [[2013_Summer_Project_Week:Deformable_transforms | Deformable transform handling in Transforms module]] (Csaba Pinter, Alex Yarmarkovich, Andras Lasso, ?)
* [[2013_Summer_Project_Week:Brachy_HDR_Ultrasound | Using ultrasound for prostate HDR brachytherapy]] (Adam Rankin)

===IGT and Device Integration with Slicer===
* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering for Neurosurgery]] (Lauren O'Donnell)
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Steven Aylward, Isaiah Norton, Tamas Ungi)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)

===Chronic Obstructive Pulmonary Disease===
* [[2013_Summer_Project_Week:Airway_Inspector_Porting | Porting Airway Inspector to Slicer 4]] (Raul San Jose, Demian Wassermann, Rola Harmouche)
* [[2013_Summer_Project_Week:MRML_Infrastructure_Airway_Inspector | Airway Inspector: Slicer Extension and MRML Infrastructure]] (Demian Wassermann, Raul San Jose, Rola Harmouche)
* [[2013_Summer_Project_Week:Nipype_CLI_Integration | Integration of Nipype with CLI modules in the Chest Imaging Platform Library ]] (Rola Harmouche,Demian Wassermann, Raul San Jose)

=== '''Additional Collaborations'''===
* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ron Kikinis)
* [[2013_Summer_Project_Week:XNAT 3D Viewer| XNAT 3D Viewer]] (Amanda Hartung, Steve Pieper, Daniel Haehn)
* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpenIGTLink]] (Sebastian Tauscher, Junichi Tokuda, Nobuhiko Hata)
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
* [[2013_Summer_Project_Week: Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease| Individualized Neuroimaging Content Analysis using 3D Slicer]] (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
* [[2013_Summer_Project_Week:CMFReg | Cranio-Maxillofacial Registration]] (Vinicius Boen)
*[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Daniel Haehn, Steve Pieper, Rudolph Pienaar, Lilla Zollei, Nathaniel Reynolds)
* [[2013_Summer_Project_Week:Biomedical_Image_Computing_Teaching_Modules|3D Slicer based Biomedical image computing teaching modules]] (A. Vilchis, J-C. Avila-Vilchis, S. Pujol)
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
* [[2013_Summer_Project_Week:3D_prostate_segmentation_of_Ultrasound_image| 3D Prostate segmentation of ultrasound image]] (Xu Li, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer|Analyzing Breast Tumor Heterogeneity Using 3D Slicer]] (Sneha Durgapal, Jayender Jagadeesan, Tobias Penzkofer, Vivek Narayan)

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin, Ron Kikinis)
* [[2013_Summer_Project_Week:Patient_hierarchy | Patient hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Andras Lasso, Csaba Pinter, Jc, Steve, Jim, ?)
* [[2013_Summer_Project_Week:CLI_Matlab | CLI module implementation in Matlab]] (Andras Lasso, Jc, Steve, Jim, ?)
* [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
* [[Plastimatch in NiPype]] (Paolo, Dave, Hans)
* [[2013_Summer_Project_Week:Optimizing start time of slicer| Optimizing start time of slicer]] (Jc, Steve)
* [[Common resampling and conversion utility functions in Slicer]] (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)
* [[2013_Summer_Project_Week:SimpleITK_GUI| Common Usage GUI for SimpleITK]] (Hans Johnson, Dave Welch, Brad Lowekamp)
* [[2013_Summer_Project_Week:Extension_dependencies| Extension dependencies]] (Jc, Adam Rankin)
* [[2013_Summer_Project_Week:Parameter_heirarchy| Parameter Hierarchy]] (Adam Rankin, ??)

== '''Background''' ==

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy 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. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 25th 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 40-50 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], [http://www.cimit.org CIMIT], and OCAIRO. 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 17-21, 2013.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' http://www.regonline.com/namic2013summerprojweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list before May 27th. See [[2013_Summer_Project_Week/RoomSharing|here]]

== '''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 projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. 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 Thursday May 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, all project leads to complete [[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 13: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## 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.)
## Where possible, 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. (Matt)
# 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.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1233699 Please click here to register.])

#Parth Amin, WIT, aminp@wit.edu
#Charles Anderson, BWH, canderson26@partners.org
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
#Juan Carlos Avila Vilchis, Univ del Estado de Mexico, jc.avila.vilchis@hotmail.com
#Salma Bengali, Univ UT, salma.bengali@carma.utah.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Matthew Brennan, MIT, brennanm@mit.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Ivan Buzurovic, BWH/HMS, ibuzurovic@lroc.harvard.edu
#Josh Cates, Univ UT, cates@sci.utah.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Laurent Chauvin, BWH - SPL, lchauvin@bwh.harvard.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Adrian Dalca, MIT, adalca@MIT.EDU
#Matthew D'Artista, BWH - SPL, mdartista7@gmail.com
#Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
#Sneha Durgapal, BWH, durgapalsneha@gmail.com
#Luping Fang, Zhejiang Univ of Technology (China), flp@zjut.edu.cn
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Gregory Fischer, WPI, gfischer@wpi.edu
#Barton Fiske, zSpace Inc, bfiske@zspace.com
#Matthew Flynn, WIT, flynnm3@wit.edu
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Maria Gonzalez-Puente, WIT, gonzalezpuentem@wit.edu
#Daniel Haehn, Boston Childrens Hospital, daniel.haehn@childrens.harvard.edu
#Michael Halle, BWH-SPL, mhalle@bwh.harvard.edu
#Rola Harmouche, BWH, rharmo@bwh.harvard.edu
#Amanda Hartung, Rochester Inst of Tech, amh1646@rit.edu
#Nobuhiko Hata, BWH, hata@bwh.harvard.edu
#Nicholas Herlambang, AZE Technology Inc, nicholas.herlambang@azetech.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Andrei Irimia, UCLA, andrei.irimia@loni.ucla.edu
#Jayender Jagadeesan, BWH-SPL, jayender@bwh.harvard.edu
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Alex Kikinis, BWH, alexkikinis@gmail.com
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Nils Klarlund, IEEE, klarlund@ieee.org
#Daniel Kostro, BWH, dkostro@bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
#Rui Li, GE Global Research, li.rui@ge.com
#Xu Li, BWH, lixu0103@gmail.com
#Lichen Liang, MGH, lichenl@nmr.mgh.harvard.edu
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
#Nikos Makris, MGH, nikos@nmr.mgh.harvard.edu
#Katie Mastrogiacomo, BWH - SPL, kmast@bwh.harvard.edu
#Alireza Mehrtash, BWH - SPL, mehrtash@bwh.harvard.edu
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Isaiah Norton, BWH, inorton@bwh.harvard.edu
#Lauren O'Donnell, BWH, odonnell@bwh.harvard.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Jian Pan, Zhejiang Univ of Technology (China), pj@zjut.edu.cn
#George Papadimitriou, MGH, georgep@nmr.mgh.harvard.edu
#Tobias Penzkofer, BWH - SPL, pt@bwh.harvard.edu
#Rudolph Pienaar, Boston Childrens Hospital, Rudolph.Pienaar@childrens.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
#Nathaniel Reynolds, MGH, reynolds@nmr.mgh.harvard.edu
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
#Peter Savadjiev, BWH, petersv@bwh.harvard.edu
#Anuja Sharma, Univ UT-SCI Institute, anuja@cs.utah.edu
#Greg Sharp, MGH, gcsharp@partners.org
#Nadya Shusharina, MGH, nshusharina@partners.org
#Sebastian Tauscher, Leibniz Univ Hannover (Germany), sebastian.tauscher@imes.uni-hannover.de
#Clare Tempany, BWH, ctempanyafdhal@partners.org
#Cyrill von Tiesenhausen, KUKA Laboratories (Germany), cyrill.tiesenhausen@kuka.com
#Gaurie Tilak, BWH, gaurie_tilak@hms.harvard.edu
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Junichi Tokuda, BWH, tokuda@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
#Kirby Vosburgh, BWH, kirby@bwh.harvard.edu
#Christian Wachinger, MIT, wachinge@mit.edu
#Bo Wang, Univ UT-SCI Institute, bowang@sci.utah.edu
#Demian Wassermann, BWH, demian@bwh.harvard.edu
#David Welch, Univ Iowa, david-welch@uiowa.edu
#William Wells, BWH/HMS, sw@bwh.harvard.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Alex Yarmarkovich, Isomics Inc, alexy@bwh.harvard.edu
#Kitaro Yoshimitsu, BWH, kitarof1@bwh.harvard.edu
#Yang Yu, Rutgers Univ, yyu@cs.rutgers.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
#Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu

2012 Summer Project Week

2012-06-12T12:39:36Z

Datar: /* Registrants */

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|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-10am:''' What's new in Slicer4 (Group. Multivolumes, Charts.) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''10-11am''' Slicer4 Python <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> <br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Computation Core PIs: closed meeting with Ron:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[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)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' Slicer4 Extensions (JC) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session: DICOM, Networking, RT, Segmentations (Steve, Greg, Andras, Andre)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-30pm: <font color="#4020ff">Breakout Session:'''</font>Qt Testing (JC)
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:Ultrasound|Ultrasound]] (Tamas)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|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
|
|}

==Projects==

This is where the list of projects goes...

