NAMIC Wiki - User contributions [en]

People

2011-06-22T21:45:17Z

Kedar p: /* Personnel at least partially funded by NA-MIC */

== Personnel at least partially funded by NA-MIC ==

#'''Leadership Core'''
## '''[[User:Kikinis|Ron Kikinis]], Harvard (BWH SPL) PI'''
## [[User:Naucoin|Nicole Aucoin]], Harvard (BWH SPL)
## [[User:Marianna|Marianna Jakab]], Harvard (BWH SPL)
## [[User:Mastrogiacom|Katie Mastrogiacomo]], Harvard (BWH SPL)
## Wendy Plesniak, Harvard (BWH SPL)
# '''Algorithms Core'''
## University of Utah C1
###'''[http://www.cs.utah.edu/~whitaker/ Ross Whitaker], PI'''
### Manasi Datar
### Samuel Gerber
### Yongshen Pan
## University of Utah
### '''[http://www.sci.utah.edu/~gerig/ Guido Gerig], PI'''
### Emmanuel Bitaud
### Stanley Dirrleman
### James Fishbaugh
### Marcel Prastawa
### [[User:Gcasey|Casey Goodlett]]
### Preston T. Fletcher
### Ran Tao
## MIT (CSAIL)
### '''[[Polina_Golland|Polina Golland]], PI'''
### [[Eric_Grimson|Eric Grimson]]
### [[User:FernD|Fern DeOliveira]]
### Michal Depa
### Tammy Riklin Raviv
## UNC
### '''[[User:Styner|Martin Styner]], PI'''
### [http://www.med.unc.edu/psych/directories/hazlett.htm/ Heather Cody Hazlett]
### Michael Garret Larson
### Gary Long
### Deepika Mahalingam
### Ipek Oguz
### Rachel Gimpel Smith
### Clement Vachet
## Georgia Tech
### '''[http://www.ece.gatech.edu/faculty/fac_profiles/bio.php?empno=502435 Allen Tannenbaum], PI'''
### Yi Gao
### Vandana Mohan
## MGH
### [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Bruce Fischl]
## Kitware, Inc.
###'''[[User:Will| Will Schroeder]], PI'''
### [[User:Barre|Sebastien Barre]]
### [http://www.kitware.com/profile/team/hoffman.html/ William Hoffman]
### [[User:Ibanez|Luis Ibanez]]
## GE
### '''[[User:Millerjv|Jim Miller]], PI'''
### Roshni Bhagalia
### Dirk Padfield
### James Ross
### [[User:Taox|Xiaodong Tao]]
### [[User:Harveerar|Harini Veeraraghavan]]
### [[User:kedar_p|Kedar Patwardhan]]
## Isomics
### '''[[User:Pieper|Steve Pieper]], PI'''
### Alex Yarmakovich
## WUSTL
### '''[http://nrg.wustl.edu Daniel Marcus], PI'''
### Kevin Archie
### Mikhail Milchenko
### Timothy Olsen
## UCSD
### '''Jeffrey S. Grethe, PI'''
### Mark Ellisman
### Marco Ruiz
# '''Driving Biological Projects (DBP)'''
## University of Utah
### '''[http://www.sci.utah.edu/~macleod/ Rob MacLeod], PI'''
### Josh Blauer
### Josh Cates
## Iowa
### '''Hans Johnson, PI'''
### Norman Williams
## MGH
### '''Gregory C. Sharp, PI'''
### Rui Li
## UCLA
### '''Jack Van Horn, PI'''
### Jeffrey Alger
### Ian Bowman
### Celia Cheung
### Nathan Hageman
### David Hovda
### Arthur W. Toga
### Paul Vespa
## Queen's University
### '''[http://www.cisst.org/~gabor/ Gabor Fichtinger], PI'''
### [http://media.cs.queensu.ca/purang/ Purang Abolmaesumi]
### [http://imaging.robarts.ca/~dgobbi/ David Gobbi]
### Siddharth Vikal
## The Mind Institute
### '''[http://www.mrn.org/principal-investigators/h-jeremy-bockholt Jeremy Bockholt], PI'''
### Mark Scully
## BWH
### '''[http://lmi.bwh.harvard.edu/~kubicki/ Marek Kubicki], PI'''
### Jorge Alvarado
### Jennifer Goodrich
### Padmapriya Srinivazan
# '''Service Core'''
## Kitware, Inc.
### '''[[User:Will|Will Schroeder]], PI'''
### Zack Galbreath
### William Hoffman
### Julien Jomier
### Zach Mullen
# '''Training Core'''
## '''[[User:Randy|Randy Gollub]], Harvard (MGH) PI'''
## [[User:SPujol|Sonia Pujol]], Harvard (BWH SPL)
# '''Dissemination Core'''
## '''[[User:Tkapur|Tina Kapur]], Harvard (BWH SPL) co-PI'''
## '''[[User:Pieper|Steve Pieper]], Isomics co-PI'''
# '''Administration Core'''
## Rachana Manandhar, Harvard (BWH SPL)
## [[User:Sanjay|Sanjay Manandhar]], Harvard (BWH SPL)

