Difference between revisions of "2016 Winter Project Week"

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__NOTOC__
 
__NOTOC__
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Back to [[Events]]
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[[image:PW-MIT2016.png|300px]]
 
[[image:PW-MIT2016.png|300px]]
  
'''Dates:''' January 4-8, 2016
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[[image:2016_Winter_Project_Week_Final_Day.JPG|1200px]]
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 +
=Welcome to the web page for the 22nd Project Week!=
 +
==Summary==
 +
The 22nd PROJECT EVENT was held on January 4-8, 2016 at MIT. It recorded 77 registered attendees, who worked on 47 projects. These attendees represented 17 academic sites (MIT, Brigham and Women’s Hospital, , École de Technologie Supérieure, (Canada), Massachusetts General Hospital, Queen’s University (Canada), Robarts Research Institute (Canada), University of Michigan, Montreal Neurosurgical Institute, Dana-Farber Cancer Institute, Boston, DKFZ - Heidelberg Cancer Research Center, JHU, University of Iowa, UNC Chapel Hill, WPI, Children's National Medical Center Washington DC, Harvard IAIC, University of Colorado at Colorado Springs (UCCS), and 8 companies (Kitware, Isomics Inc, GE, Philips Research, MEVIS, HealthMyne, KnowledgeVis, SINTEF).
  
'''Location:''' MIT, Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)
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A [[Project_Events#Past_Project_Weeks|summary]] of all past Project Events.
  
'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here].
+
==Logistics==
<br>
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*'''Dates:''' January 4-8, 2016
 +
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)
 +
*'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here].
  
 
== Introduction ==
 
== Introduction ==
 
Founded  in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built  using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.  
 
Founded  in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built  using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.  
  
[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.  
+
[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 60-120 researchers. As of August 2014, it is a [http://www.miccai.org/organization MICCAI] endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.  
  
 
Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.
 
Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.
  
 
Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO].  
 
Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO].  
 
A summary of all previous Project Events is available [[Project_Events#Past|here]].
 
  
 
This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.
 
This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.
  
Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
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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].
  
 
==Agenda==
 
==Agenda==
 
Tentative Agenda
 
  
 
{|border="1"
 
{|border="1"
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|
 
|
 
|bgcolor="#dbdbdb"|'''Project Presentations'''  
 
|bgcolor="#dbdbdb"|'''Project Presentations'''  
|bgcolor="#6494ec"|
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|bgcolor="#6494ec"| '''Work on Projects'''
|
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|bgcolor="#6494ec"| '''Work on Projects'''
 
|bgcolor="#88aaae"|'''IGT Day'''
 
|bgcolor="#88aaae"|'''IGT Day'''
 
|bgcolor="#faedb6"|'''Reporting Day'''
 
|bgcolor="#faedb6"|'''Reporting Day'''
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|bgcolor="#ffffaa"|Breakfast  
 
|bgcolor="#ffffaa"|Breakfast  
 
|-
 
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
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|bgcolor="#ffffdd"|'''9:00am-12:00pm'''
|'''10:30am-12pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 1 by Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
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|'''10:30am-12pm:''' [Tutorial] Diffeomorphic registration and geodesic shooting methods (I). (Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10-11:30am:''' <font color="#503020">Breakout Session: New Slicer Extensions'''</font><br>
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|'''10:00-11:30am:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/NewSlicerExtensions | Slicer Extensions Birds of a Feather]]
 
|
 
|
'''10-11:30am:''' <font color="#503020">Breakout Session: [[2015_Winter_Project_Week:SlicerROSIntegration| Slicer for Medical Robotics Research]] </font>
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'''10:00-11:30am:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/SlicerForMedicalRoboticsResearch| Slicer for Medical Robotics Research]]
 