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
# Intraoperative White Matter Tract Detection Module (Lauren O'Donnell, Isaiah Norton)
# [[Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury]] (Andrei Irimia, Danielle Pace, Micah Chambers, Stephen Aylward)
# [[2012_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
# [[2012_Summer_Project_Week:4D_Segmentation_TBI|4D Segmentation of longitudinal MRI of TBI patients]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig)
# An Intraoperative Transcranial Ultrasound Brain Shift Monitor (Jason White, Alex Golby, Isaiah Norton)

==='''Radiation Therapy'''===
#[[2012_Summer_Project_Week:Overlapping_structures|Overlapping structures]] (Greg Sharp, Steve Pieper)
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck|Atlas-based segmentation for head and neck]] (Greg Sharp, Nadya Shusharina, James Shackleford, Polina Golland)
#[[2012_Summer_Project_Week:SlicerRT|Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck| Deformable Registration for Head and Neck ]] (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)

==='''Huntington's Disease'''===
# [[2012_Summer_Project_Week:DTIPrep|DTIPrep]] (David Welch, Hans Johnson)
# [[2012_Summer_Project_Week:Fast Fiducial Registration|Fast Fiducial Registration Module]] (David Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)
# [[2012_Summer_Project_Week:ANTS Registation|ANTS Registation Module]] (David Welch, Hans Johnson)
# [[2012_Summer_Project_Week:Nipype Integration|Slicer/Nipype Integration]] (Hans Johnson)
# [[2012_Summer_Project_Week:DicomToNrrd|DicomToNrrdConverter Integration]] (Kent Williams)
# [[2012_Summer_Project_Week:4D shape analysis|4D shape analysis]] (James Fishbaugh, Marcel Prastawa, Guido Gerig)
# [[2012_Summer_Project_Week:DTI-Reg|DTI atlas based fiber analysis]] (Francois Budin)

==='''Atrial Fibrillation'''===
# Model-based segmentation of left Atrium using Graph-cuts (Gopal Veni, Ross Whitaker)
# [[2012_Summer_Project_Week:UtahCardiacRegistration|Cardiac MRI Registration Module]] (Alan Morris, Danny Perry, Josh Cates, Greg Gardner, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahAutoScar|Automatic Left Atrial Scar Detection]] (Danny Perry, Alan Morris, Josh Cates, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahInhomogeneity|MRI Inhomogeneity Correction Filter]] (Alan Morris, Eugene Kholmovski, Josh Cates, Danny Perry, Rob MacLeod)
# OpenIGT for realtime MRI-guided RF ablation (Rob MacLeod, Junichi Tokuda)
# [[2012_Summer_Project_Week:VecReg|Vector-Valued Cardiac MRI Registration]] (Yi Gao, Josh Cates, Liang-Jia Zhu, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
# [[2012_Summer_Project_Week:RidgeExtractionAtrialWallSegmentation|Perceptual Ridge Extraction for Atrial Wall Segmentation in MRI]] (Arie Nakhmani, Allen Tannenbaum)

==='''Device Integration with Slicer and General Image Guided Therapy'''===
# [[2012_Summer_Project_Week:iGyne|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:ProstateBxReviewWorkflow_Slicer4|Prostate biopsy multiparametric MRI review using Slicer4]] (Andrey Fedorov, Kemal Tuncali, Steve Pieper, Pat Mongkolwat)
# [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer to facilitate regulatory approval]] (Andras Lasso, Chris Wedlake)
# [[2012_Summer_Project_Week:4D_Ultrasound_Slicer4|4D Ultrasound on Slicer4]] (Nobuhiko Hata, Laurent Chauvin)
# [[2012_Summer_Project_Week:Kinect4Slicer|Kinect4Slicer]] (Nobuhiko Hata, Laurent Chauvin)

==='''General Segmentation'''===
#[[2012_Summer_Project_Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets|Semi-automated airway segmentation from 0.64mm lung CT datasets]] (Padraig Cantillon-Murphy, Raul San Jose Estepar, Pietro Nardelli)
# [[2012_Summer_Project_Week:QuantitativePETImageAnalysisModule|Quantitative PET Image Analysis Module]] (Markus Van Tol)
#Segmentation with Label Fusion (Ramesh Sridharan, Christian Wachinger, Polina Golland)
#[[Loading and segmentation of histopathology imaging for radiological-pathological correlation]] (Tobias Penzkofer)

==='''General Registration'''===
# Interactive registration (Kunlin Cao GRC, Guillaume Pernelle BWH, Simrin Nagpal Queens)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)
# [[2012_Summer_Project_Week:ElastixIntegration| Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DTIRegistration| Highly Deformable DTI Registration for cases with large pathological variations]] (Aditya Gupta, Martin Styner, Matthew Toews)
# [[2012_Summer_Project_Week:DifficultRegistration| Registration of Difficult Images]] (Matthew Toews, Stefan Klein, Marc Modat, Aditya Gupta, Martin Styner, William Wells)
# [[2012_Summer_Project_Week:PlastimatchIntegration| Plastimatch integration]] (James Shackleford, Greg Sharp)

==='''General Diffusion Tractography'''===
#
#

==='''Vessels'''===
#
#

==='''Informatics'''===
# [[2012_Summer_Project_Week:AIM_for_QIN|Applicability of AIM to QIN use cases]] (Andrey Fedorov, Reinhard Beichel, Jayashree Kalpathy-Cramer, Pat Mongkolwat, Daniel Rubin)

==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# [[2012_Summer_Project_Week:AnnotationModule|Annotation module redesign for Slicer]] (Nicole)
# [[2012_Summer_Project_Week:MultiVolumeSupport|Multivolume support]] (Andrey, Jim)
# Python CLI modules (Demian, JC, Julien). See [http://www.na-mic.org/Bug/view.php?id=2039 #2039]
# [[2012_Summer_Project_Week:Charting|Charting]] (Jim)
# [[2012_Summer_Project_Week:SimpleITK Integration|SimpleITK Integration]] (Hans Johnson, Bradley Lowekamp)
# GPU Editor Effects
# XTK/WebGL Exporter (Daniel, Nicolas - Children's Hospital Boston)
# General Usability issues (e.g. LM,FG,BG blending)
# Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
# [[2012_Summer_Project_Week:XNATSlicerIntegration|XNAT/Slicer Integration]] (Sunil, Dan, Steve,...)
# Pilot QIN use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)
# [[2012_Summer_Project_Week:ITKv4 Integration|ITKv4 Integration]] (Hans Johnson, Julien Finet, Jim). See [http://www.na-mic.org/Bug/view.php?id=2007 #2007]
# [[2012_Summer_Project_Week:Reporting|Reporting module]] (Andrey, Nicole, Steve, Ron, Pat)
# [[2012_Summer_Project_Week:LongitudinalPETCTModule|Slicer Module for longitudinal analysis of PET-CT]] (Paul, Andriy, Ron, Markus,...)
# [[2012_Summer_Project_Week:Threat Modeling|Threat Modeling]] (JC, J2, Anthony)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy 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. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th 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 40-50 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], [http://www.cimit.org CIMIT], and OCAIRO. 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 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' No room blocks have been reserved in any area hotel. Please select a [http://web.mit.edu/institute-events/visitor/stay.html |hotel of your choice] and make reservations as early as possible. Some area hotels are:
**marriott cambridge center
**marriott residence inn kendall square
**le meridien central square
**hotel marlowe cambridge
**royal sonesta hotel cambridge

== 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 26, 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 Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[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 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## 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.)
## Where possible, 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. (Matt)
# 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.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1089602 Please click here to register.])

#Anderson, Peter, retired, traneus@verizon.net
#Arbisser, Amelia, MIT, arbisser@mit.edu
#Aucoin, Nicole, BWH, Nicole@bwh.harvard.edu
#Aylward, Stephen, Kitware, stephen.aylward@kitware.com
#Blumfield, Anthony, Radnostics, Anthony.Blumfield@Radnostics.com
#Budin, Francis, NIRAL-UNC, fbudin@unc.edu
#Cao, Kunlin, GE Research, cao@ge.com
#Chauvin, Laurent, SPL, lchauvin@bwh.harvard.edu
#Chen, Elvis, Robarts, chene@robarts.ca
#Chen, Xiaojun, SPL, xiaojun@bwh.harvard.edu
#Datar, Manasi, Utah SCI, datar@sci.utah.edu
#Diedrich, Karl, AZE R&D, karl.diedrich@azeresearch.com
#Egger, Jan, BWH, egger@bwh.harvard.edu
#Fedorov, Andriy, BWH, fedorov@bwh.harvard.edu
#Fillion-Robin, Jean-Christophe, Kitware, jchris.fillionr@kitware.com
#Finet, Julien, Kitware, julien.finet@kitware.com
#Fishbaugh, James, SCI, jfishbau@sci.utah.edu
#Gardner, Greg, SCI, ggardner@sci.utah.edu
#Gouaillard, Alexandre, A*STAR, agouaillard@gmail.com
#Johnson, Hans, Univ Iowa, hans-johnson@uiowa.edu
#Kapur, Tina, BWH HMS, tkapur@bwh.harvard.edu
#Kikinis, Ron, HMS, kikinis@bwh.harvard.edu
#Klein, Stefan, Erasmus MC, s.klein@erasmusmc.nl
#Koek, Marcel, Erasmus MC, m.koek@erasmusmc.nl
#Kolesov, Ivan, GA Tech, ivan.kolesov@gatech.edu
#Kumar, Sunil, Washington Univ St Louis, kumars@mir.wustl.edu
#Lasso, Andras, Queen's Univ, lasso@cs.queensu.ca
#Macule, Raul, AZE R&D, raul.macule@azeresearch.com
#Meier, Dominik, BWH, meier@bwh.harvard.edu
#Miller, Jim, GE Research, millerjv@ge.com
#Modat, Marc, Univ College London, m.modat@ucl.ac.uk
#Moloney, Brendan, AIRC, moloney.brendan@gmail.com
#Mongkolwat, Pattanasak, Northwestern U, p-mongkolwat@northwestern.edu
#Nagpal, Simrin, Queen’s Univ, 7sn6@cs.queensu.ca
#Nakhmani, Arie, BU, nakhmani@gmail.com
#Nardelli, Pietro, Univ College Cork, pie.nardelli@gmal.com
#Nouranian, Saman, Univ BC, samann@ece.ubc.ca
#Paniagua, Beatriz, Univ NC Chapel Hill, bpaniagua@gmail.com
#Pernelle, Guillaume, BWH, gpernelle@gmail.com
#Pieper, Steve, Isomics, pieper@bwh.harvard.edu
#Pinter, Csaba, Queen's Univ, pinter@cs.queensu.ca
#Pujol, Sonia, BWH, spujol@bwh.harvard.edu
#Shackleford, James, MGH, jshackleford@partners.org
#Shusharina, Nadya, MGH, nshusharina@partners.org
#Sojoudi, Samira, Univ BC, samiras@ece.ubc.ca
#Tiwari, Pallavi, Rutgers, pallavi.tiwar@gmail.com
#Toews, Matthew, BWH HMS, mt@bwh.harvard.edu
#Ungi, Tamas, Queen's Univ, ungi@cs.queensu.ca
#Van Tol, Markus, Univ Iowa, mvantol@engineering.uiowa.edu
#Vosburgh, Kirby, BWH, kirby@bwh.harvard.edu
#Wang, Bo, SCI, bowang@sci.utah.edu
#Wedlake, Chris, Robarts, cwedlake@robarts.ca
#Welch, David, Univ Iowa, david-welch@uiowa.edu
#Yamada, Atsushi, BWH, ayamada@bwh.harvard.edu
#Yarmakovich, Alex, Isomics, alexy@bwh.harvard.edu