== NA-MIC Collaborators ==
These NA-MIC collaborators are funded under the "Collaboration with NCBC" PAR.
#Nicole Grosland, UIowa
#Vincent Magnotta, UIowa
#Steve Pieper, Isomics
#James Daunais, Wake Forest
#Robert Kraft, Wake Forest
#Chris Wyatt, Virginia Tech
#Kilian Pohl, Harvard (BWH SPL)
#Sandy Wells, Harvard (BWH SPL)
#Kevin Cleary, Georgetown
#Enrique Campos-Nanez, George Washington U.
#Patrick (Peng) Cheng, Georgetown
#Ziv Yaniv, Georgetown
#Nobuhiko Hata, Harvard (BWH)
#Curtis Lisle, KnowledgeVis

==NA-MIC EAB==

Our External Advisory Board members are listed [[EAB|here]].

== NA-MIC alumni ==
* [http://marchingcubes.org Bill Lorensen]
* [[User:Lzollei|Lilla Zollei]], MIT (CSAIL)
* Lauren O'Donnell, MIT (CSAIL)
* [http://people.csail.mit.edu/wanmei/ Wanmei Ou], MIT (CSAIL)
* [[Mahnaz_Maddah|Mahnaz Maddah]], MIT (CSAIL)
* Ramsey Al-Hakim, Georgia Tech
* [[User:Melonakos|John Melonakos]], Georgia Tech
* [[User:Lankton|Shawn Lankton]], Georgia Tech
* [[User:Nain|Delphine Nain]], Georgia Tech
* Xavier Le Faucheur, Georgia Tech
* [[User:Mohan|Vandana Mohan]], Georgia Tech
* Tom Fletcher, Utah
* [http://www.sci.utah.edu/cgi-bin/SCIpersonnel.pl?username=tolga Tolga Tasdizen], Utah
* [http://www.cs.utah.edu/~sbasu/ Saurav Basu], Utah
* Josh Snyder, Harvard (MGH)
* [[User:DavidTuch|David Tuch]], Harvard (MGH)
* [[User:Karthik|Karthik Krishnan]],Kitware
* [http://www.kitware.com/profile/team/cedilnik.html/ Andy Cedilnik], Kitware
* [[User:Mathieu|Mathieu Malaterre]], Kitware
* [http://www.stat.ucla.edu/~dinov/ Ivo Dinov], UCLA
* [[User:MichaelPan|Michael Pan]], UCLA
* Brendan Flaherty, UCSD
* [[User:Adamc|Adam Cohen]], Harvard (BWH PNL)
* [[User:Markd|Mark Dreusicke]], Harvard (BWH PNL)
* Martha Shenton, Harvard (BWH PNL) PI
* [http://lmi.bwh.harvard.edu/~sylvain/ Sylvain Bouix], Harvard (BWH PNL)
* [http://lmi.bwh.harvard.edu/~marc/ Marc Niethammer], Harvard (BWH PNL)
* [http://synapse.hitchcock.org/bios/saykin.shtml Andy Saykin], Dartmouth PI
* Bob Roth, Dartmouth
* [http://synapse.hitchcock.org/bios/flashman.shtml Laura Flashman], Dartmouth
* [http://www.dhmc.org/providers/dhmc_provider_634.html Thomas McAllister], Dartmouth
* Alan Green, Dartmouth
* John West, Dartmouth
* [http://synapse.hitchcock.org/bios/mchugh.shtml/ Tara McHugh], Dartmouth
* [http://synapse.hitchcock.org/bios/pixley.shtml Heather Pixley], Dartmouth
* Stephen Guerin, Dartmouth
* John MacDonald, Dartmouth
* [http://www.bic.uci.edu/faculty/sgpotkin.htm/ Steve Potkin], UCI PI
* [[User:Jfallon|James Fallon]], UCI
* Jessica Turner, UCI
* Martina Panzenboeck, UCI
* David Medina, UCI
* [http://www.ics.uci.edu/~smyth/ Padhraic Smyth], UCI
* [http://www.ics.uci.edu/~sternh/ Hal Stern], UCI
* Diane Highum, UCI
* [http://www.ess.uci.edu/~yu/ Yi Jin], UCI
* Liv Trondsen, UCI
* Fabio Macciardi, Toronto
* [http://www.utpsychiatry.ca/dirsearch.asp?id=130 Jim Kennedy], Toronto
* Aristotle Voineskos, Toronto
* [http://kotaro.naist.jp/~meg/eindex.html Megumi Nakao], NAIST