<br>
 
<br>
|'''9:00-10:30am''' TBD <br>
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|'''8:30-9:30am''' MR, US, Mass Spect guided Breast Surgery (Melissa Mallory, Nathalie Agar, Gabrielle Gauvin, Andras Lasso) <br>
<br>----------------------------------------<br>
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'''9:30-10:30am''' Clinical perspective on Image Guided Neurosurgery (Alexandra Golby) <br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD <br>
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'''10:30-11:30am''' Clinical perspective on Multiparametric MRI (Fiona Fennessy)<br>
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]<br>
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'''11:30am-12pm''' Drug Delivery to Brain (Jason White)  <br>
 +
|'''10:00am-12:00pm:''' [[#Projects|Project Progress Updates]]<br>  
 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>
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<br>-----------------<br>
'''12pm''' [[Events:TutorialContestJanuary2016|Tutorial Contest Winner Announcement]]<br>
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'''12pm:''' [[Winter2016TutorialContest|Tutorial Contest Winner Announcement]]<br>  
 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 
|-
 
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
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|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
 
|bgcolor="#ffffaa"|Lunch  
 
|bgcolor="#ffffaa"|Lunch  
 
|bgcolor="#ffffaa"|Lunch
 
|bgcolor="#ffffaa"|Lunch
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|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
 
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
 
|-
 
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
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|bgcolor="#ffffdd"|'''1:00-5:30pm'''
|'''1-1:05pm: <font color="#503020">Welcome</font>'''<br>
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|'''1:00pm-1:05pm: <font color="#503020">Welcome</font>'''<br>  
 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>
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<br>-----------------<br>
 
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br>
 
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br>
 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>
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<br>-----------------<br>
'''2:45-4pm:''' [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Breakout Session Ultrasound]]
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'''2:45-4:00pm:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Ultrasound]]<br>
 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>
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<br>-----------------<br>
  
'''4:00pm-5:30pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 2 by Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
+
'''4:00-5:30pm:''' [Tutorial] Diffeomorphic registration geodesic shooting methods (II). (Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''1-3pm:''' <font color="#503020"> [[2016_Winter_Project_Week/Breakout_Session/What's_Planned_for_Slicer_Core|What's Planned for Slicer Core]]<br>
 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2016_Winter_Project_Week/Breakout_Sessions/Diffusion MRI| Diffusion MRI]]
 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 
|
 
 
|
 
|
 +
|'''1:00-2:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/DiffusionMRI| Diffusion MRI]]<br>
 +
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br>
 +
'''3:00-4:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/QIICRTools| QIICR Tools]]
 +
|'''1:00-3:00pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Session/What's_Planned_for_Slicer_Core|What's Planned for Slicer Core]]<br>
 +
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br>
 +
'''3:30-5:00pm:''' Breakout Session: [[Events:TutorialContestJanuary2016 |2016 Tutorial Contest Review (Kiva)]]
 +
| [[AMIGO Tours#Project Week 22|AMIGO Tour]]
 
|-
 
|-
 
|bgcolor="#ffffdd"|'''5:30pm'''
 
|bgcolor="#ffffdd"|'''5:30pm'''
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|bgcolor="#f0e68b"|Adjourn for the day
 
|bgcolor="#f0e68b"|Adjourn for the day
 
|bgcolor="#f0e68b"|Adjourn for the day
 
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
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|bgcolor="#f0e68b"|Adjourn for the day <br> (Optional) [[2016_Winter_Project_Week/Dinner|Dinner on Thursday Night]]
 
|
 
|
 
|}
 
|}
<googlecalendar>kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com</googlecalendar>
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 +
==Calendar==
 +
{{#widget:Google Calendar
 +
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
 +
|timezone=America/New_York&dates=20160103%2F20160110
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|title=NAMIC Winter Project Week
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|view=WEEK
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|dates=20160103/20160110
 +
}}
 +
 
 +
iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics
  
 
='''Projects'''=
 
='''Projects'''=
* [[2016_Project_Week_Template | Updated Template for project pages]]
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*Use this [[2016_Project_Week_Template | Updated Template for project pages]]
  