Algorithm:Utah

2011-12-07T22:41:27Z

Datar:

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of Utah Algorithms (PI: Ross Whitaker) =

We are developing new methods in the areas of statistical shape analysis, MRI tissue segmentation, and diffusion tensor image processing and analysis. We are building shape analysis tools that can generate efficient statistical models appropriate for analyzing anatomical shape differences in the brain. We are developing a wide range of tools for diffusion tensor imaging, that span the entire pipeline from image processing to automatic white matter tract extraction to statistical testing of clinical hypotheses.

= Utah Projects =

{| cellpadding="10" style="text-align:left;"

|-
{| cellpadding="10" style="text-align:left;"

| | [[Image:sgerber_brainmanifold_oasis_manifold.png|200px]]
| |

== [[Projects:BrainManifold|Brain Manifold Learning]] ==

This work is concerned with modeling high dimensional spaces, such as the space of brain images. Common approach for representing populations are template or clustering based approaches. In this project we develop a data driven method to learn a manifold representation from a set of brain images. The presented approach is described and evaluated in the setting of brain MRI but generalizes to other application domains.

S Gerber, T Tasdizen, S Joshi, R Whitaker, On the Manifold Structure of the Space of Brain Images, MICCAI 2009.

S Gerber, T Tasdizen, R Whitaker, Dimensionality Reduction and Principal Surfaces via Kernel Map, ICCV 2009.

S. Gerber, T. Tasdizen, P.T. Fletcher, S. Joshi, R. Whitaker, Manifold Modeling for Brain Population Analysis, Medical Image Anal, 3, 2010.

|-
| style="width:15%" | [[Image:EPI.png|200px]]
| style="width:85%" |

== [[Projects:EPIDistortionCorrection| Correction for Geometric Distortion in Echo Planar Images]] ==

We have developed a variational image-based approach to correct the susceptibility artifacts in the alignment of diffusion weighted and structural MRI.The correction is formulated as an optimization of a penalty that captures the intensity difference between the jacobian corrected EPI baseline images and a corresponding T2-weighted structural image.

<font color="red"></font> R Tao, P T Fletcher, S Gerber, R Whitaker, A Variational Image-Based Approach to the Correction of Susceptibility Artifacts
in the Alignment of Diffusion Weighted and Structural MRI, IPMI 2009.

|-

| | [[Image:pipeline.png|150px]]
| |

== [[Projects:StructuralAndDWIPipeline| A Framework for Joint Analysis of Structural and Diffusion MRI]] ==

This framework addresses the simultaneous alignment and ﬁltering of DWI images to correct eddy current artifacts and the subsequent alignment of those images to structural, T1 MRI to correct for susceptibility artifacts, and this paper demonstrates the importance of performing these corrections. It also shows how a T1-based, group speciﬁc atlas can be used to generate grey-matter regions of interest that can drive subsequent connectivity analyses. The result is a system that can be combined with a variety of tools for MRI analysis for tissue classiﬁcation, morphometry, and cortical parcellation.

<font color="red"></font> Ran Tao, P. Thomas Fletcher, Ross T. Whitaker, in MICCAI 2008 on Computational Diffusion MRI.

|-

| | [[Image:Sulcaldepth.png|200px]]
| |

== [[Projects:CorticalCorrespondenceWithParticleSystem|Cortical Correspondence using Particle System]] ==

In this project, we want to compute cortical correspondence on populations, using various features such as cortical structure, DTI connectivity, vascular structure, and functional data (fMRI). This presents a challenge because of the highly convoluted surface of the cortex, as well as because of the different properties of the data features we want to incorporate together. [[Projects:CorticalCorrespondenceWithParticleSystem|More...]]

<font color="red"></font> Oguz I, Niethammer M, Cates J, Whitaker R, Fletcher T, Vachet C, Styner M. “Cortical Correspondence with Probabilistic Fiber Connectivity”. Proc. Information Processing in Medical Imaging, 2009.

|-

| | [[Image:CatesNamicFigure3.png|200px]]
| |

== [[Projects:ParticlesForShapesAndComplexes|Adaptive, Particle-Based Sampling for Shapes and Complexes]] ==

This research is a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wider range of problems than existing methods, including nonmanifold surfaces and objects of arbitrary topology. [[Projects:ParticlesForShapesAndComplexes|More...]]

<font color="red"></font> Particle-Based Shape Analysis of Multi-object Complexes. Cates J., Fletcher P.T., Styner M., Hazlett H.C., Whitaker R. Int Conf Med Image Comput Comput Assist Interv. 2008;11(Pt 1):477-485.

|-

| | [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|200px]]
| |

== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|Shape Analysis Framework using SPHARM-PDM]] ==

The UNC shape analysis is based on an analysis framework of objects with spherical topology, described mainly by sampled spherical harmonics SPHARM-PDM. The input of the shape analysis framework is a set of binary segmentations of a single brain structure, such as the hippocampus or caudate. These segmentations are converted into a shape description (SPHARM) with correspondence and analyzed via Hotelling T^2 two sample metric. [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|More...]]

<font color="red"></font> Zhao Z., Taylor W., Styner M., Steffens D., Krishnan R., Macfall J. , Hippocampus shape analysis and late-life depression. PLoS ONE. 2008 Mar 19;3(3):e1837.

|-

| | [[Image:HeadRegressionResult.png|200px]]
| |

== [[Projects:ShapeRegression|Particle Based Shape Regression]] ==

Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. We propose a new method to building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The method is applied to provide new results on clinical MRI data related to early development of the human head.

<font color="red"></font> M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging, MICCAI 2009.

|-

| | [[Image:NonRegularSurfCorres.png|200px]]
| |

== [[Projects:NonRegularSurfCorres|Geometric Correspondence for Nonregular Surfaces]] ==

To resolve the challenges posed by highly nonregular surfaces, we have proposed an efficient method which incorporates Geodesic distances and an entropy based on surface normals to improve correspondences.

<font color="red"></font> M Datar, Y Gur, B Paniagua, M Styner, R Whitaker, Geometric Correspondence for Ensembles of
Nonregular Shapes, MICCAI 2011.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|DTI Volumetric White Matter Connectivity]] ==

We have developed a PDE-based approach to white matter connectivity from DTI that is founded on the principal of minimal paths through the tensor volume. Our method computes a volumetric representation of a white matter tract given two endpoint regions. We have also developed statistical methods for quantifying the full tensor data along these pathways, which should be useful in clinical studies using DT-MRI. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

|-
| style="width:15%" | [[Image:DTIFiltering.jpg|200px]]
| style="width:85%" |

== [[Projects:DTIProcessingTools|DTI Processing and Statistics Tools]] ==

We implement the diffusion weighted image (DWI) registration model from the paper of G.K.Rohde et al. Patient head motion and eddy currents distortion cause artifacts in maps of diffusion parameters computer from DWI. This model corrects these two distortions at the same time including brightness correction.

|-

| | [[Image:Brain-seg-utah.png|200px]]
| |

== [[Projects:TissueClassificationWithNeighborhoodStatistics| Tissue Classification with Neighborhood Statistics]] ==

We have implemented an MRI tissue classification algorithm based on unsupervised non-parametric density estimation of tissue intensity classes.
[[Projects:TissueClassificationWithNeighborhoodStatistics|More...]]

|}

Projects:ShapeRegression

2011-12-07T22:35:35Z

Datar:

Back to [[Algorithm:Utah|Utah Algorithms]]
__NOTOC__
= Particle Based Shape Regression =

{|
|[[Image:HeadRegressionResult.png|thumb|512px|Changes in early head shape with log(age).]]
|}

= Description =
Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. In this paper we propose a new method to building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The statistical significance of the dependence is evaluated using permutation tests designed to estimate the likelihood of achieving the observed statistics under numerous rearrangements of the shape parameters with respect to the explanatory variable. We demonstrate the method on synthetic
data and provide a new results on clinical MRI data related to early development of the human head.

= Key Investigators =

* Utah: Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker

= Publications =

'' In Press ''

* M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging, MICCAI 2009

[[Category:Shape Analysis]] [[Category:Statistics]]

Projects:NonRegularSurfCorres

2011-12-07T22:34:29Z

Datar: Created page with ' Back to Utah Algorithms __NOTOC__ = Geometric Correspondence for Nonregular Surfaces = {| |[[Image:NonRegularSurfCorres.png|thumb|450px|Examples of chall…'

Back to [[Algorithm:Utah|Utah Algorithms]]
__NOTOC__
= Geometric Correspondence for Nonregular Surfaces =

{|
|[[Image:NonRegularSurfCorres.png|thumb|450px|Examples of challenges posed by nonregular surfaces.]]
|}

= Description =
An ensemble of biological shapes can be represented and analyzed with a dense set of point correspondences. In previous work, optimal point placement was determined by optimizing an information theoretic criterion that depends on relative spatial locations on different shapes combined with pairwise Euclidean distances between nearby points on the same shape. These choices have prevented such methods from effectively characterizing shapes with complex geometry such as thin or highly curved features. This paper extends previous methods for automatic shape correspondence by taking into account the underlying geometry of individual shapes. This is done by replacing the Euclidean distance for intrashape pairwise particle interactions by the geodesic distance. A novel set of numerical techniques for fast distance computations on curved surfaces is used to extract these distances. In addition, we introduce an entropy term that incorporates surface normal information to achieve better particle correspondences near sharp features. Finally, we demonstrate this new method on synthetic and biological datasets.

