NAMIC Wiki - User contributions [en]

User:Gfischer

2014-06-12T02:44:16Z

Gfischer:

==Personal Website==
Please see: [http://aimlab.wpi.edu/people/Gregory_Fischer http://aimlab.wpi.edu/people/Gregory_Fischer]

==Contact==
*Email: gfischer@wpi.edu
*Office Phone: 508-831-5261
*Address: WPI, Mechanical Engineering, 100 Institute Road, Higgins Lab, Rm 130, Worcester, MA 01609

User:Gfischer

2014-06-12T02:41:20Z

Gfischer:

==Personal Website==
Please see: [http://aimlab.wpi.edu/people/Gregory_Fischer http://aimlab.wpi.edu/people/Gregory_Fischer]

==Contact==
*Email: gfischer@wpi.edu
*Office Phone: 508-831-5261

User:Gfischer

2014-06-12T00:12:13Z

Gfischer:

Please See:

http://aimlab.wpi.edu/people/Gregory_Fischer

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-12T00:11:43Z

Gfischer: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* [[User:Gfischer|Greg Fischer (WPI)]]
* [[User:Nirav|Nirav Patel (WPI)]]
* [[User:Tokuda|Junichi Tokuda (BWH/SPL)]]

==Project Description==
<div style="margin: 20px;">
This Project is to further develop a workflow and communication protocol for interfacing robots with image-guided therapy systems using OpenIGTLink.

More details coming soon...

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* TBD.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* TBD
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* TBD
</div>
</div>

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-12T00:07:46Z

Gfischer: Created page with '__NOTOC__ <gallery> Image:PW-MIT2014.png|Projects List </gallery> ==Key Investigators== ==Project Description== <div style="margin: 20px;"…'

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

==Project Description==
<div style="margin: 20px;">
This Project is to further develop a workflow and communication protocol for interfacing robots with image-guided therapy systems using OpenIGTLink.

More details coming soon...

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* TBD.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* TBD
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* TBD
</div>
</div>

2014 Summer Project Week

2014-06-12T00:05:51Z

Gfischer: /* Image-Guided Therapy */

__NOTOC__

[[image:PW-MIT2014.png|300px]]

Dates: June 23-27, 2014.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 23
!style="width:18%" |Tuesday, June 24
!style="width:18%" |Wednesday, June 25
!style="width:18%" |Thursday, June 26
!style="width:18%" |Friday, June 27
|-
|
|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'''
|
|'''10-11:30pm''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|
|
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Neuro|Image-Guided Therapy - Neurosurgery]] (Alexandra Golby, Tina Kapur) <br>
[[MIT_Project_Week_Rooms#Star|Star]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
'''12pm''' [[Events:TutorialContestJune2014|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"|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''' [[2014 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:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)
TBD [[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Prostate|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Noby Hata)
<br>----------------------------------------<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
|
|}

== '''Background''' ==

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. 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 NA-MIC coverage for all. Subsequent teleconferences 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 are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

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

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]

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==TBI==

==Atrial Fibrillation==

==Huntington's Disease==

==Head and Neck Cancer==
*[[2014_Summer_Project_Week:Interactive_DIR| Interactive DIR]] (Greg, Ivan)
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg, Ivan)
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg, Paolo)

==Slicer4 Extensions==

*[[2014_Summer_Project_Week:Multidim Data| Multidim Data]] (Kevin Wang, Andras, ?)
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp)

==Cardiac==

==Stroke==

==Brain Segmentation==

==Image-Guided Therapy==

* SlicerIGT extension: testing, tutorials, website (Tamas Ungi, Junichi Tokuda)
* Gestural Point of Care Interface for IGT (Saskia, Franklin, Tobias)
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras)
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* Steered image registration using intelligent interfaces for minimal user interaction (Marcel Prastawa, Jim Miller, Steve Pieper)
* Image To Mesh Conversion for Brain MRI (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov, Ron Kikinis, Nikos Chrisochoides)
* An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer(WPI), Nirav Patel(WPI), Junichi Tokuda(BWH) )

==Radiation Therapy==
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg, ?)

==Chronic Obstructive Pulmonary Disease ==

==[http://qiicr.org QIICR]==
* Real world value mapping support (Andrey, Andras, Steve, Jim, ...)
* Segmentation object support (Andrey, Csaba, Steve, ...)
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)
*Pluggable Label Statistics (Andrey , Ethan, Steve, Brad?, Jim? Dirk?)
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras?, ?)
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc, ?)
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba, ?)
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)

==Feature Extraction==
*Breast Tumor Segmentation and Heterogeneity Analysis (Vivek Narayan, Jay Jagadeesan)
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)

==Other==
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).
*[[2014_Summer_Project_Week:Slicer_LDDMM_Shape_Analysis | Slicer Interface to LDDMM shape anlaysis]] (Saurabh Jain, JHU; Steve Pieper, Isomics; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp, Danielle Pace?)
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:Multiscale_Non_Local_Means_filter_(NLM)_for_chest_CT_images | Multiscale Non Local Means filter (NLM) for chest CT images]] (Pietro Nardelli, University College Cork (UCC), Ireland)

== '''Logistics''' ==

*'''Dates:''' June 23-27, 2014.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' https://www.regonline.com/namic2014summerprojectweek. 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: [[2014_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([https://www.regonline.com/namic2014summerprojectweek Please click here to register.])

#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
#Adrian Dalca, MIT CSAIL, adalca@mit.edu
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Yangming Li, University of Washington, ymli81@uw.edu
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu
#Jim Miller, GE Research, millerjv@ge.com
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu
#Nirav Patel, WPI, napatel@wpi.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu
#Adam Rankin, Queen's University, rankin@queensu.ca
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu
#David Welch, University of Iowa, david-welch@uiowa.edu
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

2014 Summer Project Week

2014-06-12T00:04:35Z

Gfischer: /* Other */

__NOTOC__

[[image:PW-MIT2014.png|300px]]

Dates: June 23-27, 2014.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 23
!style="width:18%" |Tuesday, June 24
!style="width:18%" |Wednesday, June 25
!style="width:18%" |Thursday, June 26
!style="width:18%" |Friday, June 27
|-
|
|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'''
|
|'''10-11:30pm''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|
|
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Neuro|Image-Guided Therapy - Neurosurgery]] (Alexandra Golby, Tina Kapur) <br>
[[MIT_Project_Week_Rooms#Star|Star]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
'''12pm''' [[Events:TutorialContestJune2014|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"|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''' [[2014 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:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)
TBD [[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Prostate|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Noby Hata)
<br>----------------------------------------<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
|
|}

== '''Background''' ==

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. 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 NA-MIC coverage for all. Subsequent teleconferences 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 are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

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

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]

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==TBI==

==Atrial Fibrillation==

==Huntington's Disease==

==Head and Neck Cancer==
*[[2014_Summer_Project_Week:Interactive_DIR| Interactive DIR]] (Greg, Ivan)
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg, Ivan)
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg, Paolo)

==Slicer4 Extensions==

*[[2014_Summer_Project_Week:Multidim Data| Multidim Data]] (Kevin Wang, Andras, ?)
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp)

==Cardiac==

==Stroke==

==Brain Segmentation==

==Image-Guided Therapy==

* SlicerIGT extension: testing, tutorials, website (Tamas Ungi, Junichi Tokuda)
* Gestural Point of Care Interface for IGT (Saskia, Franklin, Tobias)
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras)
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* Steered image registration using intelligent interfaces for minimal user interaction (Marcel Prastawa, Jim Miller, Steve Pieper)
* Image To Mesh Conversion for Brain MRI (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov, Ron Kikinis, Nikos Chrisochoides)
* An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz, Ron Kikinis, Nikos Chrisochoides)

==Radiation Therapy==
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg, ?)

==Chronic Obstructive Pulmonary Disease ==

==[http://qiicr.org QIICR]==
* Real world value mapping support (Andrey, Andras, Steve, Jim, ...)
* Segmentation object support (Andrey, Csaba, Steve, ...)
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)
*Pluggable Label Statistics (Andrey , Ethan, Steve, Brad?, Jim? Dirk?)
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras?, ?)
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc, ?)
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba, ?)
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)

==Feature Extraction==
*Breast Tumor Segmentation and Heterogeneity Analysis (Vivek Narayan, Jay Jagadeesan)
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)

==Other==
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).
*[[2014_Summer_Project_Week:Slicer_LDDMM_Shape_Analysis | Slicer Interface to LDDMM shape anlaysis]] (Saurabh Jain, JHU; Steve Pieper, Isomics; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp, Danielle Pace?)
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:Multiscale_Non_Local_Means_filter_(NLM)_for_chest_CT_images | Multiscale Non Local Means filter (NLM) for chest CT images]] (Pietro Nardelli, University College Cork (UCC), Ireland)

== '''Logistics''' ==

*'''Dates:''' June 23-27, 2014.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' https://www.regonline.com/namic2014summerprojectweek. 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: [[2014_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([https://www.regonline.com/namic2014summerprojectweek Please click here to register.])