 +
== IGT ==
 +
* [[2016_Winter_Project_Week/Projects/SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard, Jayender Jagadeesan)
 +
* [[2016_Winter_Project_Week/Projects/External_beam_planning | External Beam Radiotherapy Planning]] (Greg Sharp, others)
 +
* [[2016_Winter_Project_Week/Projects/CryoPlanningSlicerModule | CryoPlanning Module in Slicer]] (Jayender Jagadeesan, Steve Pieper, Sandy Wells)
 +
* [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin, Thomas Kirchner, Janek Groehl)
 +
*[[2016_Winter_Project_Week/Projects/IntegrationCustusX|Integration of CustusX with PLUS on BK System]] (Christian A, Andras Lasso, Adam Rankin)
 +
*[[2016_Winter_Project_Week/Projects/MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
 +
*[[2016_Winter_Project_Week/Projects/IntegrationImFusion| Integration of ImFusion MR-US Registration with BWH AMIGO Neurosurgery Setup]] (Sarah Frisken, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso, Christian Askelan)
 +
* [[2016_Winter_Project_Week/Projects/PLUS | Improvement of PLUS communication with Slicer (skip, see US standardization)]] (Adam Rankin)
 +
* [[2016_Winter_Project_Week/Projects/SliceTracker | Prostate motion tracking and navigation in Slicer ]] (Christian Herz, Andrey Fedorov, Andras Lasso)
 +
* [[2016_Winter_Project_Week/Projects/EVD |Measuring Anatomic Factors for Extraventricular Drain Placement]] (Kirby Vosburgh, P. Jason White)
 +
* [[2016_Winter_Project_Week/Projects/GABA_Delivery |Localized GABA delivery via BBB disruption]] (Nick Todd)
 +
* [[2016_Winter_Project_Week/Projects/3DNrrdSequences | Sequences extension support for 3D+t NRRD]] (Adam Rankin)
  
* [[2015_Winter_Project_Week:SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard)
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== Tractography ==
* [[2016_Winter_Project_Week:TrackedUltrasoundStandardization | Tracked ultrasound standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
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* [[2016_Winter_Project_Week/Projects/Tractography_format_interoperability | Tractography Format Interoperability]] (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)
*Integration of CustusX with PLUS on BK System (Christian A, Adam Rankin)
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* [[2016_Winter_Project_Week/Projects/SlicerDMRI_documentation | Slicer Diffusion MR / tractography workflow documentation]] (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)
*Integration of ImFusion MR-US registration with BWH AMIGO neurosurgery setup (Christian A, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso)
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* [[2016_Winter_Project_Week/Projects/TractographyModuleDevelop&Test | Tractography Analysis Module Development and Testing]] (Fan Zhang, Pegah Kahaliardabili, Isaiah Norton, Lauren O'Donnell, others)
*Digital Pathology Nuclear Segmentation (Erich Bremer, Nicole Aucoin, Andrey Fedorov)
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*Chest Imaging Platform: COPD and other pulmonary diseases (Raúl San José, Jorge Onieva)
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==Image Analysis==
*Upgrade the namic (and Slicer?) wiki (JC, Mike Halle)
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* [[2016_Winter_Project_Week/Projects/CongenitalHeart | Interactive patch-based segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)
* [[2016_Winter_Project_Week:BatchImageAnalysis  | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
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* [[2016_Winter_Project_Week/Projects/ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week:ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
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* [[2016_Winter_Project_Week/Projects/PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week:PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
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* [[2016_Winter_Project_Week/Projects/SphericalWaveletShapeAnalysis|Spherical Wavelet Shape Analysis]] (Yi Gao, Erich Bremer, Allen Tannenbaum, Ron Kikinis)
* [[2016_Winter_Project_Week:MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
+
* [[2016_Winter_Project_Week/Projects/DigitalPathologyNuclearSegmentation|Digital Pathology Nuclear Segmentation]] (Erich Bremer, Yi Gao, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week:External_beam_planning | External beam radiotherapy planning]] (Greg Sharp, others)
+
* [[2016_Winter_Project_Week/Projects/SlicerCMFNextSteps | Moving beyond SlicerCMF and Future Projects]] (Beatriz Paniagua, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week:SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
+
*[[2016_Winter_Project_Week/Projects/ChestImagingPlatform|Chest Imaging Platform: COPD and Other Pulmonary Diseases]] (Raúl San José, Jorge Onieva, James Ross)
 +
* [[2016_Winter_Project_Week/Projects/ChestImagingPlatformWorkflows|Nipype Workflows for the Chest Imaging Platform]] (James Ross, Raúl San José)
 +
* [[2016 Winter Project Week/Projects/Cluster-Driven Lung Segmentation | Cluster-Driven Segmentation of Lung Nodules]] (Vivek Narayan, Raúl San José, Daniel Blezek, Steve Pieper, Chintan Parmar)
 +
* [[2016_Winter_Project_Week/Projects/BatchImageAnalysis  | Batch Clinical Image Analysis]] (Sandy Wells, Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Randy Gollub)
 +
* [[2016_Winter_Project_Week/Projects/SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
 +
* [[2016_Winter_Project_Week/Projects/Interactive4DSegmentation | Interactive 4D Segmentation Module]] (Ethan Ulrich, Andrey Fedorov, Andras Lasso)
 +
* [[2016_Winter_Project_Week/Projects/DSCAnalysis | Dynamic Susceptibility Contrast (DSC) MRI Analysis]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)
 +
 