= Key Investigators =

* Utah: Manasi Datar, Yaniv Gur, Beatriz Paniagua, Martin Styner, Ross Whitaker

= Publications =

'' In Press ''

* M Datar, Y Gur, B Paniagua, M Styner, R Whitaker, Geometric Correspondence for Ensembles of Nonregular Shapes, MICCAI 2011

[[Category:Shape Analysis]] [[Category:Statistics]]

Algorithm:Utah

2011-12-07T22:27:11Z

Datar: /* Utah Projects */

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of Utah Algorithms (PI: Ross Whitaker) =

We are developing new methods in the areas of statistical shape analysis, MRI tissue segmentation, and diffusion tensor image processing and analysis. We are building shape analysis tools that can generate efficient statistical models appropriate for analyzing anatomical shape differences in the brain. We are developing a wide range of tools for diffusion tensor imaging, that span the entire pipeline from image processing to automatic white matter tract extraction to statistical testing of clinical hypotheses.

= Utah Projects =

{| cellpadding="10" style="text-align:left;"

| | [[Image:HeadRegressionResult.png|200px]]
| |

== [[Projects:ShapeRegression|Particle Based Shape Regression]] ==

Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. We propose a new method to building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The method is applied to provide new results on clinical MRI data related to early development of the human head.

<font color="red"></font> M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging, MICCAI 2009.

|-
{| cellpadding="10" style="text-align:left;"

| | [[Image:sgerber_brainmanifold_oasis_manifold.png|200px]]
| |

== [[Projects:BrainManifold|Brain Manifold Learning]] ==

This work is concerned with modeling high dimensional spaces, such as the space of brain images. Common approach for representing populations are template or clustering based approaches. In this project we develop a data driven method to learn a manifold representation from a set of brain images. The presented approach is described and evaluated in the setting of brain MRI but generalizes to other application domains.

S Gerber, T Tasdizen, S Joshi, R Whitaker, On the Manifold Structure of the Space of Brain Images, MICCAI 2009.

S Gerber, T Tasdizen, R Whitaker, Dimensionality Reduction and Principal Surfaces via Kernel Map, ICCV 2009.

S. Gerber, T. Tasdizen, P.T. Fletcher, S. Joshi, R. Whitaker, Manifold Modeling for Brain Population Analysis, Medical Image Anal, 3, 2010.

|-
| style="width:15%" | [[Image:EPI.png|200px]]
| style="width:85%" |

== [[Projects:EPIDistortionCorrection| Correction for Geometric Distortion in Echo Planar Images]] ==

We have developed a variational image-based approach to correct the susceptibility artifacts in the alignment of diffusion weighted and structural MRI.The correction is formulated as an optimization of a penalty that captures the intensity difference between the jacobian corrected EPI baseline images and a corresponding T2-weighted structural image.

<font color="red"></font> R Tao, P T Fletcher, S Gerber, R Whitaker, A Variational Image-Based Approach to the Correction of Susceptibility Artifacts
in the Alignment of Diffusion Weighted and Structural MRI, IPMI 2009.

|-

| | [[Image:pipeline.png|150px]]
| |

== [[Projects:StructuralAndDWIPipeline| A Framework for Joint Analysis of Structural and Diffusion MRI]] ==

This framework addresses the simultaneous alignment and ﬁltering of DWI images to correct eddy current artifacts and the subsequent alignment of those images to structural, T1 MRI to correct for susceptibility artifacts, and this paper demonstrates the importance of performing these corrections. It also shows how a T1-based, group speciﬁc atlas can be used to generate grey-matter regions of interest that can drive subsequent connectivity analyses. The result is a system that can be combined with a variety of tools for MRI analysis for tissue classiﬁcation, morphometry, and cortical parcellation.

<font color="red"></font> Ran Tao, P. Thomas Fletcher, Ross T. Whitaker, in MICCAI 2008 on Computational Diffusion MRI.

|-

| | [[Image:Sulcaldepth.png|200px]]
| |

== [[Projects:CorticalCorrespondenceWithParticleSystem|Cortical Correspondence using Particle System]] ==

In this project, we want to compute cortical correspondence on populations, using various features such as cortical structure, DTI connectivity, vascular structure, and functional data (fMRI). This presents a challenge because of the highly convoluted surface of the cortex, as well as because of the different properties of the data features we want to incorporate together. [[Projects:CorticalCorrespondenceWithParticleSystem|More...]]

<font color="red"></font> Oguz I, Niethammer M, Cates J, Whitaker R, Fletcher T, Vachet C, Styner M. “Cortical Correspondence with Probabilistic Fiber Connectivity”. Proc. Information Processing in Medical Imaging, 2009.

|-

| | [[Image:CatesNamicFigure3.png|200px]]
| |

== [[Projects:ParticlesForShapesAndComplexes|Adaptive, Particle-Based Sampling for Shapes and Complexes]] ==

This research is a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wider range of problems than existing methods, including nonmanifold surfaces and objects of arbitrary topology. [[Projects:ParticlesForShapesAndComplexes|More...]]

<font color="red"></font> Particle-Based Shape Analysis of Multi-object Complexes. Cates J., Fletcher P.T., Styner M., Hazlett H.C., Whitaker R. Int Conf Med Image Comput Comput Assist Interv. 2008;11(Pt 1):477-485.

|-

| | [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|200px]]
| |

== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|Shape Analysis Framework using SPHARM-PDM]] ==

The UNC shape analysis is based on an analysis framework of objects with spherical topology, described mainly by sampled spherical harmonics SPHARM-PDM. The input of the shape analysis framework is a set of binary segmentations of a single brain structure, such as the hippocampus or caudate. These segmentations are converted into a shape description (SPHARM) with correspondence and analyzed via Hotelling T^2 two sample metric. [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|More...]]

<font color="red"></font> Zhao Z., Taylor W., Styner M., Steffens D., Krishnan R., Macfall J. , Hippocampus shape analysis and late-life depression. PLoS ONE. 2008 Mar 19;3(3):e1837.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|DTI Volumetric White Matter Connectivity]] ==

We have developed a PDE-based approach to white matter connectivity from DTI that is founded on the principal of minimal paths through the tensor volume. Our method computes a volumetric representation of a white matter tract given two endpoint regions. We have also developed statistical methods for quantifying the full tensor data along these pathways, which should be useful in clinical studies using DT-MRI. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

|-
| style="width:15%" | [[Image:DTIFiltering.jpg|200px]]
| style="width:85%" |

== [[Projects:DTIProcessingTools|DTI Processing and Statistics Tools]] ==

We implement the diffusion weighted image (DWI) registration model from the paper of G.K.Rohde et al. Patient head motion and eddy currents distortion cause artifacts in maps of diffusion parameters computer from DWI. This model corrects these two distortions at the same time including brightness correction.

|-

| | [[Image:Brain-seg-utah.png|200px]]
| |

== [[Projects:TissueClassificationWithNeighborhoodStatistics| Tissue Classification with Neighborhood Statistics]] ==

We have implemented an MRI tissue classification algorithm based on unsupervised non-parametric density estimation of tissue intensity classes.
[[Projects:TissueClassificationWithNeighborhoodStatistics|More...]]

|-

| | [[Image:NonRegularSurfCorres.png|200px]]
| |

== [[Projects:NonRegularSurfCorres|Geometric Correspondence for Nonregular Surfaces]] ==

To resolve the challenges posed by highly nonregular surfaces, we have proposed an efficient method which incorporates Geodesic distances and an entropy based on surface normals to improve correspondences.

<font color="red"></font> M Datar, Y Gur, B Paniagua, M Styner, R Whitaker, Geometric Correspondence for Ensembles of
Nonregular Shapes, MICCAI 2011.

|}

File:NonRegularSurfCorres.png

2011-12-07T22:20:25Z

Datar: uploaded a new version of "File:NonRegularSurfCorres.png"

examples of challenges posed by nonregular surfaces

File:NonRegularSurfCorres.png

2011-12-07T22:18:41Z

Datar: examples of challenges posed by nonregular surfaces

examples of challenges posed by nonregular surfaces

2011 Summer Project Week

2011-05-26T16:38:16Z

Datar: /* Projects */

Back to [[Events]]

[[image:PW-MIT2011.png|right|200px]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="250px"|Monday, June 20
!width="250px"|Tuesday, June 21
!width="250px"|Wednesday, June 22
!width="250px"|Thursday, June 23
!width="250px"|Friday, June 24
|-
|
|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-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''9am-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''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>
'''3:30-5:00pm: NA-MIC Kit Update''' (Aylward, Miller, Pieper)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>Inter-subject Registration for EM segmenter
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
<br>'''5pm: <font color="#4020ff">Reception'''</font><br>
<br>[[MIT_Project_Week_Rooms#R&D Pub|R&D Pub]]
|'''1-2pm: <font color="#4020ff">Breakout Session:'''</font><br> TBD
<br>----------------------------------------<br>
'''2-3pm:'''Breakout Session:TBD'''
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session: TBD'''</font><br>
|
|-
|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
|
|}