#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
#Adrian Dalca, MIT CSAIL, adalca@mit.edu
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Yangming Li, University of Washington, ymli81@uw.edu
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu
#Jim Miller, GE Research, millerjv@ge.com
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu
#Nirav Patel, WPI, napatel@wpi.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu
#Adam Rankin, Queen's University, rankin@queensu.ca
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu
#David Welch, University of Iowa, david-welch@uiowa.edu
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

User:Gfischer

2014-06-12T00:04:05Z

Gfischer:

http://aimlab.wpi.edu/people/Gregory_Fischer

2009 Summer Project Week

2009-06-26T03:56:53Z

Gfischer: /* IGT */

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

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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 16th 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 that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
Breakout Rooms: 32-D451, 38-413

=== Monday===
** 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 Start project work
=== Tuesday ===
** 8:30am breakfast
** 8:30am-9:30am [[2009_Summer_Project_Week_4D_Imaging_discussion| 4D Imaging Meeting]]
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper) ([[media:2009 NA-MIC Project Week Slicer3.4.ppt|Slides]], [[2009_Summer_Project_Week_Extension_Manager|Project Page]])
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata [[Media:2009SummerProgrammingWeekHataIGT.ppt‎|Slides]], Scott Hoge [ [[Media:2009_NA-MIC_Project_Week_FastImagingLibrary.ppt|slides]] ])
** noon lunch
** 1pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W) (Star D463 Star Conference Room in Stata)
** 2:00pm-3.00pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis) (In Grier)
** 4:00pm: [[2009_Summer_Project_Week_GWE_Setup| GWE End-To-End Live Demo]] (Marco Ruiz)
** 4:30pm [http://www.cimit.org/forum-current.html CIMIT Forum (At BWH / Carl J. and Ruth Shapiro Cardiovascular Center) Open Source Software for Translational IGT Research and Commercial Use, Clif Burdette, Acoustic MedSystems, Inc. ]
** 5:30pm adjourn for day

=== Wednesday ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (32-G451) (Luis Ibanez)
** 10am - 11am 32-D451 taken by Megason Lab.
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (D463 Star conference room) (Alexandre Gouaillard, Arnaud Gelas, Lydie Souhait, Badri Roysam, Curtis Rueden)
** 5:30pm adjourn for day

=== Thursday===
** 8:30am breakfast
** 10-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]
** 11am: Breakout Session: Linking atlases, labels, and ontologies
** noon lunch
** 1:00pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (32-D451) (Dan M.)
** 5:30pm adjourn for day

=== Friday===
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#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_2010|in Utah, January 4-8, 2010]]

==Projects==

=== Segmentation ===

#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation|Lupus Lesion Segmentation]] (Mark Scully MRN)
#[[2009_Summer_Project_Week_WML_SEgmentation|White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week_Skull_Stripping|Skull Stripping]] (Snehashis Roy JHU)
#[[EMSegment|EM Segment]] (Sylvain Jaume MIT, Nicolas Rannou BWH)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation|FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_New_ITK_Level_Set_Framework|New Level Set Framework in ITK]] (Arnaud Gelas, Harvard Medical School)
#[[2009_Summer_Project_Week_TubularSurfaceSeg|Tubular Surface Segmentation in Slicer]] (Vandana Mohan, Georgia Tech)
#[[Summer2009:The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images|Segmentation of Knee Structures]] (Harish Doddi Stanford)

=== Registration ===

#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration|Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
#[[BSpline Registration in Slicer3|BSpline Registration in Slicer3]] (Samuel Gerber Utah)
#[[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
#[[2009_Summer_project_week_prostate_registration|Prostate Registration Slicer Module]] (Yi Gao, Georgia Tech)
#[[2009_Summer_Project_Week_Slicer3_registration|Slicer 3 registration ]] (Andrew Rausch BWH PNL)
#[[EPI Correction in Slicer3|EPI Correction in Slicer3]] (Ran Tao Utah)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
#[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI)
#[[2009_Summer_Project_Week_HAMMER_Registration|HAMMER Registration]] (Guorong Wu UNC)
#[[2009_Summer_Project_Week_MCMC_Cuda_Registration|Elastic Non-Rigid Registration using MCMC and CUDA]] (Petter Risholm BWH)
#[[2009_Summer_Project_Week_Cardiac_Blood_Pool_Registration|Cardiac Blood Pool Registration]] (Michal Depa MIT)

=== IGT ===

#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)
#[[2009_Summer_Project_Week_Prostate_Robotics|Prostate Robotics]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|Demo of Neuronavigation using Brainlab, Slicer3, BioImage Suite]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)
#[[2009_Summer_Project_Week_RTHawk_MR_Navigation|Using RTHawk to Implement MR Navigation]] (Ben Schwartz BWH)
#[[2009_Summer_Project_Week_Slicer|Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer]] (Jayender Jagadeesan BWH)
#[[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
#[[Enhanced Neurosuregery navigation]] (Haytham Elhawary, Brigham and Women's Hospital)
#[[GPU accelerated FEM for simulation and segmentation]] (Megumi Nakao, Brigham and Women's Hospital)
#[[Liver EM segmentation]] (Padma Akella, Brigham and Women's Hlspital)

=== Radiotherapy ===

#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
#[[2009_Summer_Project_Week_Adaptive_RT|Adaptive Radiotherapy for Head,Neck, and Thorax]] (Ivan Kolesov GATech)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](James Balter U Michigan)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
#[[2009_Summer_project_week_adaptive_radiation_planning_visualization]](Cal Hisley, Des Moines University/Mercy Des Moines Medical Center)

=== Analysis ===

#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Linking atlas data with ontologies of brain morphology and function]] (Michael Halle BWH)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
#[[2009_Summer_Project_Week_4D_Imaging|4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer|Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
#[[2009_Summer_Project_Week_Statistical_Toolbox|multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)

=== Informatics ===

#[[2009_Summer_Project_Week_XNAT_UI|XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNATFS|XNAT File System with FUSE]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
#[[2009_Summer_Project_Week_GWE_XNAT|GWE-XNAT Integration]] (Marco Ruiz UCSD)
#[[2009_Summer_Project_Week_GWE_Results_Browser|GWE Results Browser Improvements]] (Marco Ruiz UCSD)
#[[Projects:ShapeCorrespondence_UNCOrthoApp|XNAT & Ortho App]] (Beatriz Paniagua UNC)

=== Diffusion ===

#[[Summer2009:VCFS|Stochastic Tractography to study VCFS and Schizophrenia]] (Sylvain Bouix BWH)
#[[2009_Summer_Project_Week_FunctionalClusteringAnalysis|Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients]] (Doug Terry BWH)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep|DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom|DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_FMTractography|Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)

=== Python ===

#[[Summer2009:Using_ITK_in_python|Using ITK in python]] (Steve Pieper BWH)
#[[Summer2009:Using_cython|Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
#[[Summer2009:Implementing_parallelism_in_python|Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
#[[Summer2009:Using_client_server_paradigm_with_python_and_slicer|Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)

=== Slicer Internals ===

#[[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Colors_Module|Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Orthogonal_Reformat_Widget|Orthogonal Planes in Reformat Widget]] (Michal Depa MIT)
#[[Slicer3 Informatics Workflow Design & XNAT updates|Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
#[[Slicer3_FlexibleLayouts | Slicer3 Flexible Layouts]] (Wendy Plesniak BWH)
#[[2009_Summer_Project_Week_Extension_Manager|Slicer3 Extension Manager]] (Katie Hayes BWH)
#[[MeshingSummer2009|IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)

=== Execution Model ===

#[[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
#[[Summer2009:Extension of the Command Line XML Syntax/Interface|Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 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 18, 2009: 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. 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...
# 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-3-4/#dirlist Slicer-3-4 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].

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-D451 (Stata)
** Mon, noon - end
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Mon, noon-end
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*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.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Attendee List==

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''
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|80
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|81
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|84
|- style=&#34height:50px&#34
|85
|- style=&#34height:50px&#34
|86
|- style=&#34height:50px&#34
|87
|- style=&#34height:50px&#34
|88
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|89
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|- style=&#34height:50px&#34
|91
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|92
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|94
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|95
|- style=&#34height:50px&#34
|96
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|99
|- style=&#34height:50px&#34
|100
|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
|114
|- style=&#34height:50px&#34
|115
|- style=&#34height:50px&#34
|116
|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
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|- style=&#34height:50px&#34
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|
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!Last
!Affiliation
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|Blevins
|Acoustic Med
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|Clif
|Burdette
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|Peters
|Beth Israel Deaconess
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|Hayes
|BWH (NAMIC)
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|- style=&#34height:50px&#34
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|BWH (PNL)
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|BWH (PNL)
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|BWH (PNL)
|- style=&#34height:50px&#34
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|Malcolm
|BWH (PNL)
|- style=&#34height:50px&#34
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|Melonakos
|BWH (PNL)
|- style=&#34height:50px&#34
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|Rathi
|BWH (PNL)
|- style=&#34height:50px&#34
|Peter
|Savadjiev
|BWH (PNL)
|- style=&#34height:50px&#34
|Doug
|Terry
|BWH (PNL)
|- style=&#34height:50px&#34
|Andrew
|Rausch
|BWH (Mon only)
|- style=&#34height:50px&#34
|Cal
|Hisley
|Des Moines Unive
|- style=&#34height:50px&#34
|Jim
|Miller
|GE
|- style=&#34height:50px&#34
|Xiaodong
|Tao
|GE
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|GA Tech
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|GA Tech
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|Kolosev
|GA Tech
|- style=&#34height:50px&#34
|Behnood
|Gholami
|GA Tech
|- style=&#34height:50px&#34
|Ziv
|Yaniv
|Georgetown
|- style=&#34height:50px&#34
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|Gouaillard
|Harvard Systems Biology
|- style=&#34height:50px&#34
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|Gelas
|Harvard Systems Biology
|- style=&#34height:50px&#34
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|Souhait
|Harvard Systems Biology
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|Freiman
|Hebrew University of Jerusalem
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|Italy
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|Lisle
|KnowledgeVis
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|Steve
|Pieper
|Isomics
|- style=&#34height:50px&#34
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|Yarmarkovich
|Isomics
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|Cho
|JHU
|- style=&#34height:50px&#34
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|Landman
|JHU
|- style=&#34height:50px&#34
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|Roy
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|Song
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|Kitware
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|Mayo
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|Yong
|Gao
|MGH
|- style=&#34height:50px&#34
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|Gollub
|MGH
|- style=&#34height:50px&#34
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|Li
|MGH
|- style=&#34height:50px&#34
|Greg
|Sharp
|MGH
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|Yaffe
|MGH - Mon
|- style=&#34height:50px&#34
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|Jaume
|MIT
|- style=&#34height:50px&#34
|Bjoern
|Menze
|MIT
|- style=&#34height:50px&#34
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|Bockholt
|MRN (NAMIC Lupus DBP)
|- style=&#34height:50px&#34
|Mark
|Scully
|MRN (NAMIC Lupus DBP) Tue-Th
|- style=&#34height:50px&#34
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|Stam
|NVIDIA (Wed & Thurs)
|- style=&#34height:50px&#34
|Kimberly
|Powell
|NVIDIA (Wed)
|- style=&#34height:50px&#34
|Marta
|Peroni
|Politecnico di Milano
|- style=&#34height:50px&#34
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|Lasso
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|- style=&#34height:50px&#34
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|Liu
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|- style=&#34height:50px&#34
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|Grebe
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|- style=&#34height:50px&#34
|Lining
|Yang
|Siemens Corporate Research
|- style=&#34height:50px&#34
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|Doddi
|Stanford University
|- style=&#34height:50px&#34
|Marco
|Ruiz
|UCSD
|- style=&#34height:50px&#34
|Nathan
|Hageman
|UCLA (Mon-Thurs)
|- style=&#34height:50px&#34
|Hans
|Johnson
|U Iowa
|- style=&#34height:50px&#34
|Vincent
|Magnotta
|U Iowa
|- style=&#34height:50px&#34
|Jeffrey
|Yager
|U Iowa
|- style=&#34height:50px&#34
|Manasi
|Ramachandran
|U Iowa
|- style=&#34height:50px&#34
|Dave
|Welch
|U Iowa
|- style=&#34height:50px&#34
|Andrzej
|Przybyszewski
|UMass Med (Mon)
|- style=&#34height:50px&#34
|James
|Balter
|U Michigan
|- style=&#34height:50px&#34
|Dan
|McShan
|U Michigan
|- style=&#34height:50px&#34
|Zhou
|Shen
|U Michigan
|- style=&#34height:50px&#34
|Beatriz
|Paniagua
|UNC
|- style=&#34height:50px&#34
|Minjeong
|Kim
|UNC
|- style=&#34height:50px&#34
|Zhexing
|Liu
|UNC
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|Clement
|Vachet
|UNC (NAMIC DBP)
|- style=&#34height:50px&#34
|Guorong
|Wu
|UNC
|- style=&#34height:50px&#34
|Samuel
|Gerber
|SCI, Utah
|- style=&#34height:50px&#34
|Ran
|Tao
|SCI, Utah
|- style=&#34height:50px&#34
|Marcel
|Prastawa
|SCI, Utah
|- style=&#34height:50px&#34
|Ross
|Whitaker
|SCI, Utah
|- style=&#34height:50px&#34
|Curtis
|Rueden
|UW-Madison
|- style=&#34height:50px&#34
|Dan
|Marcus
|WUSTL
|- style=&#34height:50px&#34
|Misha
|Milchenko
|WUSTL
|- style=&#34height:50px&#34
|Kevin
|Archie
|WUSTL
|- style=&#34height:50px&#34
|Tim
|Olsen
|WUSTL
|- style=&#34height:50px&#34
|Mehdi
|Esteghamatian
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Diego
|Cantor
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Danielle
|Pace
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Vidya
|Rajagopalan
|VA Tech
|- style=&#34height:50px&#34
|Gregory
|Fischer
|WPI
|- style=&#34height:50px&#34
|Dominique
|Belhachemi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Alark
|Joshi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Xenios
|Papademetris
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Dustin
|Scheinost
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Michelle
|Borkin
|Harvard SEAS (Mon only)
|- style=&#34height:50px&#34
|Renxin
|Chu
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Ben
|Schwartz
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Marianna
|Jakab
|BWH (NCIGT, NAC) (Mon, Tue)
|- style=&#34height:50px&#34
|Viswanath
|Avasarala
|GE (Wed, Thurs)
|- style=&#34height:50px&#34
|Michal
|Depa
|MIT
|- style=&#34height:50px&#34
|}
|}