 +
* [[2016_Winter_Project_Week/Projects/ShapeAnalysis | Low-dimensional Principal Geodesic Analysis On the Manifold of Diffeomorphisms]] (Miaomiao Zhang, Polina Golland)
  
 
==Infrastructure==
 
==Infrastructure==
* [[2016_Winter_Project_Week:SlicerProjectName  | Project Name]] (List of people working on this project)
+
*[[2016_Winter_Project_Week/Projects/UpgradeNAMICSlicerWiki|Upgrade the NAMIC + Slicer Web Infrastructure]] (Mike Halle, JC)
* [[2016_Winter_Project_Week:CommonGL  | CommonGL]] (Steve Pieper, Jim Miller)
+
* [[2016_Winter_Project_Week/Projects/CommonDataStructure | Common Data Structure for CMF modules in Slicer]] (Jean-Baptiste Vimort, François Budin, Lucia Cevidanes, Beatriz Paniagua, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week:WebTechnologies | Web Technologies and Slicer]] (Steve Pieper, Hans Meine)
+
* [[2016_Winter_Project_Week/Projects/StatisticalShapeModeling | Statistical Shape Modeling in Slicer: OA Index]] (Laura Pascal, Beatriz Paniagua, François Budin, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week:CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab asynchronously]] (Hans Meine)
+
* [[2016_Winter_Project_Week/Projects/CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
+
* [[2016_Winter_Project_Week/Projects/CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab Asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week:CLI_Dashboard | Kibana dashboard for browsing all available CLI modules]] (Hans Meine, JC?)
+
* [[2016_Winter_Project_Week/Projects/BRAINSFit_in_MeVisLab | Interoperability Tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week:SegmentationEditorWidget | Editor widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
+
* [[2016_Winter_Project_Week/Projects/CLI_Dashboard | Kibana Dashboard for Browsing All Available CLI Modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week:SlicerTerminologyEditor | Terminology Editor]] (Csaba Pinter, Nicole Aucoin)
+
* [[2016_Winter_Project_Week/Projects/SegmentationEditorWidget | Editor Widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper)
* [[2016_Winter_Project_Week:DICOMSegObjIntegration | Integration of DICOM SegObj with Segmentations]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
+
* [[2016_Winter_Project_Week/Projects/SlicerTerminologyEditor | Terminology Editor]] (Nicole Aucoin, Csaba Pinter, Andrey Fedorov)
* [[2016_Winter_Project_Week:CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
+
* [[2016_Winter_Project_Week/Projects/DICOMSegObjIntegration | Integration of DICOM Segmentation Image Storage with Segmentations Module]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:Data Persisting | Mechanism to persist clinical user data from different modules based on SQLite and/or other database engines ]] (Raúl San José, Jorge Onieva)
+
* [[2016_Winter_Project_Week/Projects/CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week:Workflows | Workflow module that enables the navigation and data sharing between different modules in a clinical workflow ]] (Raúl San José, Jorge Onieva)
+
* [[2016_Winter_Project_Week/Projects/Data Persisting | Mechanism to Persist Clinical User Data from Different Modules Based on SQLite and/or other Database Engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week:AIMInteroperability | AIM for interoperability]] (Hans Meine, Andrey Fedorov, ??)
+
* [[2016_Winter_Project_Week/Projects/Workflows | Workflow Module that Enables the Navigation and Data Sharing between Different Modules in a Clinical Workflow ]] (Raúl San José, Jorge Onieva)
 +
* [[2016_Winter_Project_Week/Projects/CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
 +
* [[2016_Winter_Project_Week/Projects/AIMInteroperability | AIM for Interoperability]] (Hans Meine, Andrey Fedorov, ??)
 +
* [[2016_Winter_Project_Week/Projects/SlicerEnhancedMR | Developing support for Enhanced MR in Slicer]] (Michael Onken, Andrey Fedorov)
 +
* [[2016_Winter_Project_Week/Projects/CLIImprovement| Improve CLI robustness and testing]] (Johan Andruejol)
 +
* [[2016_Winter_Project_Week/Projects/ExploringCollaborationVisualization| Exploring a collaboration in visualization]] (SK Semwal)
  