==Projects==
#valuate the applicability of DICOM RT I/O facility in Slicer (via Plastimatch Extension) for Brachytherapy Planning (Tina Kapur, Greg Sharp, Robert Cormack?)
#Visualization of b-spline and vector fields (Steve, Danielle, Dominik)
#Annotation Module in Slicer4 (Nicole Aucoin, Daniel Haehn)
#Slicer4 Multivolume Containers (Ron Kikinis, Nicole Aucoin, Steve Pieper, ... )
#RECIST Slicer4 module (Nicole Aucoin)
#DicomToNrrdConverter refactoring ( Xiaodong Tao, Mark Scully)
#UNC Antialiasing Software as a Slicer extension or ITK module (Steve Pizer, Brad Davis, Petter Risholm, Andriy Fedorov)
# Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Marc Scully)
# Group-wise Automatic Mesh-Based analysis of CortIcal Thickness (GAMBIT) - TBI (Clement Vachet, Martin Styner, Randi Gollub?)
#DTIProcessing - Huntington's Disease (Clement Vachet, Joy Matsui, Martin Styner)
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] - Lucile Bompard, Clement Vachet, Mark Scully, Beatriz Paniagua, Martin Styner
# Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)
# Robust Statiistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy (Yi Gao, Kedar R, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#Mass Spectrometry for Brain Tumor Therapy (Behnood Gholami, Nathalie Agar)
#Multimodality Image Registration for TBI? (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)
# DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
# Segmentation of Longitudinal TBI data (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
# Longitudinal Shape Regression - Huntington's Disease (James Fishbaugh, Guido Gerig)
# Dose volume histograms in Slicer (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
#Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)
# Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)
# Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
# Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps (Ramesh Sridharan, Polina Golland)
# Shapeworks Shape Analysis for Atrial Fibrilliation and HD (Manasi Datar, Beatriz UNC, Marc Scully)
# Volumetric DTI into Slicer for HD for Tract based roi segmentation (Steve Callahan, Marc Scully, Jim Miller)
#Explore the applicability of RSS and Shapeworks for Ventricular Segmentation(Chiara Carminati, ?, ?)
# Integrate BRAINSCut into Slicer3(Regina Kim, ... )
# The Vascular Modeling Toolkit in 3D Slicer 4 (Daniel Haehn, Luca Antiga, Steve Pieper)
# Integration of LANDWARP into interactive registration module for MR-guided prostate biopsy (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
# Registration of mouse brains (Francois Budin)
# ShapeWorks Applications (Manasi Datar, Beatriz Paniagua, Martin Styner, Ross Whitaker, ?)

==Background==

We are pleased to announce the 13th 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. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 28th 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 40-50 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 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== 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 28, 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 Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, all project leads to complete [[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 16: 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].

2011 Winter Project Week

2010-12-08T18:41:28Z

Datar: /* Analysis */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2011]], [[Events]]

__NOTOC__
[[image:PW-SLC2010.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2011#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2011#Agenda|click here for the agenda for AHM 2011 and Project Week]].

==Background==

From January 10-14, 2011, the twelfth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

=== Segmentation ===
* Extension of ABC (Atlas-Based Classification) to detect pathology categories, with tests on TBI images (Bo Wang, Marcel Prastawa, Guido Gerig).
* Segmentation of the left atrial wall for atrial fibrillation ablation therapy (Behnood Gholami, Yi Gao, and Allen Tannenbaum)
* The Vascular Modeling Toolkit in 3D Slicer (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper)
* A stenosis detector in Slicer4 using VMTK (Suares Tamekue, Daniel Haehn, Luca Antiga)
* [[2011_Winter_Project_Week:MeshCurvolver|Surface Region Segmentation for Surgical Planning and Mapping ]] (Peter Karasev, Karol Chudy, Allen Tannenbaum)
* Integration of SPECTRE into Slicer (Nicole Aucoin)

=== Registration ===
*[[2011_Winter_Project_Week:RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
*Voxel Anisotropy and Bias Field Effects on Slicer Image Registration (Dominik Meier) (tentative)
* Efficient co-registration of multiple MR modalities using the ABC (atlas-based classification) framework, joint visualization of multiple co-registered modalities (Bo Wang, Guido Gerig)
* DTI-MRI registration: Evaluation of large deformation diffeomorphic mapping (LDDMM) with other nonlinear registration schemes (Anuja Sharma, Guido Gerig)
* Registration of CT and MRI volumes for Adaptive Radiotherapy (Ivan Kolesov, Gregory Sharp, and Allen Tannenbaum)
* Atlas Registration in Slicer3 (Daniel Haehn, Dominik Meier, Kilian Pohl)
* Registration in the presence of anatomic variation (aka. Sliding organ registration) (Danielle Pace, Marc Niethammer, Petter Risholm, Tina Kapur, Sandy Wells, Stephen Aylward)
* Visualizing registration uncertainty in Slicer3 (Petter Risholm, William Wells)

=== IGT ===
*Open IGT Link 2.0 (Junichi Tokuda, Nobuhiko Hata)
*Osteormark, navigation tool for Osteotomy (Laurent Chauvin, Nobuhiko Hata)
*Detection and compensation for prostate motion during transperineal MR-guided prostate biopsy (A.Fedorov, Andras Lasso)
*Thin Client QT Interface for IGT (Nicholas Herlambang)
*Transform recorder and (surgical) procedure annotation module (Tamas Ungi, Junichi Tokuda)

=== Radiotherapy ===
* User controlled segmentation of head and neck structures for Adaptive Radiotherapy (Ivan Kolesov, Gregory Sharp, and Allen Tannenbaum)
* DICOM-RT export (Greg Sharp)

=== Analysis ===
* GAMBIT - Cortical thickness analysis - Clement Vachet, Martin Styner
* [[2011_Winter_Project_Week:ParticleShapeAnalysis|Particle shape analysis incorporating surface normals ]] - Beatriz Paniagua, Martin Styner
* NAMIC shape analysis pipeline in Slicer 3 - Lucile Bompard, Martin Styner, Chris Gloschat
* Particle Systems for Shape Analysis - Josh Cates, Manasi Datar, Ross Whitaker

=== Informatics ===
* Share all UIowa Traveling Human Phantom DTI data with NAMIC - Mark Scully, Hans Johnson, Zack M.
* Ontology-augmented MRI brain atlas - Michael Halle, Jim Miller, Samira Farough
* Functional brain atlas (version 2) - Michael Halle, Jim Miller
* Annotation module in Slicer4: Display widget intersections (Daniel Haehn, Nicole Aucoin, Steve Pieper)

=== Diffusion ===
* Requirements gathering and test suite for refactoring DicomToNrrdConverter - Mark Scully, Zach Mullen, Xiadong Tao, Hans Johnson
* Documentation and 1st Draft Tutorial for DTIPrep - Mark Scully, Hans Johnson, Clement Vachet
* Voxelwise fiber distribution from tractography - Yinpeng Li, Martin Styner
* Two-tensor full brain tractography - Lauren O'Donnell, Yogesh Rathi, Demian Wassermann, C-F Westin
* Tract-based statistics - Demian Wassermann, Peter Savadjiev, C-F Westin
* Free-water elimination - Ofer Pasternak, Peter Savadjiev, Sylvain Bouix, C-F Westin
* Statistical analysis of Cingulum extracted using Volumetric framework - Gopal Veni, Ross Whitaker

=== NA-MIC Kit Internals ===

* Command line module logic redesign (passing paramenters, tie into workflows) - Jim, Steve
* CDash at Home / testing on demand of git topic branches - Steve and Zach M.
* 64bit Windows Builds - Dave P
* Dashboards with Subprojects - Stephen and Dave P.
* Factory Machines - Dave P. and Zack G.
* MIDAS for data hosting - Zach M and Hans
* CTK - Julien F and JC
* vtkWidgets - JC and Will
* Workflows in Python - JC
* Python Scripting - JC

=== Execution Model ===
* Extract SlicerExecutionModel (SEM) into separate entity. SEM is the only component needed to build modules compatible with Slicer3D, so it should be easy incorporate into external applications without all of Slicer3D. Jim, Hans
* Extend SEM xml to include sections for explicit grant acknowledgements, and pointers to documentation, and pointers to examples. Hans, Andriy
* Make an formal schema for the SEM xml so that eternal tools (i.e. nipype) can validate the xml. Hans Johnson, Jim Miller, Tim Olsen
* Improve documentation extractor script that converts XML to MediaWiki format so that it can directly push this information into the Slicer3D MediaWiki. (Wiki Systems Admin), Hans Johnson
* Improve merging strategies between BRAINS3Tools that are part of BRAINS3 and BRAINS3Tools that are part of Slicer. - Mark Scully, Hans Johnson

=== Workflows and Integration ===
* Workflows and Service Oriented Architecture Solutions for Slicer3 Modules. - Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 28th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 28: Engineering Infrastructure Projects
#*November 4: Engineering Infrastructure Projects
#*November 11: DPB Projects: Iowa, Outcomes from Alg Core Retreat
#*November 18: DPB Projects: MGH
#*November 25: DBP Projects, Funded External Collaborations
#*December 2: Funded External Collaborations
#*December 9: Other External Collaborations
#*December 16:Finalize Engineering Projects
#*January 6: Loose Ends
#By December 16, 2010: [[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 December 16, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (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...

