NAMIC Wiki - User contributions [en]

2017 Winter Project Week/DWI Similarity Metrics

2017-01-13T04:36:24Z

Lchauvin:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* Laurent Chauvin, ETS Montreal
* Fan Zhang, BWH
* Lauren O'Donnell, BWH
* Matthew Toews, ETS Montreal

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Investigate possible metrics for identification of information-rich patches in DWI data
|

* Discuss about DWI data structure and acquisition protocol to have a better understanding of the information available in DWI datasets (e.g. single shell / multi shell, gradient orientations, b-values)
* Identify possible metrics available to measure similarity (e.g. Mutual Information, Correlation) between datasets
* Investigate the potential of CNN for this type of application

|

* Discussed with Lauren and clarified some points on Diffusion Imaging. It also might help me to optimize some of my code.
* Discussed with Mohsen about machine learning and how I might use it for data classification in my project.
* Discussed with Henrik about information-rich patches of information in DWI data, and I learned about his LORDWI approach that could be useful to help me identify relevant information in DWI datasets.
* Attended almost all machine learning events, and got a better understanding of their utility and when it might be useful to use them and when it is not necessary.
* Participated in the tutorial contest.
|}

==Background and References==

2017 Winter Project Week/DWI Similarity Metrics

2017-01-13T04:34:31Z

Lchauvin:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* Laurent Chauvin, ETS Montreal
* Fan Zhang, BWH
* Lauren O'Donnell, BWH
* Matthew Toews, ETS Montreal

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Investigate possible metrics for identification of information-rich patches in DWI data
|

* Discuss about DWI data structure and acquisition protocol to have a better understanding of the information available in DWI datasets (e.g. single shell / multi shell, gradient orientations, b-values)
* Identify possible metrics available to measure similarity (e.g. Mutual Information, Correlation) between datasets
* Investigate the potential of CNN for this type of application

|

* Discussed with Lauren and clarified some points on Diffusion Imaging. It also might help me to optimize some of my code.
* Discussed with Mohsen about machine learning and how I might use it for data classification in my project.
* Discussed with Henrik about information-rich patches of information in DWI data, and I learned about his LORDWI approach that could be useful to help me identify relevant information in DWI datasets.
* Attended almost all machine learning events, and got a better understanding of their utility and when it might be useful to use them and when it is not necessary.
* Participated at the tutorial contest.
|}

==Background and References==

2017 Winter Project Week/DWI Similarity Metrics

2017-01-13T04:31:46Z

Lchauvin:

__NOTOC__
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* Laurent Chauvin, ETS Montreal
* Fan Zhang, BWH
* Lauren O'Donnell, BWH
* Matthew Toews, ETS Montreal

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Investigate possible metrics for identification of information-rich patches in DWI data
|

* Discuss about DWI data structure and acquisition protocol to have a better understanding of the information available in DWI datasets (e.g. single shell / multi shell, gradient orientations, b-values)
* Identify possible metrics available to measure similarity (e.g. Mutual Information, Correlation) between datasets
* Investigate the potential of CNN for this type of application

|

* Discussed with Lauren and clarified some points on Diffusion Imaging. It also might help me to optimize some of my code.
* Discussed with Mohsen about machine learning and how I might use it for data classification in my project.
* Attended almost all machine learning events, and got a better understanding of their utility and when it might be useful to use them and when it is not necessary.
* Participated at the tutorial contest.
|}

==Background and References==

2017 Tutorial Contest

2017-01-12T17:26:03Z

Lchauvin: /* Tutorials */

[[2017_Winter_Project_Week#Agenda|Back to Winter project week Agenda]]
==Introduction==
[http://www.slicer.org Slicer4.6] is used to perform meaningful research tasks. As part of the 3D Slicer Training activities we are building a curated portfolio of tutorials for the basic functions and specialized functionality available in Slicer.

The primary purpose of the Winter 2017 tutorial contest is to enrich the training materials that are available to end-users and developers using 3D Slicer. The contest provides members of the medical image computing and radiology research community a methodology and a framework for developing step-by-step tutorials on advanced image analysis methods. We believe participants will be motivated to join this event to enhance the dissemination of their own algorithms that they have incorporated into the Slicer4 platform, and to enhance training of Slicer4 functionality for their own laboratory groups.

==Organizer==
Sonia Pujol, Ph.D., Director of Training, Neuroimage Analysis Center, Brigham and Women's Hospital, Harvard Medical School

==Categories==
*Category 1 (*new*): '''DEMONSTRATION'''. This category allows new comers to the Slicer community to provide short demos based on slides and/or videos of their application.
*Category 2: '''ALGORITHM TUTORIAL'''. In this category the tutorial will teach a user how to make an algorithm work on their data.
*Category 3: '''EXTENSION TUTORIAL'''. In this category, the tutorial will teach a user how to use an Extension of Slicer.
*Category 4: '''END TO END SOLUTION TUTORIAL'''. In this category, the tutorial will teach a user how to solve a particular clinical problem using a workflow implemented in Slicer.
*Category 5: '''TUTORIAL UPGRADE/UPDATE"'. This category allows teams who participated in the past tutorial contest editions to submit an update/upgrade of their previous submission.