 
= '''Logistics''' =
 
= '''Logistics''' =
Line 144: Line 187:
 
= '''Registrants''' =
 
= '''Registrants''' =
  
Do not add your name to this list - it is maintained by the organizers based on your paid registration.  To register, visit [https://www.regonline.com/namic16 this registration url].
+
Do not add your name to this list - it is maintained by the organizers based on your paid registration.  To register, visit this [https://www.regonline.com/namic16 registration site].
 +
 
 +
# Nathalie Agar :: Brigham and Women's Hospital
 +
# Peter Anderson :: Retired
 +
# Johan Andruejol :: Kitware, Inc.
 +
# Christian Askeland :: SINTEF
 +
# Nicole Aucoin :: Brigham and Women's Hospital
 +
# Daniel Blezek :: Isomics, Inc.
 +
# Erich Bremer :: Stony Brook University
 +
# Katharine Carter :: Brigham and Women's Hospital
 +
# Lucia Cevidanes :: University of Michigan
 +
# Ye Cheng :: Brigham and Women's Hospital
 +
# Xiao Da :: Massachusetts General Hospital
 +
# Adrian Dalca :: Massachusetts Institute of Technology
 +
# Valentin Demeusy :: Brigham and Women's Hospital
 +
# Sean Doyle :: Massachusetts General Hospital
 +
# Simon Drouin :: Montreal Neurological Institute
 +
# Andriy Fedorov :: Brigham and Women's Hospital
 +
# Jean-Christophe Fillion-Robin :: Kitware, Inc.
 +
# Tobias Frank :: Leibniz Universität Hannover
 +
# Sarah Frisken :: Brigham and Women's Hospital
 +
# Yi Gao :: Stony Brook University
 +
# David Gering :: HealthMyne
 +
# Daniel Glazer :: Brigham and Women's Hospital
 +
# Polina Golland :: Massachusetts Institute of Technology
 +
# Randy Gollub :: Massachusetts General Hospital
 +
# Janek Groehl :: German Cancer Research Center
 +
# Michael Halle :: Brigham and Women's Hospital
 +
# Nobuhiko Hata :: Brigham and Women's Hospital
 +
# Christian Herz :: Brigham and Women's Hospital
 +
# Jayender Jagadeesan :: Brigham and Women's Hospital
 +
# Ameet Jain :: Phillips Research
 +
# Pegah Kahali :: Brigham and Women's Hospital
 +
# Jayashree Kalpathy-Cramer :: Massachusetts General Hospital
 +
# Tina Kapur :: Brigham and Women's Hospital
 +
# Ron Kikinis :: Brigham and Women's Hospital
 +
# Thomas Kirchner :: German Cancer Research Center
 +
# Axel Krieger :: Children's National Medical Center
 +
# Andras Lasso :: Queen's University
 +
# Simon Leoard :: Johns Hopkins University
 +
# Curtis Lisle :: KnowledgeVis, LLC
 +
# Melissa Mallory :: Brigham and Women's Hospital
 +
# Katie Mastrogiacomo :: Brigham and Women's Hospital
 +
# Hans Meine :: Fraunhofer MEVIS, Bremen
 +
# James Miller :: General Electric
 +
# Vivek Narayan :: Dana Farber Cancer Institute
 +