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''

The following was used to convert from excel to mediawiki markup: http://area23.brightbyte.de/csv2wp.php

MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement

2009-06-22T19:10:12Z

Gfischer:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
Image:MRNeuroRobot.jpg|Prototype Robot
Image:OpenIGTLink_Diagram_JHURobot.png|System Architecture based on CISST, Slicer and OpenIGTLInk
</gallery>

==Key Investigators==
* WPI: Gregory Fischer [mailto:gfischer@wpi.edu gfischer@wpi.edu]
* UMass Med.: Julie Pilitsis, Mitch Albert
* Kitware: Michel Audette

==Collaborators==
* JHU: Peter Kazanzides, Anton Deguet
* BWH: Junichi Tokuda, Noby Hata
* Kitware: Stephen Aylward, Andinet Enquobahrie

==Students==
* WPI: Greg Cole (Robot, Motor Control), Hao Su (Haptics, Sensors), Yi Wang (Controller, Pneumatics), Kevin Harrington (Controller Software and Interface)

=== Project Overview===
The objective of our research is to make conventional diagnostic closed high-field MRI scanners available for guiding deep brain stimulation electrode placement interventions. Our approach is to employ an MRI-compatible robotic assistant for guiding DBS electrode insertion under direct, real-time MR image guidance. The system will allow interactive probe alignment under real-time imaging in standard diagnostic high-field MR scanners. Use of a robotic assistant will minimize the potential for human error and mis-registration associated with the current procedure and will better address the practical issues of operating in an MR scanner bore.

=== Project Week Plan ===

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Robot control from Slicer
* Neuro navigation
* Electrode tracking in MRI
* Localization and tracking of brain anatomy (STN)
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Open to new collaborations to solve the listed objectives
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
* Prototype robot assembled
* Modular MR robot controller ready
* Robot controller architecture using CISST functional
* Communication w/ OpenIGTLink functional
</div>

</div>

==References==
*Wang Y, Cole GA, Su H, Pilitis JG, Fischer GS, MRI Compatibility Evaluation of a Piezoelectric Actuator System for a Neural Interventional Robot, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society - EMBC 2009, Minneapolis, Minnesota, September 2009 (accepted).
*Cole G, Pilitsis J, Fischer GS, Design of a Robotic System for MRI-Guided Deep Brain Stimulation Electrode Placement, International Conference on Robotics and Automation - ICRA 2009, Kobe, Japan, May 2009.
*Wang Y, Shazeeb MS, Sotak CH, Fischer GS, Optimization of Piezoelectric Motors to Enhance MR Compatiblity for Interventional Devices, 17th Scientific Meeting and Exhibition of the International Society of Magnetic Resonance in Medicine - ISMRM 2009, April 2009.

MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement

2009-06-22T19:08:02Z

Gfischer: /* Collaborators */

__NOTOC__
<gallery>
Image:MRNeuroRobot.jpg|Prototype Robot
Image:OpenIGTLink_Diagram_JHURobot.png|System Architecture based on CISST, Slicer and OpenIGTLInk
</gallery>

==Key Investigators==
* WPI: Gregory Fischer [mailto:gfischer@wpi.edu gfischer@wpi.edu]
* UMass Med.: Julie Pilitsis, Mitch Albert
* Kitware: Michel Audette

==Collaborators==
* JHU: Peter Kazanzides, Anton Deguet
* BWH: Junichi Tokuda, Noby Hata
* Kitware: Stephen Aylward, Andinet Enquobahrie

==Students==
* WPI: Greg Cole (Robot, Motor Control), Hao Su (Haptics, Sensors), Yi Wang (Controller, Pneumatics), Kevin Harrington (Controller Software and Interface)

=== Project Overview===
The objective of our research is to make conventional diagnostic closed high-field MRI scanners available for guiding deep brain stimulation electrode placement interventions. Our approach is to employ an MRI-compatible robotic assistant for guiding DBS electrode insertion under direct, real-time MR image guidance. The system will allow interactive probe alignment under real-time imaging in standard diagnostic high-field MR scanners. Use of a robotic assistant will minimize the potential for human error and mis-registration associated with the current procedure and will better address the practical issues of operating in an MR scanner bore.

=== Project Week Plan ===

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Robot control from Slicer
* Neuro navigation
* Electrode tracking in MRI
* Localization and tracking of brain anatomy (STN)
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Open to new collaborations to solve the listed objectives
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
* Prototype robot assembled
* Modular MR robot controller ready
* Robot controller architecture using CISST functional
* Communication w/ OpenIGTLink functional
</div>

</div>

==References==
*Wang Y, Cole GA, Su H, Pilitis JG, Fischer GS, MRI Compatibility Evaluation of a Piezoelectric Actuator System for a Neural Interventional Robot, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society - EMBC 2009, Minneapolis, Minnesota, September 2009 (accepted).
*Cole G, Pilitsis J, Fischer GS, Design of a Robotic System for MRI-Guided Deep Brain Stimulation Electrode Placement, International Conference on Robotics and Automation - ICRA 2009, Kobe, Japan, May 2009.
*Wang Y, Shazeeb MS, Sotak CH, Fischer GS, Optimization of Piezoelectric Motors to Enhance MR Compatiblity for Interventional Devices, 17th Scientific Meeting and Exhibition of the International Society of Magnetic Resonance in Medicine - ISMRM 2009, April 2009.

MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement

2009-06-22T18:55:20Z

Gfischer: /* Students */

__NOTOC__
<gallery>
Image:MRNeuroRobot.jpg|Prototype Robot
Image:OpenIGTLink_Diagram_JHURobot.png|System Architecture based on CISST, Slicer and OpenIGTLInk
</gallery>

==Key Investigators==
* WPI: Gregory Fischer [mailto:gfischer@wpi.edu gfischer@wpi.edu]
* UMass Med.: Julie Pilitsis, Mitch Albert
* Kitware: Michel Audette

==Collaborators==
* JHU: Peter Kazanzides
* BWH: Junichi Tokuda
* Kitware: Stephen Aylward, Andinet Enquobahrie

==Students==
* WPI: Greg Cole (Robot, Motor Control), Hao Su (Haptics, Sensors), Yi Wang (Controller, Pneumatics), Kevin Harrington (Controller Software and Interface)

=== Project Overview===
The objective of our research is to make conventional diagnostic closed high-field MRI scanners available for guiding deep brain stimulation electrode placement interventions. Our approach is to employ an MRI-compatible robotic assistant for guiding DBS electrode insertion under direct, real-time MR image guidance. The system will allow interactive probe alignment under real-time imaging in standard diagnostic high-field MR scanners. Use of a robotic assistant will minimize the potential for human error and mis-registration associated with the current procedure and will better address the practical issues of operating in an MR scanner bore.

=== Project Week Plan ===

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Robot control from Slicer
* Neuro navigation
* Electrode tracking in MRI
* Localization and tracking of brain anatomy (STN)
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Open to new collaborations to solve the listed objectives
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
* Prototype robot assembled
* Modular MR robot controller ready
* Robot controller architecture using CISST functional
* Communication w/ OpenIGTLink functional
</div>

</div>

==References==
*Wang Y, Cole GA, Su H, Pilitis JG, Fischer GS, MRI Compatibility Evaluation of a Piezoelectric Actuator System for a Neural Interventional Robot, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society - EMBC 2009, Minneapolis, Minnesota, September 2009 (accepted).
*Cole G, Pilitsis J, Fischer GS, Design of a Robotic System for MRI-Guided Deep Brain Stimulation Electrode Placement, International Conference on Robotics and Automation - ICRA 2009, Kobe, Japan, May 2009.
*Wang Y, Shazeeb MS, Sotak CH, Fischer GS, Optimization of Piezoelectric Motors to Enhance MR Compatiblity for Interventional Devices, 17th Scientific Meeting and Exhibition of the International Society of Magnetic Resonance in Medicine - ISMRM 2009, April 2009.

MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement

2009-06-22T18:50:13Z

Gfischer:

__NOTOC__
<gallery>
Image:MRNeuroRobot.jpg|Prototype Robot
Image:OpenIGTLink_Diagram_JHURobot.png|System Architecture based on CISST, Slicer and OpenIGTLInk
</gallery>

==Key Investigators==
* WPI: Gregory Fischer [mailto:gfischer@wpi.edu gfischer@wpi.edu]
* UMass Med.: Julie Pilitsis, Mitch Albert
* Kitware: Michel Audette

==Collaborators==
* JHU: Peter Kazanzides
* BWH: Junichi Tokuda
* Kitware: Stephen Aylward, Andinet Enquobahrie

==Students==
* WPI: Greg Cole (Robot), Hao Su (Haptics), Yi Wang (Controller), Kevin Harrington (Software)

=== Project Overview===
The objective of our research is to make conventional diagnostic closed high-field MRI scanners available for guiding deep brain stimulation electrode placement interventions. Our approach is to employ an MRI-compatible robotic assistant for guiding DBS electrode insertion under direct, real-time MR image guidance. The system will allow interactive probe alignment under real-time imaging in standard diagnostic high-field MR scanners. Use of a robotic assistant will minimize the potential for human error and mis-registration associated with the current procedure and will better address the practical issues of operating in an MR scanner bore.

=== Project Week Plan ===

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Robot control from Slicer
* Neuro navigation
* Electrode tracking in MRI
* Localization and tracking of brain anatomy (STN)
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Open to new collaborations to solve the listed objectives
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
* Prototype robot assembled
* Modular MR robot controller ready
* Robot controller architecture using CISST functional
* Communication w/ OpenIGTLink functional
</div>

</div>

==References==
*Wang Y, Cole GA, Su H, Pilitis JG, Fischer GS, MRI Compatibility Evaluation of a Piezoelectric Actuator System for a Neural Interventional Robot, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society - EMBC 2009, Minneapolis, Minnesota, September 2009 (accepted).
*Cole G, Pilitsis J, Fischer GS, Design of a Robotic System for MRI-Guided Deep Brain Stimulation Electrode Placement, International Conference on Robotics and Automation - ICRA 2009, Kobe, Japan, May 2009.
*Wang Y, Shazeeb MS, Sotak CH, Fischer GS, Optimization of Piezoelectric Motors to Enhance MR Compatiblity for Interventional Devices, 17th Scientific Meeting and Exhibition of the International Society of Magnetic Resonance in Medicine - ISMRM 2009, April 2009.

MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement

2009-06-22T18:46:00Z

Gfischer: /* Key Investigators */

__NOTOC__
<gallery>
Image:MRNeuroRobot.jpg|Prototype Robot
Image:OpenIGTLink_Diagram_JHURobot.png|System Architecture based on CISST, Slicer and OpenIGTLInk
</gallery>

==Key Investigators==
* WPI: Gregory Fischer [mailto:gfischer@wpi.edu gfischer@wpi.edu]
* UMass Med.: Julie Pilitsis, Mitch Albert
* Kitware: Michel Audette

==Collaborators==
* JHU: Peter Kazanzides
* BWH: Junichi Tokuda

=== Project Overview===
The objective of our research is to make conventional diagnostic closed high-field MRI scanners available for guiding deep brain stimulation electrode placement interventions. Our approach is to employ an MRI-compatible robotic assistant for guiding DBS electrode insertion under direct, real-time MR image guidance. The system will allow interactive probe alignment under real-time imaging in standard diagnostic high-field MR scanners. Use of a robotic assistant will minimize the potential for human error and mis-registration associated with the current procedure and will better address the practical issues of operating in an MR scanner bore.

=== Project Week Plan ===

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Robot control from Slicer
* Neuro navigation
* Electrode tracking in MRI
* Localization and tracking of brain anatomy (STN)
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Open to new collaborations to solve the listed objectives
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
* Prototype robot assembled
* Modular MR robot controller ready
* Robot controller architecture using CISST functional
* Communication w/ OpenIGTLink functional
</div>

</div>

==References==
*Wang Y, Cole GA, Su H, Pilitis JG, Fischer GS, MRI Compatibility Evaluation of a Piezoelectric Actuator System for a Neural Interventional Robot, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society - EMBC 2009, Minneapolis, Minnesota, September 2009 (accepted).
*Cole G, Pilitsis J, Fischer GS, Design of a Robotic System for MRI-Guided Deep Brain Stimulation Electrode Placement, International Conference on Robotics and Automation - ICRA 2009, Kobe, Japan, May 2009.
*Wang Y, Shazeeb MS, Sotak CH, Fischer GS, Optimization of Piezoelectric Motors to Enhance MR Compatiblity for Interventional Devices, 17th Scientific Meeting and Exhibition of the International Society of Magnetic Resonance in Medicine - ISMRM 2009, April 2009.

MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement

2009-06-22T18:45:21Z

Gfischer: /* Key Investigators */

__NOTOC__
<gallery>
Image:MRNeuroRobot.jpg|Prototype Robot
Image:OpenIGTLink_Diagram_JHURobot.png|System Architecture based on CISST, Slicer and OpenIGTLInk
</gallery>

==Key Investigators==
* WPI: Gregory Fischer [mailto:gfischer@wpi.edu gfischer@wpi.edu]
* UMass: Julie Pilitsis
* Kitware: Michel Audette

==Collaborators==
* JHU: Peter Kazanzides
* BWH: Junichi Tokuda

=== Project Overview===
The objective of our research is to make conventional diagnostic closed high-field MRI scanners available for guiding deep brain stimulation electrode placement interventions. Our approach is to employ an MRI-compatible robotic assistant for guiding DBS electrode insertion under direct, real-time MR image guidance. The system will allow interactive probe alignment under real-time imaging in standard diagnostic high-field MR scanners. Use of a robotic assistant will minimize the potential for human error and mis-registration associated with the current procedure and will better address the practical issues of operating in an MR scanner bore.

=== Project Week Plan ===

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Robot control from Slicer
* Neuro navigation
* Electrode tracking in MRI
* Localization and tracking of brain anatomy (STN)
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Open to new collaborations to solve the listed objectives
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
* Prototype robot assembled
* Modular MR robot controller ready
* Robot controller architecture using CISST functional
* Communication w/ OpenIGTLink functional
</div>

</div>

==References==
*Wang Y, Cole GA, Su H, Pilitis JG, Fischer GS, MRI Compatibility Evaluation of a Piezoelectric Actuator System for a Neural Interventional Robot, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society - EMBC 2009, Minneapolis, Minnesota, September 2009 (accepted).
*Cole G, Pilitsis J, Fischer GS, Design of a Robotic System for MRI-Guided Deep Brain Stimulation Electrode Placement, International Conference on Robotics and Automation - ICRA 2009, Kobe, Japan, May 2009.
*Wang Y, Shazeeb MS, Sotak CH, Fischer GS, Optimization of Piezoelectric Motors to Enhance MR Compatiblity for Interventional Devices, 17th Scientific Meeting and Exhibition of the International Society of Magnetic Resonance in Medicine - ISMRM 2009, April 2009.

MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement

2009-06-22T18:43:21Z

Gfischer: /* Project Overview */

__NOTOC__
<gallery>
Image:MRNeuroRobot.jpg|Prototype Robot
Image:OpenIGTLink_Diagram_JHURobot.png|System Architecture based on CISST, Slicer and OpenIGTLInk
</gallery>

==Key Investigators==
* WPI: Gregory Fischer
* UMass: Julie Pilitsis
* Kitware: Michel Audette

==Collaborators==
* JHU: Peter Kazanzides
* BWH: Junichi Tokuda

=== Project Overview===
The objective of our research is to make conventional diagnostic closed high-field MRI scanners available for guiding deep brain stimulation electrode placement interventions. Our approach is to employ an MRI-compatible robotic assistant for guiding DBS electrode insertion under direct, real-time MR image guidance. The system will allow interactive probe alignment under real-time imaging in standard diagnostic high-field MR scanners. Use of a robotic assistant will minimize the potential for human error and mis-registration associated with the current procedure and will better address the practical issues of operating in an MR scanner bore.

=== Project Week Plan ===

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Robot control from Slicer
* Neuro navigation
* Electrode tracking in MRI
* Localization and tracking of brain anatomy (STN)
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Open to new collaborations to solve the listed objectives
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
* Prototype robot assembled
* Modular MR robot controller ready
* Robot controller architecture using CISST functional
* Communication w/ OpenIGTLink functional
</div>

</div>

==References==
*Wang Y, Cole GA, Su H, Pilitis JG, Fischer GS, MRI Compatibility Evaluation of a Piezoelectric Actuator System for a Neural Interventional Robot, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society - EMBC 2009, Minneapolis, Minnesota, September 2009 (accepted).
*Cole G, Pilitsis J, Fischer GS, Design of a Robotic System for MRI-Guided Deep Brain Stimulation Electrode Placement, International Conference on Robotics and Automation - ICRA 2009, Kobe, Japan, May 2009.
*Wang Y, Shazeeb MS, Sotak CH, Fischer GS, Optimization of Piezoelectric Motors to Enhance MR Compatiblity for Interventional Devices, 17th Scientific Meeting and Exhibition of the International Society of Magnetic Resonance in Medicine - ISMRM 2009, April 2009.

MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement

2009-06-22T18:36:18Z

Gfischer:

__NOTOC__
<gallery>
Image:MRNeuroRobot.jpg|Prototype Robot
Image:OpenIGTLink_Diagram_JHURobot.png|System Architecture based on CISST, Slicer and OpenIGTLInk
</gallery>

==Key Investigators==
* WPI: Gregory Fischer
* UMass: Julie Pilitsis
* Kitware: Michel Audette

==Collaborators==
* JHU: Peter Kazanzides
* BWH: Junichi Tokuda

=== Project Overview===
The objective of our research is to make conventional diagnostic closed high-field MRI scanners available for guiding deep brain stimulation electrode placement interventions. Our approach is to employ an MRI-compatible robotic assistant for guiding DBS electrode insertion under direct, real-time MR image guidance. The system will allow interactive probe alignment under real-time imaging in standard diagnostic high-field MR scanners. Use of a robotic assistant will minimize the potential for human error and mis-registration associated with the current procedure and will better address the practical issues of operating in an MR scanner bore.