Entries in each category require the following material:
* scientific background and application motivation
* step-by-step instructions
* anonymized sample dataset

=Rules=
The evaluation criteria for the 2017 tutorial contest are below:
*Tutorial must be based on the Slicer 4.6 release version of the software.
*To enter the contest, you must provide 'a version of the tutorial that works on all supported platforms (Mac,Windows,Linux)
*Tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]
*Tutorial data must be anonymized
*Tutorial must include contact information of the primary author (e-mail and phone number)
*Tutorial must follow the guidelines specified above and use the [[Media:TutorialContest_Template_2016.ppt‎ | Winter 2017 contest tutorial template]].
*If applicable, the tutorial must provide clear directions for downloading and installing additional modules <br>

=Submission Process=
'''<span style="background-color: pink"> Submission dead-line: Wednesday January 11, 2017'''</span>
* To enter the contest, please follow the 5 steps below:
**1. Create a wiki page for your tutorial on the NA-MIC wiki.
**2. Upload your slides/demos and tutorial dataset. Your tutorial and data must be named as 'TutorialName_TutorialContestWinter2017.pdf' and 'TutorialData_TutorialContestWinter2017.zip'
**3. Add a link to the uploaded tutorial and datasets on your tutorial page.
**4. Copy the template of the [http://wiki.na-mic.org/Wiki/index.php/Training:Winter_2017_Contest_Table Winter 2017 test table ] on your tutorial page, and document the status of your cross-platform testing (Mac, Windows, Linux).
**5. Once you have completed step 1-4, add a link to your tutorial page in the list below and send a notification email to Sonia Pujol (spujol at bwh.harvard.edu) to receive a confirmation of your submission.

=Tutorials=
*[[Media:SimpleDiffusionGradientInformationExtractorTutorial_Chauvin_Jan2017.pptx| Simple Python Tool for Quality Control of DWI data (Laurent Chauvin)]]
*[https://www.nitrc.org/docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf SPHARM-PDM (Beatriz Paniagua)]
*[http://www.na-mic.org/Wiki/images/a/a6/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf Segmentation for 3D printing] (Csaba Pinter)
*[[Media:ROSIGTLTutorial_Tokuda_Jan2017.pptx| Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink (Junichi Tokuda)]]
*Slicer Pathology (Erich Bremer)
*[[Media:Fiber_Bundle_Volume_Measurement.pptx|Fiber Bundle Volume Measurement]], [[Media:FiberVolume_data.zip| tutorial data]] (Shun Gong)

= Review Session=
The review session of the 2017 Tutorial Contest will take place on Thursday January 12 at the Massachusetts Institute of Technology, Cambrigde, MA as part of the Winter 2017 Slicer Project Week.
All contestants will be invited to present brief highlights of their tutorials. Each presentation should be 5-minute summary of the submission.
*Judges:
**Rebekka Lauer, Humboldt-University, Berlin
**Parvin Mousavi, Brigham and Women's Hospital
**Peter Anderson

=Results=
The winner of the 2017 tutorial contest will be announced on Friday January 13 during the closing session of the Slicer Project Week.

File:SimpleDiffusionGradientInformationExtractorTutorial Chauvin Jan2017.pptx

2017-01-12T17:25:37Z

Lchauvin:

2017 Winter Project Week/DWI Similarity Metrics

2017-01-04T04:26:47Z

Lchauvin:

2017 Winter Project Week

2017-01-04T04:25:47Z

Lchauvin: /* dMRI */

__NOTOC__
[[image:PW-Winter2017.png|300px]]

=Welcome to the web page for the 24th Project Week!=

The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

==Logistics==

*'''Dates:''' January 9-13, 2017.
*'''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/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]

== Introduction ==
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and 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], enhancements to the underlying building blocks [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 open source hackathon event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon 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.

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_Project_Weeks|here]].

Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list]

==Conference Calls for Preparation==

Conference call phone number and notes are available [[TCONS:2017_Winter_Project_Week|here]].

==Calendar==

'''''<font color="maroon">The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.</font>'''''<br>

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20170108/20170114
}}

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

='''Projects'''=

*Use this [[2017_Project_Week_Template | Updated Template for project pages]]

== Learning and GPUs ==

* [[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Ziyang Wang, Guillaume Pernelle, Tina Kapur)
* [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)

== Web Technologies ==
* [[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
* [[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper)
* [[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)
* [[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
* [[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)

== Visualization ==
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)

== IGT: Navigation, Robotics, Surgical Planning ==
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
* [[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)
* [[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]] (Peter Traneus Anderson)
* [[2017 Winter Project Week/OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab | OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab ]] (Scheherazade Kraß (Shery), Junichi Tokuda, Longquan Chen, )
* [[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
* [[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov)
* [[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)

==dMRI==
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (Fan Zhang, Shun Gong, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)
* [[2017 Winter Project Week/LORDWI | Density-based DMRI registration ]] (Henrik Groenholt Jensen, Lauren J. O'Donnell, Tina Kapur, Fan Zhang, Carl-Frederik Westin)
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)
* [[2017 Winter Project Week/DiPy_in_Slicer | DiPy integration in Slicer]] (Isaiah Norton, Lauren J. O'Donnell)
* [[2017 Winter Project Week/DWI_Similarity_Metrics | Identification of information-rich patches in Diffusion-Weighted Images]] (Laurent Chauvin, Fan Zhang, Lauren J. O'Donnell, Matthew Toews)

== Infrastructure ==

* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy refactoring]] (Csaba Pinter)
* [[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)
* [[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)

==To be Categorized==

* [[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
* [[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
* [[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)
* [[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
* [[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)
* [[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)
* [[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)

= '''Registrants''' =

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/2017projectweek registration site].