# Isaiah Norton :: Brigham and Women's Hospital
 +
# Lauren O'Donnell :: Brigham and Women's Hospital
 +
# Jorge Onieva :: Brigham and Women's Hospital
 +
# Michael Onken :: Open Connections
 +
# Danielle Pace :: Massachusetts Institute of Technology
 +
# Beatriz Paniagua :: University of North Carolina
 +
# Laura Pascal :: University of Michigan
 +
# Nirav Patel :: Worcester Polytechnic Institute
 +
# Steve Pieper :: Isomics, Inc.
 +
# Csaba Pinter :: Queen's University
 +
# Stuart Pomerantz :: Massachusetts General Hospital
 +
# Sonia Pujol :: Brigham and Women's Hospital
 +
# Adam Rankin :: Robarts Research Institute
 +
# Kallirroi Retzepi :: Massachusetts General Hospital
 +
# James Ross :: Brigham and Women's Hospital
 +
# Raul San Jose Estepar :: Brigham and Women's Hospital
 +
# Sudhanshu Semwal :: University of Colorado, Colorado Springs
 +
# Gregory Sharp :: Massachusetts General Hospital
 +
# Utsav Soni :: Brigham and Women's Hospital
 +
# Kyle Sunderland :: Queen's University
 +
# Nick Todd :: Brigham and Women's Hospital
 +
# Matthew Toews :: Ecole de Technologie Superieure
 +
# Junichi Tokuda :: Brigham and Women's Hospital
 +
# Ethan Ulrich :: University of Iowa
 +
# Prashin Unadkat :: Brigham and Women's Hospital
 +
# Jean-Baptiste Vimort :: University of Michigan
 +
# Kirby Vosburgh :: Brigham and Women's Hospital
 +
# Carl-Fredrik Westin :: Brigham and Women's Hospital
 +
# Jason White :: Brigham and Women's Hospital
 +
# Kelli Xu :: Massachusetts Institute of Technology
 +
# Terry Yoo :: National Library of Medicine
 +
# Fan Zhang :: Brigham and Women's Hospital
 +
# Miaomiao Zhang :: Massachusetts Institute of Technology

Latest revision as of 11:50, 30 March 2017

Home < 2016 Winter Project Week

Back to Events

PW-MIT2016.png

2016 Winter Project Week Final Day.JPG

Welcome to the web page for the 22nd Project Week!

Summary

The 22nd PROJECT EVENT was held on January 4-8, 2016 at MIT. It recorded 77 registered attendees, who worked on 47 projects. These attendees represented 17 academic sites (MIT, Brigham and Women’s Hospital, , École de Technologie Supérieure, (Canada), Massachusetts General Hospital, Queen’s University (Canada), Robarts Research Institute (Canada), University of Michigan, Montreal Neurosurgical Institute, Dana-Farber Cancer Institute, Boston, DKFZ - Heidelberg Cancer Research Center, JHU, University of Iowa, UNC Chapel Hill, WPI, Children's National Medical Center Washington DC, Harvard IAIC, University of Colorado at Colorado Springs (UCCS), and 8 companies (Kitware, Isomics Inc, GE, Philips Research, MEVIS, HealthMyne, KnowledgeVis, SINTEF).