== "Friends and Family" ==

=== NIH ===

* [[User:Lysterp|Peter M. Lyster]]

=== mBIRN ===

* [[User:Akolasny|Anthony Kolasny]]
* [[User:Dmarcus|Dan Marcus]]
* [[User:Kikinis|Ron Kikinis]]

=== fBIRN ===

* [[User:Kikinis|Ron Kikinis]]

=== IGT ===

* [[User:Ibanez|Luis Ibanez]]
* [[User:Noby| Nobuhiko Hata]]

=== Other ===

2011 Summer Project Week RSS for AFib Ablation

2011-06-22T21:04:53Z

Kedar p: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
Image:RSSMandible.png|RSS segmentation on mandible
</gallery>
'''Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy'''...
Atrial fibrillation (AF) is characterized by rapid and dysynchronous contractions of the atria, in conjunction with structural changes in the atrial tissue. One treatment, catheter ablation, neutralizes, or isolates, the electrical sources of AF by applying radiofrequency energy with an intracardiac catheter. Magnetic resonance imaging (MRI) has been used to examine and quantify remodeling in the atrial wall before and after catheter ablation. However, the current workflow to evaluate the degree of remodeling in the atrial wall depends on a variety of tools and manual segmentation of that structure.

==Key Investigators==
* Utah: Rob MacLeod, Josh Cates, and Josh Blauer
* GE Global: Kedar Patwardhan
* Isomics: Steve Pieper
* Georgia Tech: Yi Gao, Wassim Haddad, and Allen Tannenbaum

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

<h3>Objective</h3>

'''Long-Term'''
* Automated segmentation of the atrial wall, based on RSS
* Consolidate and streamline current segmentation workflow

'''Project Week'''
* Refine registration pipeline for pre- and post-ablation contrast MRI scans
* Integrate RSS tool into the Editor module

</div>

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

<h3>Approach, Plan</h3>
* We are currently developing a registration pipeline specific to pre- and post-ablation contrast MRI scans
* We plan to use Project Week to work with collaborators to test, debug, and further refine this registration pipeline
* We will add editor module wrappers to call the RSS CLI package. We also plan to improve the clinical usability by simplifying the user interaction required for setting algorithm parameters.
</div>

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

<h3>Progress</h3>
* registration pipeline progress here ...
* First cut of integrated editor module ready (tested on windows).

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a:

::Slicer Module
::#Built-in: No
::#Extension -- commandline: No
::#Extension -- loadable: YES

==References==
'''1''' Y. Gao, B. Gholami, R.S. MacLeod, J. Blauer, W.M. Haddad, and A.R. Tannenbaum, Segmentation of the Endocardial Wall of the Left Atrium using Local-Region Based Active Contours and Statistical Shape Learning, Proceedings of SPIE Medical Imaging 2010, Vol. 7623, 76234Z.