# A, Zeina :: SHBOUL
# Aerts, Hugo :: DFCI-Harvard
# Alam, Mahbubul :: Old Dominion University
# Anderson, Peter :: Retired
# Andruejol, Johan :: Kitware, Inc.
# Bakeng, Janne Beate :: SINTEF
# Beers, Andrew :: Massachusetts General Hospital
# Bernal Rusiel, Jorge Luis :: Boston Children's Hospital
# Bremer, Erich :: Stony Brook University
# Burke, Brice :: American University of Antigua College of Medicine
# Cetin Karayumak, Suheyla :: Brigham and Women's Hospital
# Chae, Michael :: Monash University
# Chauvin, Laurent :: ETS
# Dalca, Adrian :: Massachusetts Institute of Technology
# Fedorov, Andriy :: Brigham and Women's Hospital
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.
# Fishbaugh, James :: New York University
# Frank, Tobias :: Leibniz Universität Hannover
# García Mato, David :: Queen´s University / Universidad Carlos III de Madrid
# Girault, Alexis :: Kitware, Inc.
# Golland, Polina :: Massachusetts Institute of Technology
# Gollub, Randy :: Massachusetts General Hospital
# Gong, Shun :: Brigham and Women's Hospital
# Guerrier de Dumast, Priscille :: University of Michigan
# Harris, Gordon :: Massachusetts General Hospital
# Herz, Christian :: Brigham and Women's Hospital
# Hong, Sungmin :: New York University
# Hosny, Ahmed :: Dana-Farber
# Jagadeesan, Jayender :: Brigham and Women's Hospital
# Jensen, Henrik G. :: University of Copenhagen
# Kapur, Tina :: Brigham and Women's Hospital
# Kikinis, Ron :: Brigham and Women's Hospital
# Lasso, Andras :: PerkLab, Queen's University
# Lauer, Rebekka :: Humboldt University Berlin
# Lisle, Curtis :: KnowledgeVis, LLC
# Mastrogiacomo, Katie :: Brigham and Women's Hospital
# Mateus, D. :: TUM
# Mehrtash, Alireza :: Brigham and Women's Hospital
# Meine, Hans :: University of Bremen
# Meyer, Anneke :: University of Magdeburg
# Miller, James :: GE Research
# Mirabel, Clement :: University of Michigan
# Nitsch, Jennifer :: University of Bremen
# Norton, Isaiah :: Brigham and Women's Hospital
# O'Donnell, Lauren :: Brigham and Women's Hospital
# Oram, Louise :: The Intervention Centre-Oslo University Hospital
# Paniagua, Beatriz :: Kitware, Inc.
# Parmar, Chintan :: DFCI-Harvard Medical School
# Peled, Sharon :: Brigham and Women's Hospital
# Pieper, Steve :: Isomics, Inc.
# Pinter, Csaba :: Queen's University
# Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School
# Pujol, Sonia :: Brigham and Women's Hospital/Harvard Medical School
# Rankin, Adam :: Robarts Research Institute
# Rheault, Francois :: Université de Sherbrooke
# Roethe, Anna :: Humboldt University / Charité University Hospital Berlin
# Sharp, Gregory :: Massachusetts General Hospital
# Sridharan, Patmaa :: University of Pennsylvania-CBICA
# Vidyaratne, Lasitha :: Old Dominion University
# Wang, Yaofei :: Brigham and Women's Hospital
# Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School
# Yang, Yixin :: Brigham and Women's Hospital
# Ye, Wu :: Brigham and Women's Hospital
# Zaffino, Paolo :: Magna Graecia University of Catanzaro, Italy
# Zeleznik, Roman :: DFCI
# Zhang, Fan :: Brigham and Women's Hospital
# Zhang, Miaomiao :: Massachusetts Institute of Technology
# Zhang, Yuqian :: Brigham and Women's Hospital
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital

2017 Winter Project Week/DWI Similarity Metrics

2017-01-03T22:56:22Z

Lchauvin:

2017 Winter Project Week/DWI Similarity Metrics

2017-01-03T22:55:28Z

Lchauvin: Created page with "__NOTOC__ <gallery> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|Projects List <!-- Use the "Upload file" link on the l..."

2017 Winter Project Week

2017-01-03T22:53:34Z

Lchauvin: /* dMRI */

__NOTOC__
[[image:PW-Winter2017.png|300px]]

=Welcome to the web page for the 24th Project Week!=

The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

==Logistics==

*'''Dates:''' January 9-13, 2017.
*'''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/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]

== Introduction ==
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and 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], enhancements to the underlying building blocks [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 open source hackathon event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon 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.

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_Project_Weeks|here]].

Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list]

==Conference Calls for Preparation==

Conference call phone number and notes are available [[TCONS:2017_Winter_Project_Week|here]].

==Calendar==

'''''<font color="maroon">The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.</font>'''''<br>

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20170108/20170114
}}

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

='''Projects'''=

*Use this [[2017_Project_Week_Template | Updated Template for project pages]]

== Learning and GPUs ==

* [[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Ziyang Wang, Guillaume Pernelle, Tina Kapur)
* [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)

== Web Technologies ==
* [[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
* [[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper)
* [[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)
* [[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
* [[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)

== Visualization ==
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)

== IGT: Navigation, Robotics, Surgical Planning ==
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
* [[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)
* [[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]] (Peter Traneus Anderson)
* [[2017 Winter Project Week/OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab | OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab ]] (Scheherazade Kraß (Shery), Junichi Tokuda, Longquan Chen, )
* [[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
* [[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov)
* [[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)

==dMRI==
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (Fan Zhang, Shun Gong, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)
* [[2017 Winter Project Week/LORDWI | Density-based DMRI registration ]] (Henrik Groenholt Jensen, Lauren J. O'Donnell, Tina Kapur, Fan Zhang, Carl-Frederik Westin)
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)
* [[2017 Winter Project Week/DiPy_in_Slicer | DiPy integration in Slicer]] (Isaiah Norton, Lauren J. O'Donnell)
* [[2017 Winter Project Week/DWI_Similarity_Metrics | Identification of information-rich patches in Diffusion-Weighted Images]] (Laurent Chauvin, Matthew Toews)

== Infrastructure ==

* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy refactoring]] (Csaba Pinter)
* [[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)
* [[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)

==To be Categorized==

* [[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
* [[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
* [[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)
* [[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
* [[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)
* [[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)
* [[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)

= '''Registrants''' =

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/2017projectweek registration site].