A summary of all past Project Events.

Logistics

  • Dates: January 4-8, 2016
  • Location: MIT CSAIL, Cambridge, MA. (Rooms: Kiva, R&D)
  • REGISTRATION: Register here.

Introduction

Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded NCBC program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform 3D Slicer, built using VTK, ITK, CMake, and CDash, and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

Project Week is a semi-annual event which draws 60-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include NAC, NCIGT, QIICR, and OCAIRO.

This project week is an event endorsed by the MICCAI society.

Please make sure that you are on the NA-MIC Project Week mailing list.

Agenda

Time Monday, January 4 Tuesday, January 5 Wednesday, January 6 Thursday, January 7 Friday, January 8
Project Presentations Work on Projects Work on Projects IGT Day Reporting Day
8:30am Breakfast Breakfast Breakfast Breakfast
9:00am-12:00pm 10:30am-12pm: [Tutorial] Diffeomorphic registration and geodesic shooting methods (I). (Sarang Joshi)
Room: 32-D507.
10:00-11:30am: Breakout Session: Slicer Extensions Birds of a Feather

10:00-11:30am: Breakout Session: Slicer for Medical Robotics Research

8:30-9:30am MR, US, Mass Spect guided Breast Surgery (Melissa Mallory, Nathalie Agar, Gabrielle Gauvin, Andras Lasso)

9:30-10:30am Clinical perspective on Image Guided Neurosurgery (Alexandra Golby)
10:30-11:30am Clinical perspective on Multiparametric MRI (Fiona Fennessy)
11:30am-12pm Drug Delivery to Brain (Jason White)

10:00am-12:00pm: Project Progress Updates

Kiva
-----------------
12pm: Tutorial Contest Winner Announcement
Kiva

12:00pm-1:00pm Lunch Lunch Lunch Lunch Lunch boxes; Adjourn by 1:30pm
1:00-5:30pm 1:00pm-1:05pm: Welcome

Kiva
-----------------
1:05-2:30pm: Project Introductions (all Project Leads)
Kiva
-----------------
2:45-4:00pm: Breakout Session: Ultrasound
Kiva
-----------------

4:00-5:30pm: [Tutorial] Diffeomorphic registration geodesic shooting methods (II). (Sarang Joshi)
Room: 32-D507.

1:00-2:30pm: Breakout Session: Diffusion MRI

Kiva
3:00-4:30pm: Breakout Session: QIICR Tools

1:00-3:00pm: Breakout Session:What's Planned for Slicer Core

Kiva
3:30-5:00pm: Breakout Session: 2016 Tutorial Contest Review (Kiva)

AMIGO Tour
5:30pm Adjourn for the day Adjourn for the day Adjourn for the day Adjourn for the day
(Optional) Dinner on Thursday Night

Calendar

iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics

Projects

IGT

Tractography

Image Analysis

Infrastructure

Logistics

  • Dates: January 4-8, 2016
  • Location: MIT, Kiva Conference room; 4th floor of Building 32.
  • REGISTRATION: Register here. 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 here

Registrants

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this registration site.