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*TBA
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*TBA
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
*TBA
</div>

</div>

==References==
*Wang Y, Cole GA, Su H, Pilitis JG, Fischer GS, MRI Compatibility Evaluation of a Piezoelectric Actuator System for a Neural Interventional Robot, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society - EMBC 2009, Minneapolis, Minnesota, September 2009 (accepted).
*Cole G, Pilitsis J, Fischer GS, Design of a Robotic System for MRI-Guided Deep Brain Stimulation Electrode Placement, International Conference on Robotics and Automation - ICRA 2009, Kobe, Japan, May 2009.
*Wang Y, Shazeeb MS, Sotak CH, Fischer GS, Optimization of Piezoelectric Motors to Enhance MR Compatiblity for Interventional Devices, 17th Scientific Meeting and Exhibition of the International Society of Magnetic Resonance in Medicine - ISMRM 2009, April 2009.

MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement

2009-06-22T18:34:00Z

Gfischer:

__NOTOC__
<gallery>
Image:MRNeuroRobot.jpg|Prototyope Robot
Image:OpenIGTLink_Diagram_JHURobot.png|System Architecture
</gallery>

==Key Investigators==
* WPI: Gregory Fischer
* UMass: Julie Pilitsis
* Kitware: Michel Audette

==Collaborators==
* JHU: Peter Kazanzides
* BWH: Junichi Tokuda

=== Project Overview===
The objective of our research is to make conventional diagnostic closed high-field MRI scanners available for guiding deep brain stimulation electrode placement interventions. Our approach is to employ an MRI-compatible robotic assistant for guiding DBS electrode insertion under direct, real-time MR image guidance. The system will allow interactive probe alignment under real-time imaging in standard diagnostic high-field MR scanners. Use of a robotic assistant will minimize the potential for human error and mis-registration associated with the current procedure and will better address the practical issues of operating in an MR scanner bore.

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*TBA
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*TBA
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
*TBA
</div>

</div>

===Detailed plan ===
*TBA

==References==
*Wang Y, Cole GA, Su H, Pilitis JG, Fischer GS, MRI Compatibility Evaluation of a Piezoelectric Actuator System for a Neural Interventional Robot, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society - EMBC 2009, Minneapolis, Minnesota, September 2009 (accepted).
*Cole G, Pilitsis J, Fischer GS, Design of a Robotic System for MRI-Guided Deep Brain Stimulation Electrode Placement, International Conference on Robotics and Automation - ICRA 2009, Kobe, Japan, May 2009.
*Wang Y, Shazeeb MS, Sotak CH, Fischer GS, Optimization of Piezoelectric Motors to Enhance MR Compatiblity for Interventional Devices, 17th Scientific Meeting and Exhibition of the International Society of Magnetic Resonance in Medicine - ISMRM 2009, April 2009.

MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement

2009-06-22T18:32:28Z

Gfischer: /* Key Investigators */

MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement

2009-06-22T18:28:13Z

Gfischer: /* References */

__NOTOC__
<gallery>
Image:MRNeuroRobot.jpg|Prototyope Robot
Image:OpenIGTLink_Diagram_JHURobot.png|System Architecture
</gallery>

==Key Investigators==
* WPI: Gregory Fischer
* UMass: Julie Pilitsis
* JHU: Peter Kazanzides

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*TBA
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*TBA
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
*TBA
</div>

</div>

===Detailed plan ===
*TBA

==References==
*Wang Y, Cole GA, Su H, Pilitis JG, Fischer GS, MRI Compatibility Evaluation of a Piezoelectric Actuator System for a Neural Interventional Robot, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society - EMBC 2009, Minneapolis, Minnesota, September 2009 (accepted).
*Cole G, Pilitsis J, Fischer GS, Design of a Robotic System for MRI-Guided Deep Brain Stimulation Electrode Placement, International Conference on Robotics and Automation - ICRA 2009, Kobe, Japan, May 2009.
*Wang Y, Shazeeb MS, Sotak CH, Fischer GS, Optimization of Piezoelectric Motors to Enhance MR Compatiblity for Interventional Devices, 17th Scientific Meeting and Exhibition of the International Society of Magnetic Resonance in Medicine - ISMRM 2009, April 2009.

User:Gfischer

2009-06-22T18:26:30Z

Gfischer: Created page with 'http://aimlab.wpi.edu/AIM-lab/index.php/Gregory_Fischer'

http://aimlab.wpi.edu/AIM-lab/index.php/Gregory_Fischer

MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement

2009-06-22T18:25:39Z

Gfischer:

__NOTOC__
<gallery>
Image:MRNeuroRobot.jpg|Prototyope Robot
Image:OpenIGTLink_Diagram_JHURobot.png|System Architecture
</gallery>

==Key Investigators==
* WPI: Gregory Fischer
* UMass: Julie Pilitsis
* JHU: Peter Kazanzides

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*TBA
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*TBA
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
*TBA
</div>

</div>

===Detailed plan ===
*TBA

==References==
*Wang Y, Cole GA, Su H, Pilitis JG, Fischer GS, MRI Compatibility Evaluation of a Piezoelectric Actuator System for a Neural Interventional Robot, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society - EMBC 2009, Minneapolis, Minnesota, September 2009 (accepted).
*Cole G, Pilitsis J, Fischer GS, Design of a Robotic System for MRI-Guided Deep Brain Stimulation Electrode Placement, International Conference on Robotics and Automation - ICRA 2009, Kobe, Japan, May 2009.

File:MRNeuroRobot.jpg

2009-06-22T18:24:21Z

Gfischer:

MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement

2009-06-22T18:21:23Z

Gfischer:

__NOTOC__
<gallery>
Image:MRNeuroRobot.jpg|Prototyope Robot
Image:MRNeuroRobotArchitecture.jpg|System Architecture
</gallery>

==Key Investigators==
* WPI: Gregory Fischer
* UMass: Julie Pilitsis
* JHU: Peter Kazanzides

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*TBA
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*TBA
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
*TBA
</div>

</div>

===Detailed plan ===
*TBA

==References==
*Wang Y, Cole GA, Su H, Pilitis JG, Fischer GS, MRI Compatibility Evaluation of a Piezoelectric Actuator System for a Neural Interventional Robot, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society - EMBC 2009, Minneapolis, Minnesota, September 2009 (accepted).
*Cole G, Pilitsis J, Fischer GS, Design of a Robotic System for MRI-Guided Deep Brain Stimulation Electrode Placement, International Conference on Robotics and Automation - ICRA 2009, Kobe, Japan, May 2009.

MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement

2009-06-22T18:16:19Z

Gfischer: Created page with 'Direct MR image guidance during deep brain stimulation (DBS) insertion offers many benefits; most significantly, interventional MRI can be used for planning, monitoring of tissue...'

Direct MR image guidance during deep brain stimulation (DBS) insertion offers many benefits; most significantly, interventional MRI can be used for planning, monitoring of tissue deformation, real-time visualization of insertion, and confirmation of placement. The accuracy of standard stereotactic insertion is limited by registration errors and brain movement during surgery. With real-time acquisition of high-resolution MR images during insertion, probe placement can be confirmed intra-operatively. Direct MR guidance has not taken hold because it is often confounded by a number of issues including: MR-compatibility of existing stereotactic surgery equipment and patient access in the scanner bore. The high resolution images required for neurosurgical planning and guidance require high-field MR (1.5-3T); thus, any system must be capable of working within the constraints of a closed, long-bore diagnostic magnet. Currently, no technological solution exists to assist MRI guided neurosurgical interventions in an accurate, simple, and economical manner.

The objective of our research is to make conventional diagnostic closed high-field MRI scanners available for guiding deep brain stimulation electrode placement interventions.
Our approach is to employ an MRI-compatible robotic assistant for guiding DBS electrode insertion under direct, real-time MR image guidance. The system will allow interactive probe alignment under real-time imaging in standard diagnostic high-field MR scanners. Use of a robotic assistant will minimize the potential for human error and mis-registration associated with the current procedure and will better address the practical issues of operating in an MR scanner bore.

[[Image:NeuroBot.jpg|400px]]

==Key Investigators==
* WPI: Gregory Fischer
* UMass: Julie Pilitsis
* JHU: Peter Kazanzides

==Participants==
* WPI: Greg Fischer

=== References ===
#Wang Y, Cole GA, Su H, Pilitis JG, Fischer GS, MRI Compatibility Evaluation of a Piezoelectric Actuator System for a Neural Interventional Robot, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society - EMBC 2009, Minneapolis, Minnesota, September 2009 (accepted).
#Cole G, Pilitsis J, Fischer GS, Design of a Robotic System for MRI-Guided Deep Brain Stimulation Electrode Placement, International Conference on Robotics and Automation - ICRA 2009, Kobe, Japan, May 2009.

2009 Summer Project Week

2009-06-22T18:11:05Z

Gfischer: /* IGT */

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

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-D451 (Stata)
** Mon, noon - end
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Mon, noon-end
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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 16th 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 that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
Breakout Rooms: 32-D451, 38-413

=== Monday===
** 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 Start project work
=== Tuesday ===
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper) ([[media:2009 NA-MIC Project Week Slicer3.4.ppt|Slides]], [[2009_Summer_Project_Week_Extension_Manager|Project Page]])
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W) (32-D451)
** noon lunch
** 2:00pm-3.00pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis) (In Griers)
** 4:30pm [http://www.cimit.org/forum-current.html CIMIT Forum (At BWH / Carl J. and Ruth Shapiro Cardiovascular Center) Open Source Software for Translational IGT Research and Commercial Use, Clif Burdette, Acoustic MedSystems, Inc. ]
** 5:30pm adjourn for day
=== Wednesday ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] ((Alexandre Gouaillard)(32-D451)
** 5:30pm adjourn for day
=== Thursday===
** 8:30am breakfast
** 9-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (Dan M.)
** 5:30pm adjourn for day
=== Friday===
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#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_2010|in Utah, January 4-8, 2010]]

==Projects==

=== Segmentation ===

#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation|Lupus Lesion Segmentation]] (Mark Scully MRN)
#[[2009_Summer_Project_Week_WML_SEgmentation|White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week_Skull_Stripping|Skull Stripping]] (Snehasish Roy JHU)
#[[EMSegment|EM Segment]] (Sylvain Jaume MIT, Nicolas Rannou BWH)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation|FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_New_ITK_Level_Set_Framework|New Level Set Framework in ITK]] (Arnaud Gelas, Harvard Medical School)
#[[2009_Summer_Project_Week_TubularSurfaceSeg|Tubular Surface Segmentation in Slicer]] (Vandana Mohan, Georgia Tech)
#[[Summer2009:The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images|Segmentation of Knee Structures]] (Harish Doddi Stanford)
#[[2009 Summer Project Week Quantify VMTK seg error|Quantifying VMTK User Segmentation Error]] (Dave Welch UIowa)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Atrium_wall|Atrium Wall Segmentation]] (Behnood Gholami Georgia Tech)