# A, Zeina :: SHBOUL
# Aerts, Hugo :: DFCI-Harvard
# Alam, Mahbubul :: Old Dominion University
# Anderson, Peter :: Retired
# Andruejol, Johan :: Kitware, Inc.
# Bakeng, Janne Beate :: SINTEF
# Beers, Andrew :: Massachusetts General Hospital
# Bernal Rusiel, Jorge Luis :: Boston Children's Hospital
# Bremer, Erich :: Stony Brook University
# Burke, Brice :: American University of Antigua College of Medicine
# Cetin Karayumak, Suheyla :: Brigham and Women's Hospital
# Chae, Michael :: Monash University
# Chauvin, Laurent :: ETS
# Dalca, Adrian :: Massachusetts Institute of Technology
# Fedorov, Andriy :: Brigham and Women's Hospital
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.
# Fishbaugh, James :: New York University
# Frank, Tobias :: Leibniz Universität Hannover
# García Mato, David :: Queen´s University / Universidad Carlos III de Madrid
# Girault, Alexis :: Kitware, Inc.
# Golland, Polina :: Massachusetts Institute of Technology
# Gollub, Randy :: Massachusetts General Hospital
# Gong, Shun :: Brigham and Women's Hospital
# Guerrier de Dumast, Priscille :: University of Michigan
# Harris, Gordon :: Massachusetts General Hospital
# Herz, Christian :: Brigham and Women's Hospital
# Hong, Sungmin :: New York University
# Hosny, Ahmed :: Dana-Farber
# Jagadeesan, Jayender :: Brigham and Women's Hospital
# Jensen, Henrik G. :: University of Copenhagen
# Kapur, Tina :: Brigham and Women's Hospital
# Kikinis, Ron :: Brigham and Women's Hospital
# Lasso, Andras :: PerkLab, Queen's University
# Lauer, Rebekka :: Humboldt University Berlin
# Lisle, Curtis :: KnowledgeVis, LLC
# Mastrogiacomo, Katie :: Brigham and Women's Hospital
# Mateus, D. :: TUM
# Mehrtash, Alireza :: Brigham and Women's Hospital
# Meine, Hans :: University of Bremen
# Meyer, Anneke :: University of Magdeburg
# Miller, James :: GE Research
# Mirabel, Clement :: University of Michigan
# Nitsch, Jennifer :: University of Bremen
# Norton, Isaiah :: Brigham and Women's Hospital
# O'Donnell, Lauren :: Brigham and Women's Hospital
# Oram, Louise :: The Intervention Centre-Oslo University Hospital
# Paniagua, Beatriz :: Kitware, Inc.
# Parmar, Chintan :: DFCI-Harvard Medical School
# Peled, Sharon :: Brigham and Women's Hospital
# Pieper, Steve :: Isomics, Inc.
# Pinter, Csaba :: Queen's University
# Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School
# Pujol, Sonia :: Brigham and Women's Hospital/Harvard Medical School
# Rankin, Adam :: Robarts Research Institute
# Rheault, Francois :: Université de Sherbrooke
# Roethe, Anna :: Humboldt University / Charité University Hospital Berlin
# Sharp, Gregory :: Massachusetts General Hospital
# Sridharan, Patmaa :: University of Pennsylvania-CBICA
# Vidyaratne, Lasitha :: Old Dominion University
# Wang, Yaofei :: Brigham and Women's Hospital
# Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School
# Yang, Yixin :: Brigham and Women's Hospital
# Ye, Wu :: Brigham and Women's Hospital
# Zaffino, Paolo :: Magna Graecia University of Catanzaro, Italy
# Zeleznik, Roman :: DFCI
# Zhang, Fan :: Brigham and Women's Hospital
# Zhang, Miaomiao :: Massachusetts Institute of Technology
# Zhang, Yuqian :: Brigham and Women's Hospital
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital

2015 Summer Project Week

2015-04-02T00:15:37Z

Lchauvin:

__NOTOC__

[[image:PW-Summer2015.png|300px]]
<br>

==Logistics==

Location: NH COLLECTION CONSTANZA Hotel, Barcelona

Dates:

*Start: Sunday, June 21st (early evening start with project presentations)
**3 days of work: Monday June 22, Tuesday June 23, Wednesday June 24
*Adjourn: Wednesday June 24th at 5pm

Registration Fee: zero. We will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.

== '''Background''' ==

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.

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]. The next event in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Summer_Project_Week Barcelona, Spain] in June 2015.

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.