2010 Summer Project Week

2010-06-10T03:13:49Z

Datar: /* Shape Analysis */

__NOTOC__

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

[[Image:PW-MIT2010.png|300px]]

==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]]

==Agenda==
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanez)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast

** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. 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, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* [[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)
*[[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)
*[[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)

=== 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)

=== Analysis ===
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, 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)
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

===[[Microscopy Image Analysis]] ===
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* [[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)
* [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
* [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason, Badri Roysam)
* [[ITK GPAC level set]] (K. Palaniappan, Kishore Mosaliganti, Sean Megason)
* [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)

=== Shape Analysis ===
*[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
* [[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)

=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== 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, Ross Whitaker)

=== NA-MIC Kit Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., 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)
*XNAT Enterprise webservices client for Slicer (Wendy, Mark)
*[[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, Ron Kikinis)
*Superbuild (Dave Partika, Steve Pieper, Katie Hayes)
*[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== 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>

# Aucoin Nicole , BWH
# Audette Michel , Kitware
# Aylward Stephen , Kitware, Inc
# Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
# Bouix Sylvain , BWH
# Budin Francois , UNC
# Burdette Everette , Acoustic MedSystems, Inc.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# Datar Manasi , SCI Institute
# Eckbo Ryan , BWH
# Fedorov Andriy , Surgical Planning Lab
# Fillion-Robin Jean-Christophe , Kitware Inc.
# Finet Julien , Kitware Inc
# Fishbaugh James , SCI Institute
#Fritscher, Karl, UMIT
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Haehn Daniel , University of Pennsylvania
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
#Halle, Michael, BWH
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# Johnson Hans , University of Iowa
# Kapur Tina , Brigham and Women's Hospital
# Kikinis Ron , Brigham and Women's Hospital
# Kim Minjeong , UNC-Chapel Hill
# Kolesov Ivan , Georgia Institute of Technology
# Larson Garrett , UNC-CH
# Li Rui , MGH
# Lisle Curtis , KnowledgeVis, LLC
# Liu Haiying , Brigham and Women's Hospital
# Liu Yanling , SAIC-Frederick, Inc.
# Magnotta Vincent , The University of Iowa
# malaterre mathieu , CoSMo Software
# Marcus Daniel , Washington University
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# Mosaliganti Kishore , Harvard Medical School
# Niethammer Marc , UNC Chapel Hill
# Norton Isaiah , BWH Neurosurgery
# Paniagua Beatriz , University of North Caolina at Chapel Hill
# Papademetris Xenophon , Yale University
# Partyka David , Kitware Inc
# Pathak Sudhir , Univeristy Of Pittsburgh
# Peroni Marta , Politecnico di Milano, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , Brigham and Women's Hospital
# Tao Xiaodong , GE Research
#Tokuda, Junichi, BWH
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
#Weinrich, Adam, Nokia
# Wells Sandy , BWH
# Wu Guorong , University of North Carolina at Chapel Hill
#Yarmarkovich, Alexander, ISOMICS

Particle Based Shape Regression

2010-06-08T17:42:09Z

Datar:

__NOTOC__

[[Image:HeadRegressionResult.png‎|500px|Changes in early head shape with log(age).]]

==Key Investigators==
* Utah: Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker

==Project==
<div style="margin: 10px;">
<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Objective</h3>
Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. We propose a new method to
building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The statistical signiﬁcance of the dependence is evaluated using permutation tests designed to estimate the likelihood of achieving the observed statistics
under numerous rearrangements of the shape parameters with respect to the explanatory variable.
</div>

<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Approach, Plan</h3>
The general strategy of this method is to represent correspondences as point sets that are distributed across an ensemble of similar shapes by a gradient descent optimization of an objective function that quantiﬁes the entropy of the system [1]. Our proposed extension to this method incorporates a linear regression model into the correspondence optimization. We also present a new methodology for correspondence optimization on open surfaces where surface boundaries are deﬁned by arbitrary geometric
constraints.
</div>

<div style="width: 35%; float: left;">
<h3>Progress</h3>
The proposed method has been implemented and integrated with the [http://www.sci.utah.edu/cibc/software/131-shapeworks.html ShapeWorks] package. The figure above shows results on clinical MRI data related to early development of the human head, described in [2]
</div>

<div style="width: 35%; float: left;">
<h3>References</h3>
1. J Cates, P T Fletcher, M Styner, M Shenton, R Whitaker, "Shape modeling
and analysis with entropy-based particle systems," Information Processing in
Medical Imaging (IPMI 2007), LNCS 4584. (2007) 333–345

2. M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, "Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging," MICCAI 2009
</div>

Back to [[2010_Summer_Project_Week#Projects|Projects List]]

Particle Based Shape Regression

2010-06-08T17:41:00Z

Datar:

__NOTOC__

Back to [[2010_Summer_Project_Week#Projects|Projects List]]

[[Image:HeadRegressionResult.png‎|500px|Changes in early head shape with log(age).]]

==Key Investigators==
* Utah: Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker

==Project==
<div style="margin: 10px;">
<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Objective</h3>
Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. We propose a new method to
building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The statistical signiﬁcance of the dependence is evaluated using permutation tests designed to estimate the likelihood of achieving the observed statistics
under numerous rearrangements of the shape parameters with respect to the explanatory variable.
</div>

<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Approach, Plan</h3>
The general strategy of this method is to represent correspondences as point sets that are distributed across an ensemble of similar shapes by a gradient descent optimization of an objective function that quantiﬁes the entropy of the system [1]. Our proposed extension to this method incorporates a linear regression model into the correspondence optimization. We also present a new methodology for correspondence optimization on open surfaces where surface boundaries are deﬁned by arbitrary geometric
constraints.
</div>

<div style="width: 35%; float: left;">
<h3>Progress</h3>
The proposed method has been implemented and integrated with the [http://www.sci.utah.edu/cibc/software/131-shapeworks.html ShapeWorks] package. The figure above shows results on clinical MRI data related to early development of the human head, described in [2]
</div>

<div style="width: 35%; float: left;">
<h3>References</h3>
1. J Cates, P T Fletcher, M Styner, M Shenton, R Whitaker, "Shape modeling
and analysis with entropy-based particle systems," Information Processing in
Medical Imaging (IPMI 2007), LNCS 4584. (2007) 333–345

2. M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, "Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging," MICCAI 2009
</div>

Particle Based Shape Regression

2010-06-08T17:37:26Z

Datar: /* Project */

__NOTOC__

Back to [[2010_Summer_Project_Week#Projects|Projects List]]

<gallery>
Image:HeadRegressionResult.png|Changes in early head shape with log(age).
</gallery>

==Key Investigators==
* Utah: Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker

==Project==
<div style="margin: 10px;">
<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Objective</h3>
Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. We propose a new method to
building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The statistical signiﬁcance of the dependence is evaluated using permutation tests designed to estimate the likelihood of achieving the observed statistics
under numerous rearrangements of the shape parameters with respect to the explanatory variable.
</div>

<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Approach, Plan</h3>
The general strategy of this method is to represent correspondences as point sets that are distributed across an ensemble of similar shapes by a gradient descent optimization of an objective function that quantiﬁes the entropy of the system [1]. Our proposed extension to this method incorporates a linear regression model into the correspondence optimization. We also present a new methodology for correspondence optimization on open surfaces where surface boundaries are deﬁned by arbitrary geometric
constraints.
</div>

<div style="width: 35%; float: left;">
<h3>Progress</h3>
The proposed method has been implemented and integrated with the [http://www.sci.utah.edu/cibc/software/131-shapeworks.html ShapeWorks] package. The figure above shows results on clinical MRI data related to early development of the human head, described in [2]
</div>

<div style="width: 35%; float: left;">
<h3>References</h3>
1. J Cates, P T Fletcher, M Styner, M Shenton, R Whitaker, "Shape modeling
and analysis with entropy-based particle systems," Information Processing in
Medical Imaging (IPMI 2007), LNCS 4584. (2007) 333–345

2. M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, "Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging," MICCAI 2009
</div>

Particle Based Shape Regression

2010-06-08T17:36:17Z

Datar:

__NOTOC__

Back to [[2010_Summer_Project_Week#Projects|Projects List]]

<gallery>
Image:HeadRegressionResult.png|Changes in early head shape with log(age).
</gallery>

==Key Investigators==
* Utah: Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker

==Project==
<div style="margin: 10px;">
<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Objective</h3>
Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. We propose a new method to
building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The statistical signiﬁcance of the dependence is evaluated using permutation tests designed to estimate the likelihood of achieving the observed statistics
under numerous rearrangements of the shape parameters with respect to the explanatory variable.
</div>

<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Approach, Plan</h3>
The general strategy of this method is to represent correspondences as point sets that are distributed across an ensemble of similar shapes by a gradient descent optimization of an objective function that quantiﬁes the entropy of the system [1]. Our proposed extension to this method incorporates a linear regression model into the correspondence optimization. We also present a new methodology for correspondence optimization on open surfaces where surface boundaries are deﬁned by arbitrary geometric
constraints.
</div>

<div style="width: 35%; float: left;">
<h3>Progress</h3>
The proposed method has been implemented and integrated with the [http://www.sci.utah.edu/cibc/software/131-shapeworks.html | ShapeWorks] package. The figure above shows results on clinical MRI data related to early development of the human head, described in [2]
</div>

<div style="width: 35%; float: left;">
<h3>References</h3>
1. J Cates, P T Fletcher, M Styner, M Shenton, R Whitaker, "Shape modeling
and analysis with entropy-based particle systems," Information Processing in
Medical Imaging (IPMI 2007), LNCS 4584. (2007) 333–345

2. M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, "Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging," MICCAI 2009
</div>

Particle Based Shape Regression

2010-06-08T17:33:01Z

Datar: Created page with '__NOTOC__ <gallery> Image:HeadRegressionResult.png|Changes in early head shape with log(age). </gallery> ==Key Investigators== * Utah: Manasi Datar, Joshua Cates, P. Thomas Flet…'

__NOTOC__
<gallery>
Image:HeadRegressionResult.png|Changes in early head shape with log(age).
</gallery>

==Key Investigators==
* Utah: Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker

==Project==
<div style="margin: 10px;">
<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Objective</h3>
Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. We propose a new method to
building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The statistical signiﬁcance of the dependence is evaluated using permutation tests designed to estimate the likelihood of achieving the observed statistics
under numerous rearrangements of the shape parameters with respect to the explanatory variable.
</div>

<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Approach, Plan</h3>
The general strategy of this method is to represent correspondences as point sets that are distributed across an ensemble of similar shapes by a gradient descent optimization of an objective function that quantiﬁes the entropy of the system [1]. Our proposed extension to this method incorporates a linear regression model into the correspondence optimization. We also present a new methodology for correspondence optimization on open surfaces where surface boundaries are deﬁned by arbitrary geometric
constraints.
</div>