=== Registration ===

#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration|Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
#[[BSpline Registration in Slicer3|BSpline Registration in Slicer3]] (Samuel Gerber Utah)
#[[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
#[[2009_Summer_project_week_prostate_registration|Prostate Registration Slicer Module]] (Yi Gao, Georgia Tech)
#[[2009_Summer_Project_Week_Slicer3_registration|Slicer 3 registration ]] (Andrew Rausch BWH PNL)
#[[EPI Correction in Slicer3|EPI Correction in Slicer3]] (Ran Tao Utah)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
#[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI)
#[[2009_Summer_Project_Week_HAMMER_Registration|HAMMER Registration]] (Guorong Wu UNC)

=== IGT ===

#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)
#[[2009_Summer_Project_Week_Prostate_Robotics|Prostate Robotics]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|Demo of Neuronavigation using Brainlab, Slicer3, BioImage Suite]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)
#[[2009_Summer_Project_Week_RTHawk_MR_Navigation|Using RTHawk to Implement MR Navigation]] (Ben Schwartz BWH)
#[[2009_Summer_Project_Week_Slicer|Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer]] (Jayender Jagadeesan BWH)
#[[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
#[[Enhanced Neurosuregery navigation]] (Haytham Elhawary, Brigham and Women's Hospital)
#[[GPU accelerated FEM for simulation and segmentation]] (Megumi Nakao, Brigham and Women's Hospital)
#[[Liver EM segmentation]] (Padma Akella, Brigham and Women's Hlspital)
#[[MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement]] (Greg Fischer, WPI)

=== Radiotherapy ===

#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
#[[2009_Summer_Project_Week_Adaptive_RT|Adaptive Radiotherapy for Head,Neck, and Thorax]] (Ivan Kolesov GATech)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](James Balter U Michigan)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
#[[2009_Summer_project_week_adaptive_radiation_planning_visualization]](Cal Hisley, Des Moines University/Mercy Des Moines Medical Center)

=== Analysis ===

#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Linking atlas data with ontologies of brain morphology and function]] (Michael Halle BWH)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
#[[2009_Summer_Project_Week_4D_Imaging|4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer|Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
#[[2009_Summer_Project_Week_Statistical_Toolbox|multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)

=== Informatics ===

#[[2009_Summer_Project_Week_Slicer3_XNAT_UI|XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNATFS|XNAT File System with FUSE]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
#[[2009_Summer_Project_Week_GWE_XNAT|GWE-XNAT Integration]] (Marco Ruiz UCSD)
#[[2009_Summer_Project_Week_GWE_Results_Browser|GWE Results Browser Improvements]] (Marco Ruiz UCSD)
#[[Projects:ShapeCorrespondence_UNCOrthoApp|XNAT & Ortho App]] (Beatriz Paniagua UNC)

=== Diffusion ===

#[[Summer2009:VCFS|Stochastic Tractography to study VCFS and Schizophrenia]] (Sylvain Bouix BWH)
#[[2009_Summer_Project_Week_FunctionalClusteringAnalysis|Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients]] (Doug Terry BWH)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep|DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom|DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_FMTractography|Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)

=== Python ===

#[[Summer2009:Using_ITK_in_python|Using ITK in python]] (Steve Pieper BWH)
#[[Summer2009:Using_cython|Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
#[[Summer2009:Implementing_parallelism_in_python|Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
#[[Summer2009:Using_client_server_paradigm_with_python_and_slicer|Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)

=== Slicer Internals ===

#[[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Colors_Module|Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Orthogonal_Reformat_Widget|Orthogonal Planes in Reformat Widget]] (Michal Depa MIT)
#[[Slicer3 Informatics Workflow Design & XNAT updates|Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
#[[Slicer3_FlexibleLayouts | Slicer3 Flexible Layouts]] (Wendy Plesniak BWH)
#[[2009_Summer_Project_Week_Extension_Manager|Slicer3 Extension Manager]] (Katie Hayes BWH)
#[[MeshingSummer2009|IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)

=== Execution Model ===

#[[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
#[[Summer2009:Extension of the Command Line XML Syntax/Interface|Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 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 18, 2009: 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. 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...
# 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-3-4/#dirlist Slicer-3-4 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].

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-D451 (Stata)
** Mon, noon - end
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Mon, noon-end
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*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.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Attendee List==

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''
{|
|-
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{|class="wikitable"
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|}
|
{| class="wikitable sortable"
!First
!Last
!Affiliation
|- style=&#34height:50px&#34
|John
|Melonakos
|AccelerEyes (Wed & Thu morning)
|- style=&#34height:50px&#34
|Jack
|Blevins
|Acoustic Med
|- style=&#34height:50px&#34
|Clif
|Burdette
|Acoustic Med (Mon-Wed)
|- style=&#34height:50px&#34
|Dana
|Peters
|Beth Israel Deaconess
|- style=&#34height:50px&#34
|Nicole
|Aucoin
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Giovanna
|Danagoulian
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haytham
|Elhawary
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Andriy
|Fedorov
|BWH (NAMIC Collaborator)
|- style=&#34height:50px&#34
|Daniel
|Haehn
|BWH (NAC)
|- style=&#34height:50px&#34
|Michael
|Halle
|BWH (NAC)
|- style=&#34height:50px&#34
|Nobuhiko
|Hata
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Katie
|Hayes
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Scott
|Hoge
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Tina
|Kapur
|BWH (NCIGT, NAMIC)
|- style=&#34height:50px&#34
|Ron
|Kikinis
|BWH (NAMIC, NAC, NCIGT)
|- style=&#34height:50px&#34
|Jayender
|Jagadeesan
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haying
|Liu
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Lauren
|O'Donnell
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Wendy
|Plesniak
|BWH (NAC)
|- style=&#34height:50px&#34
|Megumi
|Nakao
|BWH (NAIST)
|- style=&#34height:50px&#34
|Sonia
|Pujol
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Lei
|Qin
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Nicolas
|Rannou
|BWH (NAC)
|- style=&#34height:50px&#34
|Petter
|Risholm
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Florin
|Talos
|BWH (NAC)
|- style=&#34height:50px&#34
|Clare
|Tempany
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Junichi
|Tokuda
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Demian
|Wasserman
|BWH (INRIA)
|- style=&#34height:50px&#34
|Carl-Fredrik
|Westin
|BWH (NAC)
|- style=&#34height:50px&#34
|Sandy
|Wells
|BWH (NAC, NCIGT)
|- style=&#34height:50px&#34
|Lilla
|Zollei
|MGH (NAC)
|- style=&#34height:50px&#34
|Padma
|Akella
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Sylvain
|Bouix
|BWH (PNL)
|- style=&#34height:50px&#34
|Julien
|de Siebenthal
|BWH (PNL)
|- style=&#34height:50px&#34
|Marek
|Kubicki
|BWH (NAMIC DBP PNL)
|- style=&#34height:50px&#34
|Juhana
|Frosen
|BWH Tues only
|- style=&#34height:50px&#34
|Sun Woo
|Lee
|BWH (PNL)
|- style=&#34height:50px&#34
|Jimi
|Malcolm
|BWH (PNL)
|- style=&#34height:50px&#34
|Eric
|Melonakos
|BWH (PNL)
|- style=&#34height:50px&#34
|Yogesh
|Rathi
|BWH (PNL)
|- style=&#34height:50px&#34
|Peter
|Savadjiev
|BWH (PNL)
|- style=&#34height:50px&#34
|Doug
|Terry
|BWH (PNL)
|- style=&#34height:50px&#34
|Andrew
|Rausch
|BWH (Mon only)
|- style=&#34height:50px&#34
|Cal
|Hisley
|Des Moines Unive
|- style=&#34height:50px&#34
|Jim
|Miller
|GE
|- style=&#34height:50px&#34
|Xiaodong
|Tao
|GE
|- style=&#34height:50px&#34
|Vandana
|Mohan
|GA Tech
|- style=&#34height:50px&#34
|Yi
|Gao
|GA Tech
|- style=&#34height:50px&#34
|Ivan
|Kolosev
|GA Tech
|- style=&#34height:50px&#34
|Behnood
|Gholami
|GA Tech
|- style=&#34height:50px&#34
|Ziv
|Yaniv
|Georgetown
|- style=&#34height:50px&#34
|Alex
|Gouaillard
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Arnaud
|Gelas
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Sean
|Megason
|Harvard Systems Biology (Wed only)
|- style=&#34height:50px&#34
|Lydie
|Souhait
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Moti
|Freiman
|Hebrew University of Jerusalem
|- style=&#34height:50px&#34
|Amanda
|Peters
|Harvard SEAS
|- style=&#34height:50px&#34
|Maria Francesca
|Spadea
|Italy
|- style=&#34height:50px&#34
|Curtis
|Lisle
|KnowledgeVis
|- style=&#34height:50px&#34
|Steve
|Pieper
|Isomics
|- style=&#34height:50px&#34
|Alex
|Yarmarkovich
|Isomics
|- style=&#34height:50px&#34
|Nathan
|Cho
|JHU
|- style=&#34height:50px&#34
|Bennett
|Landman
|JHU
|- style=&#34height:50px&#34
|Snehashis
|Roy
|JHU
|- style=&#34height:50px&#34
|Sam
|Song
|JHU
|- style=&#34height:50px&#34
|Sebastien
|Barre
|Kitware
|- style=&#34height:50px&#34
|Luis
|Ibanez
|Kitware
|- style=&#34height:50px&#34
|Daniel
|Blezek
|Mayo
|- style=&#34height:50px&#34
|Yong
|Gao
|MGH
|- style=&#34height:50px&#34
|Randy
|Gollub
|MGH
|- style=&#34height:50px&#34
|Rui
|Li
|MGH
|- style=&#34height:50px&#34
|Greg
|Sharp
|MGH
|- style=&#34height:50px&#34
|Robert
|Yaffe
|MGH - Mon
|- style=&#34height:50px&#34
|Sylvain
|Jaume
|MIT
|- style=&#34height:50px&#34
|Bjoern
|Menze
|MIT
|- style=&#34height:50px&#34
|Jeremy
|Bockholt
|MRN (NAMIC Lupus DBP)
|- style=&#34height:50px&#34
|Mark
|Scully
|MRN (NAMIC Lupus DBP) Tue-Th
|- style=&#34height:50px&#34
|Joe
|Stam
|NVIDIA (Wed & Thurs)
|- style=&#34height:50px&#34
|Kimberly
|Powell
|NVIDIA (Wed)
|- style=&#34height:50px&#34
|Marta
|Peroni
|Politecnico di Milano
|- style=&#34height:50px&#34
|Andras
|Lasso
|Queen's (NAMIC DBP)
|- style=&#34height:50px&#34
|Yanling
|Liu
|SAIC/NCI-Frederick
|- style=&#34height:50px&#34
|Melanie
|Grebe
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Lining
|Yang
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Harish
|Doddi
|Stanford University
|- style=&#34height:50px&#34
|Marco
|Ruiz
|UCSD
|- style=&#34height:50px&#34
|Nathan
|Hageman
|UCLA (Mon-Thurs)
|- style=&#34height:50px&#34
|Hans
|Johnson
|U Iowa
|- style=&#34height:50px&#34
|Vincent
|Magnotta
|U Iowa
|- style=&#34height:50px&#34
|Jeffrey
|Yager
|U Iowa
|- style=&#34height:50px&#34
|Manasi
|Ramachandran
|U Iowa
|- style=&#34height:50px&#34
|Dave
|Welch
|U Iowa
|- style=&#34height:50px&#34
|Andrzej
|Przybyszewski
|UMass Med (Mon)
|- style=&#34height:50px&#34
|James
|Balter
|U Michigan
|- style=&#34height:50px&#34
|Dan
|McShan
|U Michigan
|- style=&#34height:50px&#34
|Zhou
|Shen
|U Michigan
|- style=&#34height:50px&#34
|Beatriz
|Paniagua
|UNC
|- style=&#34height:50px&#34
|Minjeong
|Kim
|UNC
|- style=&#34height:50px&#34
|Zhexing
|Liu
|UNC
|- style=&#34height:50px&#34
|Clement
|Vachet
|UNC (NAMIC DBP)
|- style=&#34height:50px&#34
|Guorong
|Wu
|UNC
|- style=&#34height:50px&#34
|Samuel
|Gerber
|SCI, Utah
|- style=&#34height:50px&#34
|Ran
|Tao
|SCI, Utah
|- style=&#34height:50px&#34
|Marcel
|Prastawa
|SCI, Utah
|- style=&#34height:50px&#34
|Ross
|Whitaker
|SCI, Utah
|- style=&#34height:50px&#34
|Curtis
|Rueden
|UW-Madison
|- style=&#34height:50px&#34
|Dan
|Marcus
|WUSTL
|- style=&#34height:50px&#34
|Misha
|Milchenko
|WUSTL
|- style=&#34height:50px&#34
|Kevin
|Archie
|WUSTL
|- style=&#34height:50px&#34
|Tim
|Olsen
|WUSTL
|- style=&#34height:50px&#34
|Mehdi
|Esteghamatian
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Diego
|Cantor
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Danielle
|Pace
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Vidya
|Rajagopalan
|VA Tech
|- style=&#34height:50px&#34
|Gregory
|Fischer
|WPI
|- style=&#34height:50px&#34
|Dominique
|Belhachemi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Alark
|Joshi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Xenios
|Papademetris
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Dustin
|Scheinost
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Michelle
|Borkin
|Harvard SEAS (Mon only)
|- style=&#34height:50px&#34
|Renxin
|Chu
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Ben
|Schwartz
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Marianna
|Jakab
|BWH (NCIGT, NAC) (Mon, Tue)
|- style=&#34height:50px&#34
|Viswanath
|Avasarala
|GE (Wed, Thurs)
|- style=&#34height:50px&#34
|}
|}