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

=Projects=
* [[2015_Summer_Project_Week_Template | Template for project pages]]

==Image-Guided Therapy==
*[[2015 Orthognatic Surgery|Orthognatic Surgery]]

==Huntington's Disease==
==TBI==

==Stroke==

==Cardiac==

==Chronic Obstructive Pulmonary Disease, Lung, Chest ==

==[http://qiicr.org QIICR]==

==Feature Extraction==
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells)

==Additional Brain Image Analysis==
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]

==Slicer4 Extensions==

==TMJOA RO1 - Collaboration with NAMIC==

==Infrastructure==
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC)
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, ??)
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin, Jim Miller)

== '''Logistics''' ==

*'''Dates:''' June 21-24, 2015.
*'''Location:''' Barcelona, Spain
*'''REGISTRATION:''' 0
*'''Registration Fee:''' TBD
*'''Hotel:''' TBD
*'''Room sharing''': If interested, add your name to the list: [[2015_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Please add your name to the list. This is the registration mechanism for this project week.

#Tina Kapur, BWH
#Ron Kikinis, BWH & Fraunhofer
#Steve Pieper, Isomics
#Tamas Ungi (Queen's University, Canada)
#Andras Lasso, Queen's University, Canada
#Paolo Zaffino (ImagEngLab, Magna Graecia University, Italy)
#Salvatore Scaramuzzino (ImagEngLab, Magna Graecia University, Italy)
#Giampaolo Pileggi (ImagEngLab, Magna Graecia University, Italy)
#Hans Meine (Fraunhofer MEVIS, Bremen, Germany)
#Nicole Aucoin (BWH)
#Sonia Pujol (BWH)
#Dženan Zukić (Kitware, Carrboro, NC, USA)
#Jayender Jagadeesan (BWH)
#Guido Gerig
#Sandy Wells, BWH
#Matthew Toews (École de Technologie Supérieure, Montreal, Canada)
#Frank Preiswerk, BWH
#Junichi Tokuda, BWH
#Jonathan Scalera, BWH
#Raul San Jose, BWH
#Jorge Onieva, BWH
#James Ross, BWH
#Yulong Zhao, Université de Rennes
#Laurent Chauvin, BWH

2015 Summer Project Week

2015-03-30T18:39:14Z

Lchauvin: /* Registrants */

__NOTOC__

[[image:PW-Summer2015.png|300px]]
<br>

==Logistics==

Location: NH COLLECTION CONSTANZA Hotel, Barcelona

Dates:

*Start: Sunday, June 21st (early evening start with project presentations)
**3 days of work: Monday June 22, Tuesday June 23, Wednesday June 24
*Adjourn: Wednesday June 24th at 5pm

Registration Fee: zero. We will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.

== '''Background''' ==

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.

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]. The next event in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Summer_Project_Week Barcelona, Spain] in June 2015.

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.

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

=Projects=
* [[2015_Summer_Project_Week_Template | Template for project pages]]

==Image-Guided Therapy==
*[[2015 Orthognatic Surgery|Orthognatic Surgery]]

==Huntington's Disease==
==TBI==

==Stroke==

==Cardiac==

==Chronic Obstructive Pulmonary Disease, Lung, Chest ==

==[http://qiicr.org QIICR]==

==Feature Extraction==
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells)

==Additional Brain Image Analysis==
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]

==Slicer4 Extensions==

==TMJOA RO1 - Collaboration with NAMIC==

==Infrastructure==
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC)
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, ??)
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin, Jim Miller)

== '''Logistics''' ==

*'''Dates:''' June 21-24, 2015.
*'''Location:''' Barcelona, Spain
*'''REGISTRATION:''' 0
*'''Registration Fee:''' TBD
*'''Hotel:''' TBD
*'''Room sharing''': If interested, add your name to the list: [[2015_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Please add your name to the list. This is the registration mechanism for this project week.

#Tina Kapur
#Ron Kikinis
#Steve Pieper
#Tamas Ungi (Queen's University, Canada)
#Paolo Zaffino (ImagEngLab, Magna Graecia University, Italy)
#Salvatore Scaramuzzino (ImagEngLab, Magna Graecia University, Italy)
#Giampaolo Pileggi (ImagEngLab, Magna Graecia University, Italy)
#Hans Meine (Fraunhofer MEVIS, Bremen, Germany)
#Nicole Aucoin (BWH)
#Sonia Pujol (BWH)
#Dženan Zukić (Kitware, Carrboro, NC, USA)
#Jayender Jagadeesan (BWH)
#Guido Gerig
#Matthew Toews (École de Technologie Supérieure, Montreal, Canada)
#Frank Preiswerk

2014 Summer Project Week:PathExplorer Extension

2014-06-26T22:08:17Z

Lchauvin: /* Project Description */

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

==Key Investigators==
* BWH: Laurent Chauvin, Nobuhiko Hata
* Queen's University: Tamas Ungi

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Refactor code to be able to use PathExplorer from other modules
* Maybe update UI to be more user friendly
* Update documentation
* Create tutorial
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Will meet with Tamas to discuss how to refactor source code, and user interface
* Update documentation accordingly
* Create tutorial
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Refactoring the code into the logic was more complicated than expected. It requires to modify the whole module implementation.
* During this process, I decided to re-design the interface to be more user friendly. In the same time, after attending some discussions and breakout sessions, I thought it would be useful to include curved trajectories into PathExplorer (currently only linear trajectories).
* We brainstormed with Tamas about the new design and features. Tamas suggested to reuse Fiducial Registration Wizard module (from SlicerIGT) to place fiducials, and CurveMaker (after some modifications) to generate the trajectory, then we would use VolumeResliceDriver (with some modifications) to reslice along the path.
* Implementation of new UI has started
</div>
</div>

2014 Summer Project Week:PathExplorer Extension

2014-06-26T22:07:34Z

Lchauvin: /* Project Description */

2014 Summer Project Week:PathExplorer Extension

2014-06-26T22:07:13Z

Lchauvin: /* Project Description */

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

==Key Investigators==
* BWH: Laurent Chauvin, Nobuhiko Hata
* Queen's University: Tamas Ungi

