NAMIC Wiki - User contributions [en]

2014 Summer Project Week

2014-06-19T16:16:28Z

Tannenba: /* Head and Neck Cancer */

__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''' Breakout Session:''' [[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)]] 
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
 ---------------------------------------- 
'''10am-12pm: Breakout Session:''' [[2014 Project Week Breakout Session: IGT Neuro|Image-Guided Therapy - Neurosurgery]] (Alexandra Golby, Tina Kapur) 
[[MIT_Project_Week_Rooms#Star|Star]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] 
'''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: Ron Kikinis: Welcome'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
 ---------------------------------------- 
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
 ---------------------------------------- 
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) 
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' Breakout Session:''' [[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' Breakout Session:''' [[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' Breakout Session:''' [[2014 Project Week Breakout Session: IGT Prostate|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Noby Hata)
[[MIT_Project_Week_Rooms#Star|Star]]
 ---------------------------------------- 
|
|-
|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 Sharp, Ivan Kolesov, Allen Tannenbaum)
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp)

==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, Paolo Zaffino, Andras, Csaba, Kevin)

==Cardiac==

==Stroke==

==Brain Segmentation==

==Image-Guided Therapy==

* SlicerIGT extension: testing, tutorials, website (Tamas Ungi, Nobuhiko Hata)
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, 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)
* [[2014_Summer_Project_Week:Image To Mesh Conversion for Brain MRI | Image To Mesh Conversion for Brain MRI]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift | 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), Nobuhiko Hata (BWH) )
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)

==Radiation Therapy==
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques, ?)
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)

==Chronic Obstructive Pulmonary Disease ==

==[http://qiicr.org QIICR]==
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim, ...)
* [[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)
*[[2014_Summer_Project_Week:Pluggable Label Statistics |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)
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)

==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)
*[[2014_Summer_Project_Week:Intraoperative_Registration_of_preoperative_CT_and_C-arm_CT_of_the_lung | Intraoperative Registration of preoperative CT and C-arm CT of the lung]] (Katharina Breininger, Jay Jagadeesan)
*[[2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders | CAD Toolbox for Neurological Disorders]] (Sidong Liu, Siqi Liu, Fan Zhang, {Yang Song, Weidong Cai}, Sonia Pujol, Ron Kikinis {remotely})

== '''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
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Saskia Camps, SPL, saskiacamps@gmail.com
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu
#Laurent Chauvin, SPL, lchauvin@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
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com
#Polina Golland, MIT CSAIL, polina@csail.mit.edu
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Franklin King, Queen's University, franklin.king@queensu.ca
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu
#Yangming Li, University of Washington, ymli81@uw.edu
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.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
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu
#Jim Miller, GE Research, millerjv@ge.com
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu
#Danielle Pace, MIT CSAIL, dfpace@mit.edu
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org
#Nirav Patel, WPI, napatel@wpi.edu
#Tobias Penzkofer, SPL, pt@bwh.harvard.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
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu
#Tamas Ungi, Queen's University, ungi@queensu.ca
#David Welch, University of Iowa, david-welch@uiowa.edu
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.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

2014-06-04T13:32:55Z

Tannenba: /* Head and Neck Cancer */

__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 and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11:30pm''' Breakout Session:''' [[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11am: Breakout Session:''' [[2014 Project Week Breakout Session:Registration Algorithms|Registration Algorithms]]'''(Sandy Wells)
[[MIT_Project_Week_Rooms#Star|Star]]
|
'''9:30-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] 
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
 ---------------------------------------- 
'''10am-12pm: Breakout Session:''' [[2014 Project Week Breakout Session: IGT|Image-Guided Therapy - Neurosurgery]] (Alexandra Golby, Tina Kapur) 
[[MIT_Project_Week_Rooms#Star|Star]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] 
'''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: Ron Kikinis: Welcome'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
 ---------------------------------------- 
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
 ---------------------------------------- 
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) 
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' Breakout Session:''' [[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' Breakout Session:''' [[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)
TBD [[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' Breakout Session:''' [[2014 Project Week Breakout Session: IGT|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Tina Kapur)
 ---------------------------------------- 
'''3-5:30pm: Breakout Session:''' TBD
[[MIT_Project_Week_Rooms#Star|Star]]
|
|-
|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)

==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)
* MR-Ultrasound Registration for Prostate Interventions (Chenxi Zhang, Andriy Fedorov, Andras)
* 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, ?)

==TMJ-OA==

==Chronic Obstructive Pulmonary Disease ==

==[http://qiicr.org QIICR]==
* Real world value mapping support (Andrey, Andras, Steve, Jim, ...)
* Segmentation object support (Andrey, Csaba, Steve, ...)

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
*Chronicle (Steve Pieper)
*Volume Registration (Steve Pieper)
*OpenCL (Steve Pieper, Marcel Prastawa)
*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, Matt, 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)

== '''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 before May 27th. See [[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
#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
#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
#Jim Miller, GE Research, millerjv@ge.com
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
#Adam Rankin, Queen's University, rankin@queensu.ca
#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
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

Tannenba:

AHM 2013 alg core presentations

2013-01-05T21:23:48Z

2012-11-19T01:28:23Z

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

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

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

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

==NA-MIC EAB==

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

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

== "Friends and Family" ==

=== NIH ===

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

=== mBIRN ===

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

=== fBIRN ===

* [[User:Kikinis|Ron Kikinis]]

=== IGT ===

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

=== Other ===