<div style="width: 35%; float: left;">
<h3>Progress</h3>
The proposed method has been implemented and integrated with the [http://www.sci.utah.edu/cibc/software/131-shapeworks.html | ShapeWorks] package. The figure above shows results on clinical MRI data related to early development of the human head, described in [2]
</div>

<div style="width: 35%; float: left;">
<h3>References</h3>
1. J Cates, P T Fletcher, M Styner, M Shenton, R Whitaker, "Shape modeling
and analysis with entropy-based particle systems," Information Processing in
Medical Imaging (IPMI 2007), LNCS 4584. (2007) 333–345

2. M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, "Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging," MICCAI 2009
</div>

2010 Summer Project Week

2010-06-08T17:11:54Z

Datar: /* Shape Analysis */

__NOTOC__

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

[[Image:PW-MIT2010.png|300px]]

==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]]

==Agenda==
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanesz)
**3-4pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast

** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. 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, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* BrainLab-Aurora HybridNav (Isaiah Norton, Dan Marcus)
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
* PerkStation Module (Tamas Ungi)
*[[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)

=== 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)

=== Analysis ===
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, 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)
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

===[[Microscopy Image Analysis]] ===
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* [[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)
* [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
* [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason, Badri Roysam)
* [[ITK GPAC level set]] (K. Palaniappan, Kishore Mosaliganti, Sean Megason)
* [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)

=== Shape Analysis ===
*[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
* [[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)

=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== 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)

=== NA-MIC Kit Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., 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)
*XNAT Enterprise webservices client for Slicer (Wendy, Mark)
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)

*VTKWidgets (JC, will, Schroeder, Nicole, Ron)
*Superbuild (Dave Partika, Steve Pieper, Katie Hayes)
*[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== 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>

# Aucoin Nicole , BWH
# Audette Michel , Kitware
# Aylward Stephen , Kitware, Inc
# Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
# Bouix Sylvain , BWH
# Budin Francois , UNC
# Burdette Everette , Acoustic MedSystems, Inc.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# Datar Manasi , SCI Institute
# Eckbo Ryan , BWH
# Fedorov Andriy , Surgical Planning Lab
# Fillion-Robin Jean-Christophe , Kitware Inc.
# Finet Julien , Kitware Inc
# Fishbaugh James , SCI Institute
#Fritscher, Karl, UMIT
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Haehn Daniel , University of Pennsylvania
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
#Halle, Michael, BWH
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# Johnson Hans , University of Iowa
# Kapur Tina , Brigham and Women's Hospital
# Kikinis Ron , Brigham and Women's Hospital
# Kim Minjeong , UNC-Chapel Hill
# Kolesov Ivan , Georgia Institute of Technology
# Larson Garrett , UNC-CH
# Li Rui , MGH
# Lisle Curtis , KnowledgeVis, LLC
# Liu Haiying , Brigham and Women's Hospital
# Liu Yanling , SAIC-Frederick, Inc.
# Magnotta Vincent , The University of Iowa
# malaterre mathieu , CoSMo Software
# Marcus Daniel , Washington University
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# Mosaliganti Kishore , Harvard Medical School
# Niethammer Marc , UNC Chapel Hill
# Norton Isaiah , BWH Neurosurgery
# Paniagua Beatriz , University of North Caolina at Chapel Hill
# Papademetris Xenophon , Yale University
# Partyka David , Kitware Inc
# Pathak Sudhir , Univeristy Of Pittsburgh
# Peroni Marta , Politecnico di Milano, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , Brigham and Women's Hospital
# Tao Xiaodong , GE Research
#Tokuda, Junichi, BWH
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
#Weinrich, Adam, Nokia
# Wells Sandy , BWH
# Wu Guorong , University of North Carolina at Chapel Hill
#Yarmarkovich, Alexander, ISOMICS

Algorithm:Utah

2009-10-05T17:14:25Z

Datar:

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of Utah Algorithms (PI: Ross Whitaker) =

We are developing new methods in the areas of statistical shape analysis, MRI tissue segmentation, and diffusion tensor image processing and analysis. We are building shape analysis tools that can generate efficient statistical models appropriate for analyzing anatomical shape differences in the brain. We are developing a wide range of tools for diffusion tensor imaging, that span the entire pipeline from image processing to automatic white matter tract extraction to statistical testing of clinical hypotheses.

= Utah Projects =

{| cellpadding="10" style="text-align:left;"

| | [[Image:HeadRegressionResult.png|200px]]
| |

== [[Projects:ShapeRegression|Particle Based Shape Regression]] ==

Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. We propose a new method to building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The method is applied to provide new results on clinical MRI data related to early development of the human head.

<font color="red">'''New: '''</font> M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging, MICCAI 2009.

|-

{| cellpadding="10" style="text-align:left;"

| | [[Image:sgerber_brainmanifold_oasis_manifold.png|200px]]
| |

== [[Projects:BrainManifold|Brain Manifold Learning]] ==

This work is concerned with modeling the space of brain images. Common approach for representing populations are template or clustering based approaches. In this project we develop a data driven method to learn a manifold representation from a set of brain images. The presented approach is described and evaluated in the setting of brain MRI but generalizes to other application domains.

<font color="red">'''New: '''</font> S Gerber, T Tasdizen, S Joshi, R Whitaker, On the Manifold Structure of the Space of Brain Images, MICCAI 2009.

<font color="red">'''New: '''</font> S Gerber, T Tasdizen, R Whitaker, Dimensionality Reduction and Principal Surfaces via Kernel Map, ICCV 2009.
|-
| style="width:15%" | [[Image:DTIregistration200.png|200px]]
| style="width:85%" |

== [[Projects:DTIProcessingTools|Diffusion Tensor Image Processing Tools]] ==

We implement the diffusion weighted image (DWI) registration model from the paper of G.K.Rohde et al. Patient head motion and eddy currents distortion cause artifacts in maps of diffusion parameters computer from DWI. This model corrects these two distortions at the same time including brightness correction.

|-

| | [[Image:f_27.png|100px]] [[Image:r_27.png|100px]]
| |

== [[Projects:DTIProcessingTools| Correction for Geometric Distortion in Echo Planar Images]] ==

We have developed a variational image-based approach to correct the susceptibility artifacts in the alignment of diffusion weighted and structural MRI.The correction is formulated as an optimization of a penalty that captures the intensity difference between the jacobian corrected EPI baseline images and a corresponding T2-weighted structural image.

<font color="red">'''New: '''</font> R Tao, PT Fletcher, S Gerber, R Whitaker, A Variational Image-Based Approach to the Correction of Susceptibility Artifacts
in the Alignment of Diffusion Weighted and Structural MRI, IPMI 2009,

|-

| | [[Image:Sulcaldepth.png|200px]]
| |

== [[Projects:CorticalCorrespondenceWithParticleSystem|Cortical Correspondence using Particle System]] ==

In this project, we want to compute cortical correspondence on populations, using various features such as cortical structure, DTI connectivity, vascular structure, and functional data (fMRI). This presents a challenge because of the highly convoluted surface of the cortex, as well as because of the different properties of the data features we want to incorporate together. [[Projects:CorticalCorrespondenceWithParticleSystem|More...]]

<font color="red">'''New: '''</font> Oguz I, Niethammer M, Cates J, Whitaker R, Fletcher T, Vachet C, Styner M. “Cortical Correspondence with Probabilistic Fiber Connectivity”. Proc. Information Processing in Medical Imaging, 2009.

|-

| | [[Image:CatesNamicFigure3.png|200px]]
| |

== [[Projects:ParticlesForShapesAndComplexes|Adaptive, Particle-Based Sampling for Shapes and Complexes]] ==

This research is a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wider range of problems than existing methods, including nonmanifold surfaces and objects of arbitrary topology. [[Projects:ParticlesForShapesAndComplexes|More...]]

<font color="red">'''New: '''</font> Particle-Based Shape Analysis of Multi-object Complexes. Cates J., Fletcher P.T., Styner M., Hazlett H.C., Whitaker R. Int Conf Med Image Comput Comput Assist Interv. 2008;11(Pt 1):477-485.

|-

| | [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|200px]]
| |

== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|Shape Analysis Framework using SPHARM-PDM]] ==

The UNC shape analysis is based on an analysis framework of objects with spherical topology, described mainly by sampled spherical harmonics SPHARM-PDM. The input of the shape analysis framework is a set of binary segmentations of a single brain structure, such as the hippocampus or caudate. These segmentations are converted into a shape description (SPHARM) with correspondence and analyzed via Hotelling T^2 two sample metric. [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|More...]]

<font color="red">'''New: '''</font> Zhao Z., Taylor W., Styner M., Steffens D., Krishnan R., Macfall J. , Hippocampus shape analysis and late-life depression. PLoS ONE. 2008 Mar 19;3(3):e1837.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|DTI Volumetric White Matter Connectivity]] ==

We have developed a PDE-based approach to white matter connectivity from DTI that is founded on the principal of minimal paths through the tensor volume. Our method computes a volumetric representation of a white matter tract given two endpoint regions. We have also developed statistical methods for quantifying the full tensor data along these pathways, which should be useful in clinical studies using DT-MRI. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

|-

| | [[Image:Brain-seg-utah.png|200px]]
| |

== [[Projects:TissueClassificationWithNeighborhoodStatistics| Tissue Classification with Neighborhood Statistics]] ==

We have implemented an MRI tissue classification algorithm based on unsupervised non-parametric density estimation of tissue intensity classes.
[[Projects:TissueClassificationWithNeighborhoodStatistics|More...]]

|}

Projects:ShapeRegression

2009-10-05T17:10:47Z

Datar:

Back to [[Algorithm:Utah|Utah Algorithms]]
__NOTOC__
= Particle Based Shape Regression =

{|
|[[Image:HeadRegressionResult.png|thumb|512px|Changes in early head shape with log(age).]]
|}

= Description =

= Key Investigators =

* Utah: Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker

= Publications =

[[Category:Shape Analysis]] [[Category:Statistics]]

Projects:ShapeRegression

2009-10-05T17:08:24Z

Datar: Created page with ' Back to Utah Algorithms __NOTOC__ = Particle Based Shape Regression = {| |[[Image:HeadRegressionResult.png|thumb|512px|Changes in early head shape with lo…'

Back to [[Algorithm:Utah|Utah Algorithms]]
__NOTOC__
= Particle Based Shape Regression =

{|
|[[Image:HeadRegressionResult.png|thumb|512px|Changes in early head shape with log(age).]]
|}

= Description =

= Key Investigators =

* Utah: Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker

= Publications =

[[Category:Atlas]] [[Category:Statistics]] [[Category:Registration]] [[Category:Population Analysis]]

File:HeadRegressionResult.png

2009-10-05T17:03:49Z

Datar:

Algorithm:Utah

2009-10-05T17:02:53Z

Datar:

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of Utah Algorithms (PI: Ross Whitaker) =

We are developing new methods in the areas of statistical shape analysis, MRI tissue segmentation, and diffusion tensor image processing and analysis. We are building shape analysis tools that can generate efficient statistical models appropriate for analyzing anatomical shape differences in the brain. We are developing a wide range of tools for diffusion tensor imaging, that span the entire pipeline from image processing to automatic white matter tract extraction to statistical testing of clinical hypotheses.