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Refactor code to be able to use PathExplorer from other modules
* Maybe update UI to be more user friendly
* Update documentation
* Create tutorial
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Will meet with Tamas to discuss how to refactor source code, and user interface
* Update documentation accordingly
* Create tutorial
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Refactoring the code into the logic was more complicated than expected. It requires to modify all module implementation.
* During this process, I decided to re-design the interface to be more user friendly. In the same time, after attending some discussions and breakout sessions, I thought it would be useful to include curved trajectories into PathExplorer (currently only linear trajectories).
* We brainstormed with Tamas about the new design and features. Tamas suggested to reuse Fiducial Registration Wizard module (from SlicerIGT) to place fiducials, and CurveMaker (after some modifications) to generate the trajectory, then we would use VolumeResliceDriver (with some modifications) to reslice along the path.
* Implementation of UI has been started
</div>
</div>

2014 Summer Project Week:PathExplorer Extension

2014-06-23T14:26:22Z

Lchauvin:

2014 Summer Project Week:PathExplorer Extension

2014-06-23T14:23:45Z

Lchauvin: 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;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Refactor code to be able to use PathExplorer from other modules
* Maybe update UI to be more user friendly
* Update documentation
* Create tutorial
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Summer Project Week

2014-06-23T14:22:18Z

Lchauvin: /* 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'''
|
|'''10-11:30am''' <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>
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)
<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]]

<br>----------------------------------------<br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
|-
|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)
[[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)
[[MIT_Project_Week_Rooms#Star|Star]]
<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/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

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

==Image-Guided Therapy==

* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata)
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras Lasso)
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer WPI, Nirav Patel WPI, Nobuhiko Hata BWH)
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias)
* [[2014_Summer_Project_Week:Intelligent_Steering | 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:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
*[[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:Image guided neuroendoscope | Making realistic clinical story board for image guided skull base endoscopic surgery]] (Keryn Palmer, Nobuhiko Hata)
*[[2014_Summer_Project_Week:Cortical_Dysplasia_Identification | Tools for Dysplasia Identification in Epilepsy]] (Luiz Murta; Emylin Souza; Tina Kapur; Ron Kikinis)
*[[2014_Summer_Project_Week:PathExplorer_Extension | PathExplorer Extension (code refactoring, documentation, tutorial)]] (Laurent Chauvin, Tamas Ungi, Nobuhiko Hata)

==Huntington's Disease==
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)

==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)
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)
*[[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)

==TBI==
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Stroke==
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)

==Chronic Obstructive Pulmonary Disease, Lung, Chest ==

*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, 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, Raul San Jose)

==[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})
* [[2014_Summer_Project_Week: DICOM SEG conversion to support archival of QIN Grand challenges results|DICOM SEG conversion to support archival of QIN Grand challenges results]] (Jayashree, Andrey, Steve, {David remotely})

==Feature Extraction==
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor 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)

==Brain==
*[[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:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)
*[[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)
*[[2014_Summer_Project_Week:Longitudinal_patient_specific_DTI_analysis | Longitudinal patient-specific DTI analysis using Slicer for neonatal asphyxia]] (Anuja Sharma, SCI, Utah; Francois Budin, UNC; Martin Styner, UNC; Guido Gerig, SCI, Utah)
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)

==Slicer4 Extensions==

*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Kevin Wang, Andras Lasso)
*[[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)
*[[2014_Summer_Project_Week:DRAMMS_Slicer| Integrating DRAMMS deformable registration into Slicer]] (Yangming Ou, Steve Pieper, Andriy Fedorov, Tina Kapur, Christos Davatzikos, Ron Kikinis, Randy Gollub, Jayashree Kalpathy-Cramer)

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)
* [[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)
*[[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)

== '''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
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com
#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
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@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
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu
#Polina Golland, MIT CSAIL, polina@csail.mit.edu
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com
#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
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.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
#Robin Kouver, BWH/SPL, r.kouver@gmail.com
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca
#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
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com
#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
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca
#David Welch, University of Iowa, david-welch@uiowa.edu
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu
#Phillip White, BWH/Harvard Medical School, white@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

ProstateBRP OpenIGTLink Communication June 2013

2014-03-19T20:58:43Z

Lchauvin:

The following table shows message exchange diagram for the communication between 3D Slicer (and other navigation software) and the robot in each workhpase.

==Notations==
*STRING(NN, SS) (see http://openigtlink.org/protocols/v2_string.html)
**NN: Device name in the OpenIGTLink header. (Max. 20 bytes)
**SS: String in the message body. (Max. 65536 bytes)
*STATE(NN, CC:SS:EE:MM) (see http://openigtlink.org/protocols/v2_status.html )
**NN: Device type in the OpenIGTLink header. (Max. 20 bytes)
**CC: Code
**SS: Subcode
**EE: Error name (Max 20 bytes) -- no predefined name. It will logged or show up on navigation screen as it is.
**MM: Message -- no predefined text. It will logged or show up on navigation screen as it is.
*TRANSFORM(NN, TT) (see http://openigtlink.org/protocols/v2_transform.html)
**NN: Device type in the OpenIGTLink header. (Max. 20 bytes)
**TT: 4x4 linear transformation matrix