'''2''' C.J. McGann, E.G. Kholmovski, R.S. Oakes, J.J. Blauer, M. Daccarett, N. Segerson, K.J. Airey, N. Akoum, E. Fish, T.J. Badger, E.V. DiBella, D. Parker, R.S. MacLeod, N.F. Marrouche. “New Magnetic Resonance Imaging-Based Method for Defining the Extent of Left Atrial Wall Injury After the Ablation of Atrial Fibrillation,” In Journal of the American College of Cardiology, Vol. 52, No. 15, pp. 1263--1271. Oct 7, 2008. http://www.sci.utah.edu/publications/mcgann08/mcg2008.pdf
</div>

2011 Summer Project Week RSS for AFib Ablation

2011-06-20T18:00:54Z

Kedar p: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
Image:RSSMandible.png|RSS segmentation on mandible
</gallery>
'''Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy'''...
Atrial fibrillation (AF) is characterized by rapid and dysynchronous contractions of the atria, in conjunction with structural changes in the atrial tissue. One treatment, catheter ablation, neutralizes, or isolates, the electrical sources of AF by applying radiofrequency energy with an intracardiac catheter. Magnetic resonance imaging (MRI) has been used to examine and quantify remodeling in the atrial wall before and after catheter ablation. However, the current workflow to evaluate the degree of remodeling in the atrial wall depends on a variety of tools and manual segmentation of that structure.

==Key Investigators==
* Utah: Rob MacLeod, Josh Cates, and Josh Blauer
* Georgia Tech: Yi Gao, Wassim Haddad, and Allen Tannenbaum
* GE Global: Kedar Patwardhan

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

<h3>Objective</h3>

'''Long-Term'''
* Automated segmentation of the atrial wall, based on RSS
* Consolidate and streamline current segmentation workflow

'''Project Week'''
* Refine registration pipeline for pre- and post-ablation contrast MRI scans
* Integrate RSS tool into the Editor module

</div>

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

<h3>Approach, Plan</h3>
* We are currently developing a registration pipeline specific to pre- and post-ablation contrast MRI scans
* We plan to use Project Week to work with collaborators to test, debug, and further refine this registration pipeline
* We will add editor module wrappers to call the RSS CLI package. We also plan to improve the clinical usability by simplifying the user interaction required for setting algorithm parameters.
</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a:

::Slicer Module
::#Built-in: No
::#Extension -- commandline: No
::#Extension -- loadable: YES

==References==
'''1''' Y. Gao, B. Gholami, R.S. MacLeod, J. Blauer, W.M. Haddad, and A.R. Tannenbaum, Segmentation of the Endocardial Wall of the Left Atrium using Local-Region Based Active Contours and Statistical Shape Learning, Proceedings of SPIE Medical Imaging 2010, Vol. 7623, 76234Z.

'''2''' C.J. McGann, E.G. Kholmovski, R.S. Oakes, J.J. Blauer, M. Daccarett, N. Segerson, K.J. Airey, N. Akoum, E. Fish, T.J. Badger, E.V. DiBella, D. Parker, R.S. MacLeod, N.F. Marrouche. “New Magnetic Resonance Imaging-Based Method for Defining the Extent of Left Atrial Wall Injury After the Ablation of Atrial Fibrillation,” In Journal of the American College of Cardiology, Vol. 52, No. 15, pp. 1263--1271. Oct 7, 2008. http://www.sci.utah.edu/publications/mcgann08/mcg2008.pdf
</div>

2011 Summer Project Week RSS for AFib Ablation

2011-06-14T20:01:20Z

Kedar p: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>
'''Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy'''...
Atrial fibrillation (AF) is characterized by rapid and dysynchronous contractions of the atria, in conjunction with structural changes in the atrial tissue. One treatment, catheter ablation, neutralizes, or isolates, the electrical sources of AF by applying radiofrequency energy with an intracardiac catheter. Magnetic resonance imaging (MRI) has been used to examine and quantify remodeling in the atrial wall before and after catheter ablation. However, the current workflow to evaluate the degree of remodeling in the atrial wall depends on a variety of tools and manual segmentation of that structure.