  1. Nathalie Agar :: Brigham and Women's Hospital
  2. Peter Anderson :: Retired
  3. Johan Andruejol :: Kitware, Inc.
  4. Christian Askeland :: SINTEF
  5. Nicole Aucoin :: Brigham and Women's Hospital
  6. Daniel Blezek :: Isomics, Inc.
  7. Erich Bremer :: Stony Brook University
  8. Katharine Carter :: Brigham and Women's Hospital
  9. Lucia Cevidanes :: University of Michigan
  10. Ye Cheng :: Brigham and Women's Hospital
  11. Xiao Da :: Massachusetts General Hospital
  12. Adrian Dalca :: Massachusetts Institute of Technology
  13. Valentin Demeusy :: Brigham and Women's Hospital
  14. Sean Doyle :: Massachusetts General Hospital
  15. Simon Drouin :: Montreal Neurological Institute
  16. Andriy Fedorov :: Brigham and Women's Hospital
  17. Jean-Christophe Fillion-Robin :: Kitware, Inc.
  18. Tobias Frank :: Leibniz Universität Hannover
  19. Sarah Frisken :: Brigham and Women's Hospital
  20. Yi Gao :: Stony Brook University
  21. David Gering :: HealthMyne
  22. Daniel Glazer :: Brigham and Women's Hospital
  23. Polina Golland :: Massachusetts Institute of Technology
  24. Randy Gollub :: Massachusetts General Hospital
  25. Janek Groehl :: German Cancer Research Center
  26. Michael Halle :: Brigham and Women's Hospital
  27. Nobuhiko Hata :: Brigham and Women's Hospital
  28. Christian Herz :: Brigham and Women's Hospital
  29. Jayender Jagadeesan :: Brigham and Women's Hospital
  30. Ameet Jain :: Phillips Research
  31. Pegah Kahali :: Brigham and Women's Hospital
  32. Jayashree Kalpathy-Cramer :: Massachusetts General Hospital
  33. Tina Kapur :: Brigham and Women's Hospital
  34. Ron Kikinis :: Brigham and Women's Hospital
  35. Thomas Kirchner :: German Cancer Research Center
  36. Axel Krieger :: Children's National Medical Center
  37. Andras Lasso :: Queen's University
  38. Simon Leoard :: Johns Hopkins University
  39. Curtis Lisle :: KnowledgeVis, LLC
  40. Melissa Mallory :: Brigham and Women's Hospital
  41. Katie Mastrogiacomo :: Brigham and Women's Hospital
  42. Hans Meine :: Fraunhofer MEVIS, Bremen
  43. James Miller :: General Electric
  44. Vivek Narayan :: Dana Farber Cancer Institute
  45. Isaiah Norton :: Brigham and Women's Hospital
  46. Lauren O'Donnell :: Brigham and Women's Hospital
  47. Jorge Onieva :: Brigham and Women's Hospital
  48. Michael Onken :: Open Connections
  49. Danielle Pace :: Massachusetts Institute of Technology
  50. Beatriz Paniagua :: University of North Carolina
  51. Laura Pascal :: University of Michigan
  52. Nirav Patel :: Worcester Polytechnic Institute
  53. Steve Pieper :: Isomics, Inc.
  54. Csaba Pinter :: Queen's University
  55. Stuart Pomerantz :: Massachusetts General Hospital
  56. Sonia Pujol :: Brigham and Women's Hospital
  57. Adam Rankin :: Robarts Research Institute
  58. Kallirroi Retzepi :: Massachusetts General Hospital
  59. James Ross :: Brigham and Women's Hospital
  60. Raul San Jose Estepar :: Brigham and Women's Hospital
  61. Sudhanshu Semwal :: University of Colorado, Colorado Springs
  62. Gregory Sharp :: Massachusetts General Hospital
  63. Utsav Soni  :: Brigham and Women's Hospital
  64. Kyle Sunderland :: Queen's University
  65. Nick Todd :: Brigham and Women's Hospital
  66. Matthew Toews :: Ecole de Technologie Superieure
  67. Junichi Tokuda :: Brigham and Women's Hospital
  68. Ethan Ulrich :: University of Iowa
  69. Prashin Unadkat :: Brigham and Women's Hospital
  70. Jean-Baptiste Vimort :: University of Michigan
  71. Kirby Vosburgh  :: Brigham and Women's Hospital
  72. Carl-Fredrik Westin :: Brigham and Women's Hospital
  73. Jason White :: Brigham and Women's Hospital
  74. Kelli Xu :: Massachusetts Institute of Technology
  75. Terry Yoo :: National Library of Medicine
  76. Fan Zhang :: Brigham and Women's Hospital
  77. Miaomiao Zhang :: Massachusetts Institute of Technology