==Diagram==
<span style="color:#800000">
</span>

{| border="1" cellpadding="5" cellspacing="0" align="center"
|-
| align="left style="background:#e0e0e0;" | ''3D Slicer (operator)''
| align="left style="background:#e0e0e0;" | ''Message''
| align="left style="background:#e0e0e0;" | ''Robot Controller''
| align="left style="background:#e0e0e0;" | ''Radiologist''
| align="left style="background:#e0e0e0;" | ''Note''
|-
| colspan=5 align="center" style="background:#f0f0f0;" | Start-up
|-
| align="left" | The operator presses "Start-up" button
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" | Send command to robot
| align="left" | >> STRING(CMD_XXXX, START_UP) >>
| align="left" |
| align="left" |
| align="left" | XXXX is a unique query ID (string of any ASCII letters up to 16 bytes)
|-
| align="left" |
| align="left" | << STRING(ACK_XXXX, START_UP) <<
| align="left" | Echo back an acknowledgement command was received, but not yet completed
| align="left" |
| align="left" | XXXX is the same unique query ID as the START_UP message.
|-
| align="left" style="background:#f8f8f8;" |
| align="left" style="background:#f8f8f8;;" | << STATUS(CURRENT_STATUS, Code:0:Phase) <<
| align="left" style="background:#f8f8f8;;" | '''Code=OK:''' Confirm that the robot is transition to START_UP mode. Phase should be "START_UP". ''Code=DNR:'' Fails to transition. Phase should be the name of the current workphase
| align="left" style="background:#f8f8f8;;" |
| align="left" style="background:#f8f8f8;;" | DNR: Device not ready (13)
|-
| align="left" |
| align="left" |
| align="left" | Start up and initialize the hardware. Run the robot homing procedure if necessary (skip if already successfully completed). Move robot to home (loading) configuration.
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << STATUS(START_UP, Code:??:??) <<
| align="left" | '''Code=OK:''' Confirm when robot is initialized <br>'''Code>=2''': Error. See [http://openigtlink.org/protocols/v2_status.html error list]
| align="left" |
| align="left" |
|-
| align="left" | Display the result of start up process.
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| colspan=5 align="center" style="background:#f0f0f0;" | Planning
|-
| align="left" | The operator opens the planning panel
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | >> STRING(CMD_XXXX, PLANNING) >>
| align="left" |
| align="left" |
| align="left" | XXXX is a unique query ID (string of any ASCII letters up to 16 bytes)
|-
| align="left" |
| align="left" | << STRING(ACK_XXXX, PLANNING) <<
| align="left" | Echo back an acknowledgement command was received
| align="left" |
| align="left" | XXXX is the same unique query ID as the PLANNING message.
|-
| align="left" style="background:#f8f8f8;" |
| align="left" style="background:#f8f8f8;;" | << STATUS(CURRENT_STATUS, Code:0:Phase) <<
| align="left" style="background:#f8f8f8;;" | '''Code=OK:''' Confirm that the robot is transition to PLANNING mode. Phase should be "PLANNING". ''Code=DNR:'' Fails to transition. Phase should be the name of the current workphase
| align="left" style="background:#f8f8f8;;" |
| align="left" style="background:#f8f8f8;;" | DNR: Device not ready (13)
|-
| align="left" |
| align="left" |
| align="left" | Do nothing except keep track of current state, robot is awaiting next workphase.
| align="left" |
| align="left" |
|-
| align="left" | Show that the robot is in PLANNING phase.
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| colspan=5 align="center" style="background:#f0f0f0;" | Calibration
|-
| align="left" | The operator opens the calibration panel
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | >> STRING(CMD_XXXX, CALIBRATION) >>
| align="left" |
| align="left" |
| align="left" | XXXX is a unique query ID (string of any ASCII letters up to 16 bytes)
|-
| align="left" |
| align="left" | << STRING(ACK_XXXX, CALIBRATION) <<
| align="left" | Echo back an acknowledgement command was received
| align="left" |
| align="left" | XXXX is the same unique query ID as the CALIBRATION message.
|-
| align="left" style="background:#f8f8f8;" |
| align="left" style="background:#f8f8f8;;" | << STATUS(CURRENT_STATUS, Code:0:Phase) <<
| align="left" style="background:#f8f8f8;;" | '''Code=OK:''' Confirm that the robot is transition to CALIBRATION mode. Phase should be "CALIBRATION". ''Code=DNR:'' Fails to transition. Phase should be the name of the current workphase
| align="left" style="background:#f8f8f8;;" |
| align="left" style="background:#f8f8f8;;" | DNR: Device not ready (13)
|-
| align="left" |
| align="left" |
| align="left" | Do nothing except keep track of current state, robot is awaiting calibration transform
| align="left" |
| align="left" |
|-
| align="left" | Show that the robot is in CALIBRATION phase.
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" | Nav Software (3D Slicer or RadVision) calculates calibration matrix
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | >> TRANSFORM(CLB_XXXX, 4x4 calibration matrix in RAS coordinates) >>
| align="left" |
| align="left" |
| align="left" |XXXX is a unique query ID (string of any ASCII letters up to 16 bytes)
|-
| align="left" |
| align="left" | << TRANSFORM(ACK_XXXX, Calibration matrix in RAS coordinates) <<
| align="left" | Echo back an acknowledgement transform was received
| align="left" |
| align="left" | XXXX is the same unique query ID as the CLB message.
|-
| align="left" |
| align="left" |
| align="left" | Update calibration transform, set flag that registration has been set externally, reply with confirmation
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << STATUS(CALIBRATION, Code:??:??) <<
| align="left" | '''Code=OK:''' Confirm that calibration was received and robot is ready for next workphase <br>'''Code=CE''': Error.
| align="left" |
| align="left" | CE: Configuration Error (code 10)
|-
| align="left" | Show that calibration successfully sent to robot or failed.