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''

The following was used to convert from excel to mediawiki markup: http://area23.brightbyte.de/csv2wp.php

2009 Summer Project Week

2009-06-22T18:10:29Z

Gfischer: /* IGT */

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

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-D451 (Stata)
** Mon, noon - end
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Mon, noon-end
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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 16th 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 that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
Breakout Rooms: 32-D451, 38-413

=== Monday===
** 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 Start project work
=== Tuesday ===
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper) ([[media:2009 NA-MIC Project Week Slicer3.4.ppt|Slides]], [[2009_Summer_Project_Week_Extension_Manager|Project Page]])
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W) (32-D451)
** noon lunch
** 2:00pm-3.00pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis) (In Griers)
** 4:30pm [http://www.cimit.org/forum-current.html CIMIT Forum (At BWH / Carl J. and Ruth Shapiro Cardiovascular Center) Open Source Software for Translational IGT Research and Commercial Use, Clif Burdette, Acoustic MedSystems, Inc. ]
** 5:30pm adjourn for day
=== Wednesday ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] ((Alexandre Gouaillard)(32-D451)
** 5:30pm adjourn for day
=== Thursday===
** 8:30am breakfast
** 9-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (Dan M.)
** 5:30pm adjourn for day
=== Friday===
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#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_2010|in Utah, January 4-8, 2010]]

==Projects==

=== Segmentation ===

#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation|Lupus Lesion Segmentation]] (Mark Scully MRN)
#[[2009_Summer_Project_Week_WML_SEgmentation|White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week_Skull_Stripping|Skull Stripping]] (Snehasish Roy JHU)
#[[EMSegment|EM Segment]] (Sylvain Jaume MIT, Nicolas Rannou BWH)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation|FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_New_ITK_Level_Set_Framework|New Level Set Framework in ITK]] (Arnaud Gelas, Harvard Medical School)
#[[2009_Summer_Project_Week_TubularSurfaceSeg|Tubular Surface Segmentation in Slicer]] (Vandana Mohan, Georgia Tech)
#[[Summer2009:The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images|Segmentation of Knee Structures]] (Harish Doddi Stanford)
#[[2009 Summer Project Week Quantify VMTK seg error|Quantifying VMTK User Segmentation Error]] (Dave Welch UIowa)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Atrium_wall|Atrium Wall Segmentation]] (Behnood Gholami Georgia Tech)

=== Registration ===

#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration|Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
#[[BSpline Registration in Slicer3|BSpline Registration in Slicer3]] (Samuel Gerber Utah)
#[[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
#[[2009_Summer_project_week_prostate_registration|Prostate Registration Slicer Module]] (Yi Gao, Georgia Tech)
#[[2009_Summer_Project_Week_Slicer3_registration|Slicer 3 registration ]] (Andrew Rausch BWH PNL)
#[[EPI Correction in Slicer3|EPI Correction in Slicer3]] (Ran Tao Utah)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
#[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI)
#[[2009_Summer_Project_Week_HAMMER_Registration|HAMMER Registration]] (Guorong Wu UNC)

=== IGT ===

#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)
#[[2009_Summer_Project_Week_Prostate_Robotics|Prostate Robotics]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|Demo of Neuronavigation using Brainlab, Slicer3, BioImage Suite]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)
#[[2009_Summer_Project_Week_RTHawk_MR_Navigation|Using RTHawk to Implement MR Navigation]] (Ben Schwartz BWH)
#[[2009_Summer_Project_Week_Slicer|Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer]] (Jayender Jagadeesan BWH)
#[[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
#[[Enhanced Neurosuregery navigation]] (Haytham Elhawary, Brigham and Women's Hospital)
#[[GPU accelerated FEM for simulation and segmentation]] (Megumi Nakao, Brigham and Women's Hospital)
#[[Liver EM segmentation]] (Padma Akella, Brigham and Women's Hospital)
#[[MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement]] (Greg Fischer, WPI)

=== Radiotherapy ===

#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
#[[2009_Summer_Project_Week_Adaptive_RT|Adaptive Radiotherapy for Head,Neck, and Thorax]] (Ivan Kolesov GATech)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](James Balter U Michigan)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
#[[2009_Summer_project_week_adaptive_radiation_planning_visualization]](Cal Hisley, Des Moines University/Mercy Des Moines Medical Center)

=== Analysis ===

#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Linking atlas data with ontologies of brain morphology and function]] (Michael Halle BWH)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
#[[2009_Summer_Project_Week_4D_Imaging|4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer|Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
#[[2009_Summer_Project_Week_Statistical_Toolbox|multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)

=== Informatics ===

#[[2009_Summer_Project_Week_Slicer3_XNAT_UI|XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNATFS|XNAT File System with FUSE]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
#[[2009_Summer_Project_Week_GWE_XNAT|GWE-XNAT Integration]] (Marco Ruiz UCSD)
#[[2009_Summer_Project_Week_GWE_Results_Browser|GWE Results Browser Improvements]] (Marco Ruiz UCSD)
#[[Projects:ShapeCorrespondence_UNCOrthoApp|XNAT & Ortho App]] (Beatriz Paniagua UNC)

=== Diffusion ===

#[[Summer2009:VCFS|Stochastic Tractography to study VCFS and Schizophrenia]] (Sylvain Bouix BWH)
#[[2009_Summer_Project_Week_FunctionalClusteringAnalysis|Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients]] (Doug Terry BWH)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep|DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom|DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_FMTractography|Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)

=== Python ===

#[[Summer2009:Using_ITK_in_python|Using ITK in python]] (Steve Pieper BWH)
#[[Summer2009:Using_cython|Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
#[[Summer2009:Implementing_parallelism_in_python|Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
#[[Summer2009:Using_client_server_paradigm_with_python_and_slicer|Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)

=== Slicer Internals ===

#[[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Colors_Module|Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Orthogonal_Reformat_Widget|Orthogonal Planes in Reformat Widget]] (Michal Depa MIT)
#[[Slicer3 Informatics Workflow Design & XNAT updates|Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
#[[Slicer3_FlexibleLayouts | Slicer3 Flexible Layouts]] (Wendy Plesniak BWH)
#[[2009_Summer_Project_Week_Extension_Manager|Slicer3 Extension Manager]] (Katie Hayes BWH)
#[[MeshingSummer2009|IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)

=== Execution Model ===

#[[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
#[[Summer2009:Extension of the Command Line XML Syntax/Interface|Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 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 18, 2009: 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. 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...
# 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-3-4/#dirlist Slicer-3-4 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].