= Utah Projects =

{| cellpadding="10" style="text-align:left;"

| | [[Image:HeadRegressionResult.png|200px]]
| |

== [[Projects:ShapeRegression|Particle Based Shape Regression]] ==

Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. In this paper we propose a new method to building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The statistical signi¯cance of the dependence is evaluated using permutation tests designed to estimate the likelihood of achieving the observed statistics under numerous rearrangements of the shape parameters with respect to the explanatory variable. We demonstrate the method on synthetic data and provide a new results on clinical MRI data related to early development of the human head.

<font color="red">'''New: '''</font> M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging, MICCAI 2009.

|-

{| cellpadding="10" style="text-align:left;"

| | [[Image:sgerber_brainmanifold_oasis_manifold.png|200px]]
| |

== [[Projects:BrainManifold|Brain Manifold Learning]] ==

This work is concerned with modeling the space of brain images. Common approach for representing populations are template or clustering based approaches. In this project we develop a data driven method to learn a manifold representation from a set of brain images. The presented approach is described and evaluated in the setting of brain MRI but generalizes to other application domains.

<font color="red">'''New: '''</font> S Gerber, T Tasdizen, S Joshi, R Whitaker, On the Manifold Structure of the Space of Brain Images, MICCAI 2009.

<font color="red">'''New: '''</font> S Gerber, T Tasdizen, R Whitaker, Dimensionality Reduction and Principal Surfaces via Kernel Map, ICCV 2009.
|-
| style="width:15%" | [[Image:DTIregistration200.png|200px]]
| style="width:85%" |

== [[Projects:DTIProcessingTools|Diffusion Tensor Image Processing Tools]] ==

We implement the diffusion weighted image (DWI) registration model from the paper of G.K.Rohde et al. Patient head motion and eddy currents distortion cause artifacts in maps of diffusion parameters computer from DWI. This model corrects these two distortions at the same time including brightness correction.

<font color="red">'''New: '''</font> R Tao, PT Fletcher, S Gerber, R Whitaker, A Variational Image-Based Approach to the Correction of Susceptibility Artifacts in the Alignment of Diffusion Weighted and Structural MRI, IPMI 2009.

|-

| | [[Image:f_27.png|100px]] [[Image:r_27.png|100px]]
| |

== [[Projects:DTIProcessingTools| Correction for Geometric Distortion in Echo Planar Images]] ==

We have developed a variational image-based approach to correct the susceptibility artifacts in the alignment of diffusion weighted and structural MRI.The correction is formulated as an optimization of a penalty that captures the intensity difference between the jacobian corrected EPI baseline images and a corresponding T2-weighted structural image.

<font color="red">'''New: '''</font> R Tao, PT Fletcher, S Gerber, R Whitaker, A Variational Image-Based Approach to the Correction of Susceptibility Artifacts
in the Alignment of Diffusion Weighted and Structural MRI, IPMI 2009,

|-

| | [[Image:Sulcaldepth.png|200px]]
| |

== [[Projects:CorticalCorrespondenceWithParticleSystem|Cortical Correspondence using Particle System]] ==

In this project, we want to compute cortical correspondence on populations, using various features such as cortical structure, DTI connectivity, vascular structure, and functional data (fMRI). This presents a challenge because of the highly convoluted surface of the cortex, as well as because of the different properties of the data features we want to incorporate together. [[Projects:CorticalCorrespondenceWithParticleSystem|More...]]

<font color="red">'''New: '''</font> Oguz I, Niethammer M, Cates J, Whitaker R, Fletcher T, Vachet C, Styner M. “Cortical Correspondence with Probabilistic Fiber Connectivity”. Proc. Information Processing in Medical Imaging, 2009.

|-

| | [[Image:CatesNamicFigure3.png|200px]]
| |

== [[Projects:ParticlesForShapesAndComplexes|Adaptive, Particle-Based Sampling for Shapes and Complexes]] ==

This research is a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wider range of problems than existing methods, including nonmanifold surfaces and objects of arbitrary topology. [[Projects:ParticlesForShapesAndComplexes|More...]]

<font color="red">'''New: '''</font> Particle-Based Shape Analysis of Multi-object Complexes. Cates J., Fletcher P.T., Styner M., Hazlett H.C., Whitaker R. Int Conf Med Image Comput Comput Assist Interv. 2008;11(Pt 1):477-485.

|-

| | [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|200px]]
| |

== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|Shape Analysis Framework using SPHARM-PDM]] ==

The UNC shape analysis is based on an analysis framework of objects with spherical topology, described mainly by sampled spherical harmonics SPHARM-PDM. The input of the shape analysis framework is a set of binary segmentations of a single brain structure, such as the hippocampus or caudate. These segmentations are converted into a shape description (SPHARM) with correspondence and analyzed via Hotelling T^2 two sample metric. [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|More...]]

<font color="red">'''New: '''</font> Zhao Z., Taylor W., Styner M., Steffens D., Krishnan R., Macfall J. , Hippocampus shape analysis and late-life depression. PLoS ONE. 2008 Mar 19;3(3):e1837.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|DTI Volumetric White Matter Connectivity]] ==

We have developed a PDE-based approach to white matter connectivity from DTI that is founded on the principal of minimal paths through the tensor volume. Our method computes a volumetric representation of a white matter tract given two endpoint regions. We have also developed statistical methods for quantifying the full tensor data along these pathways, which should be useful in clinical studies using DT-MRI. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

|-

| | [[Image:Brain-seg-utah.png|200px]]
| |

== [[Projects:TissueClassificationWithNeighborhoodStatistics| Tissue Classification with Neighborhood Statistics]] ==

We have implemented an MRI tissue classification algorithm based on unsupervised non-parametric density estimation of tissue intensity classes.
[[Projects:TissueClassificationWithNeighborhoodStatistics|More...]]

|}

2009 Winter Project Week ShapePipeline

2009-01-09T15:25:43Z

Datar: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|}

__NOTOC__

===Key Investigators===
* Univ Utah, SCI Institute: Manasi Datar, Josh Cates, Ross Whitaker
* Kitware: Stephen Aylward
* UNC: Martin Styner

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

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

<h1>Objective</h1>
We will investigate the use of BatchMake for automating and packaging
our particle-based shape analysis pipeline. Major tasks include learning
to use BatchMake, and designing compatible command-line interfaces for our
existing software.

</div>

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

<h1>Approach, Plan</h1>
Our goal during project week is to spec out a design and API for a shape analysis
pipeline that strings together a number of our existing software tools. If time
allows, we will also construct a prototype system. Existing code that we hope to
convert for use by BatchMake includes preprocessing routines, correspondence optimization
routines, and visualization tools.

</div>

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

<h1>Progress</h1>
Strategy:<br>
Create individual Batchmake scripts for the various components identified during discussions with the UNC group <br>
String these (as required) into a master Batchmake script to run a customized pipeline <br>
As a separate step, integrate these into Slicer3 as command line modules <br>

Action: <br>
Created a prototype Batchmake script which: <br>
requires the user to set the data directory <br>
dynamically creates the parameter file required for one of the pre-processing operations <br>
runs the pre-processing operation on all images present in the data directory <br>

Problems: <br>
1. The command appendFile(...) is used to create the parameter file dynamically - unable to print '(' and ')' to the file - e.g. appendFile('<path>/xyz.params','(inputs\n') does not work <br>
2. What are the components that need to be bundled with this script when distributing it ? <br>

</div>

<br style="clear: both;" />

</div>

===References===
* J Cates, P T Fletcher, M Styner, H Hazlett, R Whitaker. Particle-Based Shape Analysis of Multi-Object Complexes. Proceedings of the 11th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI '08), to appear.

* J Cates, P T Fletcher, Z Warnock, R Whitaker. A Shape Analysis Framework for Small Animal Phenotyping with Application to Mice with a Targeted Disruption of Hoxd11. Proceedings of the 5th IEEE International Symposium on Biomedical Imaging (ISBI '08), pp. 512-516, 2008.

* I Oguz, J Cates, P T Fletcher, R Whitaker, D Cool, S Aylward, M Styner. Entropy-Based Particle Systems and Local Features for Cortical Correspondence Optimization Proceedings of the 5th IEEE International Symposium on Biomedical Imaging (ISBI '08), pp. 1637-1641, 2008.

* J Cates, P T Fletcher, M Styner, M Shenton, R Whitaker. Shape Modeling and Analysis with Entropy-Based Particle Systems. Information Processing in Medical Imaging IPMI 2007, LNCS 4584, pp. 333-345, 2007.

* J Cates, P T Fletcher, R Whitaker. Entropy-Based Particle Systems for Shape Correspondence. Mathematical Foundations of Computational Anatomy Workshop, MICCAI 2006. pp. 90-99 Oct 2006. pdf