==Key Investigators==
* Utah: Rob MacLeod, Josh Cates, and Josh Blauer
* Georgia Tech: Yi Gao, Wassim Haddad, and Allen Tannenbaum
* GE Global: Kedar Patwardhan

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

<h3>Objective</h3>

'''Long-Term'''
* Automated segmentation of the atrial wall, based on RSS
* Consolidate and streamline current segmentation workflow

'''Project Week'''
* Refine registration pipeline for pre- and post-ablation contrast MRI scans
* Integrate RSS tool into the Editor module

</div>

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

<h3>Approach, Plan</h3>
* We are currently developing a registration pipeline specific to pre- and post-ablation contrast MRI scans
* We plan to use Project Week to work with collaborators to test, debug, and further refine this registration pipeline
* We will add editor module wrappers to call the RSS CLI package. We plan to use the project week to complete the editor module integration of the RSS tool and simplify the user interaction required for setting parameters required by the RSS algorithm.
</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a:

::Slicer Module
::#Built-in: No
::#Extension -- commandline: No
::#Extension -- loadable: YES

==References==
'''1''' Y. Gao, B. Gholami, R.S. MacLeod, J. Blauer, W.M. Haddad, and A.R. Tannenbaum, Segmentation of the Endocardial Wall of the Left Atrium using Local-Region Based Active Contours and Statistical Shape Learning, Proceedings of SPIE Medical Imaging 2010, Vol. 7623, 76234Z.

'''2''' C.J. McGann, E.G. Kholmovski, R.S. Oakes, J.J. Blauer, M. Daccarett, N. Segerson, K.J. Airey, N. Akoum, E. Fish, T.J. Badger, E.V. DiBella, D. Parker, R.S. MacLeod, N.F. Marrouche. “New Magnetic Resonance Imaging-Based Method for Defining the Extent of Left Atrial Wall Injury After the Ablation of Atrial Fibrillation,” In Journal of the American College of Cardiology, Vol. 52, No. 15, pp. 1263--1271. Oct 7, 2008. http://www.sci.utah.edu/publications/mcgann08/mcg2008.pdf
</div>

2011 Summer Project Week RSS for AFib Ablation

2011-06-13T19:39:11Z

Kedar p: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>
'''Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy'''...
Atrial fibrillation (AF) is characterized by rapid and dysynchronous contractions of the atria, in conjunction with structural changes in the atrial tissue. One treatment, catheter ablation, neutralizes, or isolates, the electrical sources of AF by applying radiofrequency energy with an intracardiac catheter. Magnetic resonance imaging (MRI) has been used to examine and quantify remodeling in the atrial wall before and after catheter ablation. However, the current workflow to evaluate the degree of remodeling in the atrial wall depends on a variety of tools and manual segmentation of that structure.

==Key Investigators==
* Utah: Rob MacLeod, Josh Cates, and Josh Blauer
* Georgia Tech: Yi Gao, Wassim Haddad, and Allen Tannenbaum
* GE Global: Kedar Patwardhan

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

<h3>Objective</h3>

'''Long-Term'''
* Automated segmentation of the atrial wall, based on RSS
* Consolidate and streamline current segmentation workflow

'''Project Week'''
* Refine registration pipeline for pre- and post-ablation contrast MRI scans
* Integrate RSS tool into the Editor module

</div>

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

<h3>Approach, Plan</h3>
* We are currently developing a registration pipeline specific to pre- and post-ablation contrast MRI scans
* We plan to use Project Week to work with collaborators to test, debug, and further refine this registration pipeline

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a:

::Slicer Module
::#Built-in: No
::#Extension -- commandline: No
::#Extension -- loadable: YES

==References==
'''1''' Y. Gao, B. Gholami, R.S. MacLeod, J. Blauer, W.M. Haddad, and A.R. Tannenbaum, Segmentation of the Endocardial Wall of the Left Atrium using Local-Region Based Active Contours and Statistical Shape Learning, Proceedings of SPIE Medical Imaging 2010, Vol. 7623, 76234Z.