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-D451 (Stata)
** Mon, noon - end
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Mon, noon-end
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*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.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Attendee List==

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''
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|- style=&#34height:50px&#34
|91
|- style=&#34height:50px&#34
|92
|- style=&#34height:50px&#34
|94
|- style=&#34height:50px&#34
|95
|- style=&#34height:50px&#34
|96
|- style=&#34height:50px&#34
|97
|- style=&#34height:50px&#34
|98
|- style=&#34height:50px&#34
|99
|- style=&#34height:50px&#34
|100
|- style=&#34height:50px&#34
|101
|- style=&#34height:50px&#34
|102
|- style=&#34height:50px&#34
|103
|- style=&#34height:50px&#34
|104
|- style=&#34height:50px&#34
|105
|- style=&#34height:50px&#34
|106
|- style=&#34height:50px&#34
|107
|- style=&#34height:50px&#34
|108
|- style=&#34height:50px&#34
|109
|- style=&#34height:50px&#34
|110
|- style=&#34height:50px&#34
|111
|- style=&#34height:50px&#34
|112
|- style=&#34height:50px&#34
|113
|- style=&#34height:50px&#34
|114
|- style=&#34height:50px&#34
|115
|- style=&#34height:50px&#34
|116
|- style=&#34height:50px&#34
|117
|- style=&#34height:50px&#34
|118
|- style=&#34height:50px&#34
|119
|- style=&#34height:50px&#34
|120
|- style=&#34height:50px&#34
|121
|- style=&#34height:50px&#34
|122
|- style=&#34height:50px&#34
|123
|- style=&#34height:50px&#34
|124
|- style=&#34height:50px&#34
|}
|
{| class="wikitable sortable"
!First
!Last
!Affiliation
|- style=&#34height:50px&#34
|John
|Melonakos
|AccelerEyes (Wed & Thu morning)
|- style=&#34height:50px&#34
|Jack
|Blevins
|Acoustic Med
|- style=&#34height:50px&#34
|Clif
|Burdette
|Acoustic Med (Mon-Wed)
|- style=&#34height:50px&#34
|Dana
|Peters
|Beth Israel Deaconess
|- style=&#34height:50px&#34
|Nicole
|Aucoin
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Giovanna
|Danagoulian
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haytham
|Elhawary
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Andriy
|Fedorov
|BWH (NAMIC Collaborator)
|- style=&#34height:50px&#34
|Daniel
|Haehn
|BWH (NAC)
|- style=&#34height:50px&#34
|Michael
|Halle
|BWH (NAC)
|- style=&#34height:50px&#34
|Nobuhiko
|Hata
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Katie
|Hayes
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Scott
|Hoge
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Tina
|Kapur
|BWH (NCIGT, NAMIC)
|- style=&#34height:50px&#34
|Ron
|Kikinis
|BWH (NAMIC, NAC, NCIGT)
|- style=&#34height:50px&#34
|Jayender
|Jagadeesan
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haying
|Liu
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Lauren
|O'Donnell
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Wendy
|Plesniak
|BWH (NAC)
|- style=&#34height:50px&#34
|Megumi
|Nakao
|BWH (NAIST)
|- style=&#34height:50px&#34
|Sonia
|Pujol
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Lei
|Qin
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Nicolas
|Rannou
|BWH (NAC)
|- style=&#34height:50px&#34
|Petter
|Risholm
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Florin
|Talos
|BWH (NAC)
|- style=&#34height:50px&#34
|Clare
|Tempany
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Junichi
|Tokuda
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Demian
|Wasserman
|BWH (INRIA)
|- style=&#34height:50px&#34
|Carl-Fredrik
|Westin
|BWH (NAC)
|- style=&#34height:50px&#34
|Sandy
|Wells
|BWH (NAC, NCIGT)
|- style=&#34height:50px&#34
|Lilla
|Zollei
|MGH (NAC)
|- style=&#34height:50px&#34
|Padma
|Akella
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Sylvain
|Bouix
|BWH (PNL)
|- style=&#34height:50px&#34
|Julien
|de Siebenthal
|BWH (PNL)
|- style=&#34height:50px&#34
|Marek
|Kubicki
|BWH (NAMIC DBP PNL)
|- style=&#34height:50px&#34
|Juhana
|Frosen
|BWH Tues only
|- style=&#34height:50px&#34
|Sun Woo
|Lee
|BWH (PNL)
|- style=&#34height:50px&#34
|Jimi
|Malcolm
|BWH (PNL)
|- style=&#34height:50px&#34
|Eric
|Melonakos
|BWH (PNL)
|- style=&#34height:50px&#34
|Yogesh
|Rathi
|BWH (PNL)
|- style=&#34height:50px&#34
|Peter
|Savadjiev
|BWH (PNL)
|- style=&#34height:50px&#34
|Doug
|Terry
|BWH (PNL)
|- style=&#34height:50px&#34
|Andrew
|Rausch
|BWH (Mon only)
|- style=&#34height:50px&#34
|Cal
|Hisley
|Des Moines Unive
|- style=&#34height:50px&#34
|Jim
|Miller
|GE
|- style=&#34height:50px&#34
|Xiaodong
|Tao
|GE
|- style=&#34height:50px&#34
|Vandana
|Mohan
|GA Tech
|- style=&#34height:50px&#34
|Yi
|Gao
|GA Tech
|- style=&#34height:50px&#34
|Ivan
|Kolosev
|GA Tech
|- style=&#34height:50px&#34
|Behnood
|Gholami
|GA Tech
|- style=&#34height:50px&#34
|Ziv
|Yaniv
|Georgetown
|- style=&#34height:50px&#34
|Alex
|Gouaillard
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Arnaud
|Gelas
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Sean
|Megason
|Harvard Systems Biology (Wed only)
|- style=&#34height:50px&#34
|Lydie
|Souhait
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Moti
|Freiman
|Hebrew University of Jerusalem
|- style=&#34height:50px&#34
|Amanda
|Peters
|Harvard SEAS
|- style=&#34height:50px&#34
|Maria Francesca
|Spadea
|Italy
|- style=&#34height:50px&#34
|Curtis
|Lisle
|KnowledgeVis
|- style=&#34height:50px&#34
|Steve
|Pieper
|Isomics
|- style=&#34height:50px&#34
|Alex
|Yarmarkovich
|Isomics
|- style=&#34height:50px&#34
|Nathan
|Cho
|JHU
|- style=&#34height:50px&#34
|Bennett
|Landman
|JHU
|- style=&#34height:50px&#34
|Snehashis
|Roy
|JHU
|- style=&#34height:50px&#34
|Sam
|Song
|JHU
|- style=&#34height:50px&#34
|Sebastien
|Barre
|Kitware
|- style=&#34height:50px&#34
|Luis
|Ibanez
|Kitware
|- style=&#34height:50px&#34
|Daniel
|Blezek
|Mayo
|- style=&#34height:50px&#34
|Yong
|Gao
|MGH
|- style=&#34height:50px&#34
|Randy
|Gollub
|MGH
|- style=&#34height:50px&#34
|Rui
|Li
|MGH
|- style=&#34height:50px&#34
|Greg
|Sharp
|MGH
|- style=&#34height:50px&#34
|Robert
|Yaffe
|MGH - Mon
|- style=&#34height:50px&#34
|Sylvain
|Jaume
|MIT
|- style=&#34height:50px&#34
|Bjoern
|Menze
|MIT
|- style=&#34height:50px&#34
|Jeremy
|Bockholt
|MRN (NAMIC Lupus DBP)
|- style=&#34height:50px&#34
|Mark
|Scully
|MRN (NAMIC Lupus DBP) Tue-Th
|- style=&#34height:50px&#34
|Joe
|Stam
|NVIDIA (Wed & Thurs)
|- style=&#34height:50px&#34
|Kimberly
|Powell
|NVIDIA (Wed)
|- style=&#34height:50px&#34
|Marta
|Peroni
|Politecnico di Milano
|- style=&#34height:50px&#34
|Andras
|Lasso
|Queen's (NAMIC DBP)
|- style=&#34height:50px&#34
|Yanling
|Liu
|SAIC/NCI-Frederick
|- style=&#34height:50px&#34
|Melanie
|Grebe
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Lining
|Yang
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Harish
|Doddi
|Stanford University
|- style=&#34height:50px&#34
|Marco
|Ruiz
|UCSD
|- style=&#34height:50px&#34
|Nathan
|Hageman
|UCLA (Mon-Thurs)
|- style=&#34height:50px&#34
|Hans
|Johnson
|U Iowa
|- style=&#34height:50px&#34
|Vincent
|Magnotta
|U Iowa
|- style=&#34height:50px&#34
|Jeffrey
|Yager
|U Iowa
|- style=&#34height:50px&#34
|Manasi
|Ramachandran
|U Iowa
|- style=&#34height:50px&#34
|Dave
|Welch
|U Iowa
|- style=&#34height:50px&#34
|Andrzej
|Przybyszewski
|UMass Med (Mon)
|- style=&#34height:50px&#34
|James
|Balter
|U Michigan
|- style=&#34height:50px&#34
|Dan
|McShan
|U Michigan
|- style=&#34height:50px&#34
|Zhou
|Shen
|U Michigan
|- style=&#34height:50px&#34
|Beatriz
|Paniagua
|UNC
|- style=&#34height:50px&#34
|Minjeong
|Kim
|UNC
|- style=&#34height:50px&#34
|Zhexing
|Liu
|UNC
|- style=&#34height:50px&#34
|Clement
|Vachet
|UNC (NAMIC DBP)
|- style=&#34height:50px&#34
|Guorong
|Wu
|UNC
|- style=&#34height:50px&#34
|Samuel
|Gerber
|SCI, Utah
|- style=&#34height:50px&#34
|Ran
|Tao
|SCI, Utah
|- style=&#34height:50px&#34
|Marcel
|Prastawa
|SCI, Utah
|- style=&#34height:50px&#34
|Ross
|Whitaker
|SCI, Utah
|- style=&#34height:50px&#34
|Curtis
|Rueden
|UW-Madison
|- style=&#34height:50px&#34
|Dan
|Marcus
|WUSTL
|- style=&#34height:50px&#34
|Misha
|Milchenko
|WUSTL
|- style=&#34height:50px&#34
|Kevin
|Archie
|WUSTL
|- style=&#34height:50px&#34
|Tim
|Olsen
|WUSTL
|- style=&#34height:50px&#34
|Mehdi
|Esteghamatian
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Diego
|Cantor
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Danielle
|Pace
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Vidya
|Rajagopalan
|VA Tech
|- style=&#34height:50px&#34
|Gregory
|Fischer
|WPI
|- style=&#34height:50px&#34
|Dominique
|Belhachemi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Alark
|Joshi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Xenios
|Papademetris
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Dustin
|Scheinost
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Michelle
|Borkin
|Harvard SEAS (Mon only)
|- style=&#34height:50px&#34
|Renxin
|Chu
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Ben
|Schwartz
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Marianna
|Jakab
|BWH (NCIGT, NAC) (Mon, Tue)
|- style=&#34height:50px&#34
|Viswanath
|Avasarala
|GE (Wed, Thurs)
|- style=&#34height:50px&#34
|}
|}

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''

The following was used to convert from excel to mediawiki markup: http://area23.brightbyte.de/csv2wp.php