'''2''' C.J. McGann, E.G. Kholmovski, R.S. Oakes, J.J. Blauer, M. Daccarett, N. Segerson, K.J. Airey, N. Akoum, E. Fish, T.J. Badger, E.V. DiBella, D. Parker, R.S. MacLeod, N.F. Marrouche. “New Magnetic Resonance Imaging-Based Method for Defining the Extent of Left Atrial Wall Injury After the Ablation of Atrial Fibrillation,” In Journal of the American College of Cardiology, Vol. 52, No. 15, pp. 1263--1271. Oct 7, 2008. http://www.sci.utah.edu/publications/mcgann08/mcg2008.pdf
</div>

2011 Summer Project Week RSS for AFib Ablation

2011-06-13T19:38:35Z

Kedar p: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>
'''Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy'''...
Atrial fibrillation (AF) is characterized by rapid and dysynchronous contractions of the atria, in conjunction with structural changes in the atrial tissue. One treatment, catheter ablation, neutralizes, or isolates, the electrical sources of AF by applying radiofrequency energy with an intracardiac catheter. Magnetic resonance imaging (MRI) has been used to examine and quantify remodeling in the atrial wall before and after catheter ablation. However, the current workflow to evaluate the degree of remodeling in the atrial wall depends on a variety of tools and manual segmentation of that structure.

==Key Investigators==
* Utah: Rob MacLeod, Josh Cates, and Josh Blauer
* Georgia Tech: Yi Gao, Wassim Haddad, and Allen Tannenbaum
* GE Global: Kedar Patwardhan

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

<h3>Objective</h3>

'''Long-Term'''
* Automated segmentation of the atrial wall, based on RSS
* Consolidate and streamline current segmentation workflow

'''Project Week'''
* Refine registration pipeline for pre- and post-ablation contrast MRI scans
* Integrate RSS tool into the Editor module

</div>

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

<h3>Approach, Plan</h3>
* We are currently developing a registration pipeline specific to pre- and post-ablation contrast MRI scans
* We plan to use Project Week to work with collaborators to test, debug, and further refine this registration pipeline
* We
</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a:

::Slicer Module
::#Built-in: No
::#Extension -- commandline: No
::#Extension -- loadable: YES

==References==
'''1''' Y. Gao, B. Gholami, R.S. MacLeod, J. Blauer, W.M. Haddad, and A.R. Tannenbaum, Segmentation of the Endocardial Wall of the Left Atrium using Local-Region Based Active Contours and Statistical Shape Learning, Proceedings of SPIE Medical Imaging 2010, Vol. 7623, 76234Z.

'''2''' C.J. McGann, E.G. Kholmovski, R.S. Oakes, J.J. Blauer, M. Daccarett, N. Segerson, K.J. Airey, N. Akoum, E. Fish, T.J. Badger, E.V. DiBella, D. Parker, R.S. MacLeod, N.F. Marrouche. “New Magnetic Resonance Imaging-Based Method for Defining the Extent of Left Atrial Wall Injury After the Ablation of Atrial Fibrillation,” In Journal of the American College of Cardiology, Vol. 52, No. 15, pp. 1263--1271. Oct 7, 2008. http://www.sci.utah.edu/publications/mcgann08/mcg2008.pdf
</div>

2011 Summer Project Week

2011-06-02T19:35:37Z

Kedar p: /* 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 Patwardhan, 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)
# [[2011_Summer_Project__Week_DICOM_RT|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, ?)
# Wireless joystick controlling Slicer4 (Szymon Kostrzewski)
# Live Tracked Ultrasound in 3D Slicer 4 (Tamas Heffter)
# [http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
#Nifti Support for Diffusion Tensor Images
# Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
# Refactoring of the tractography display widget (Isaiah)
# Laterality (Lauren)
# Selection for models and bundles post-clustering (Lauren)
#ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
#Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
#Add ODF estimation / visualization (Antonio)
# Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
# [[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
# Stenosis Detector in 3D Slicer 4 (Suares Tamekue, Daniel Haehn, Luca Antiga)

==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].