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| colspan=5 align="center" style="background:#f0f0f0;" | Targeting
|-
| align="left" | The operator enters "Targeting" mode
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | >> STRING(CMD_XXXX, TARGETING) >>
| align="left" |
| align="left" |
| align="left" |XXXX is a unique query ID (string of any ASCII letters up to 16 bytes)
|-
| align="left" |
| align="left" | << STRING(ACK_XXXX, TARGETING) <<
| align="left" | Acknowledge receiving targeting command
| align="left" |
| align="left" | XXXX is the same unique query ID as the TARGETING message.
|-
| align="left" style="background:#f8f8f8;" |
| align="left" style="background:#f8f8f8;;" | << STATUS(CURRENT_STATUS, Code:0:Phase) <<
| align="left" style="background:#f8f8f8;;" | '''Code=OK:''' Confirm that the robot is transition to TARGETING mode. Phase should be "TARGETING". ''Code=DNR:'' Fails to transition. Phase should be the name of the current workphase
| align="left" style="background:#f8f8f8;;" |
| align="left" style="background:#f8f8f8;;" | DNR: Device not ready (13)
|-
| align="left" |
| align="left" |
| align="left" | Confirm if robot is ready for targeting; check if calibration was received; return robot to home (loading) position, if needed.
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << STATUS(TARGETING, Code:??:??) <<
| align="left" | '''Code=OK:''' Confirm robot has entered targeting mode. <br>'''Code=DNR:''' If not able to enter targeting mode (i.e. calibration not received)
| align="left" |
| align="left" | DNR: Device Not Ready (code 13)
|-
| align="left" | The operator select a target, Nav software creates a 4x4 matrix for desired 6-DOF robot pose to reach the target
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | >> TRANSFORM(TGT_XXXXX, 4x4 target matrix in RAS coordinates) >>
| align="left" |
| align="left" |
| align="left" | XXXX is a unique query ID (string of any ASCII letters up to 16 bytes). The unique ID may be used as a human-readable target name on the robot control software. For example, TGT_LeftApex-2 is for the second targeting attempt on a lesion in the left-apex.
|-
| align="left" |
| align="left" | << TRANSFORM(ACK_XXXXX, 4x4 target matrix) <<
| align="left" | Acknowledge receipt of target transformation by echoing back
| align="left" |
| align="left" | XXXX is the same unique query ID as the TARGETING message.
|-
| align="left" |
| align="left" |
| align="left" | Calculate if target pose is reachable based on the kinematics, reply with status and set target
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << STATUS(TARGET, Code:??:??) <<
| align="left" | '''Code=OK:''' Reply with OK if target was accepted <br/>'''Code=DNR:''' Not in targeting mode <br/> '''Code=CE:''' Not a valid target (i.e. out of workspace)
| align="left" |
| align="left" | DNR: Device Not Ready (code 13) <br> CE: Configuration Error (code 10)
|-
| align="left" |
| align="left" | << TRANSFORM(TARGET, 4x4 target matrix) <<
| align="left" | Send actual target pose in robot controller if one was set (corresponds to when status comes back OK)
| align="left" |
| align="left" |
|-
| align="left" | Display the reachable target position set in robot controller.
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" | The operator confirms the target position set in the controller, and press "MOVE"
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | >> STRING(CMD_XXXX, MOVE_TO_TARGET) >>
| align="left" |
| align="left" |
| align="left" | XXXX is a unique query ID (string of any ASCII letters up to 16 bytes)
|-
| align="left" |
| align="left" | << STRING(ACK_XXXX, MOVE_TO_TARGET) <<
| align="left" | Echo back an acknowledgement command was received (not yet completed)
| align="left" |
| align="left" | XXXX is the same unique query ID as the MOVE_TO_TARGET message. <font color=red>See the note below</font>
|-
| align="left" | Alert the clinician to hold footpedal to align the robot
| align="left" |
| align="left" |
| align="left" | Clinician engages interlock (footpedal in scanner room) to enable robot motion. Robot will only move when interlock is engaged following a move command.
| align="left" |
|-
| align="left" |
| align="left" |
| align="left" | The robot moves to the target and streams its pose during motion
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << TRANSFORM(CURRENT_POSITION, Current robot pose matrix in RAS coordinates) <<
| align="left" | Stream current robot pose in RAS coords as moving. Can also be requested (see below).
| align="left" |
| align="left" |
|-
| align="left" | Display the current robot position as it moves toward the target.
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" |
| align="left" | Display that the robot is at the target. Send confirmation.
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << STATUS(MOVE_TO_TARGET, Code:??:??) <<
| align="left" | '''Code=OK:''' Robot reaches target <br> '''Code >= 3:''' Return error code when the device fails to move to the target. See [http://openigtlink.org/protocols/v2_status.html error list]
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << TRANSFORM(CURRENT_POSITION, Current robot pose matrix in RAS coordinates) <<
| align="left" | Push out final robot pose in RAS coords as moving. (same format as previous stream - ensures last one is at final position)
| align="left" |
| align="left" |
|-
| align="left" | Display the current final robot position at the target.
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| colspan=5 align="center" style="background:#f0f0f0;" | Needle Insertion (Manual)
|-
| align="left" | Ask to lock the robot
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" |
| align="left" |
| align="left" | The operator presses "Lock" button
| align="left" |
|-
| align="left" |
| align="left" | >> STRING (CMD_XXXX, MANUAL) >>
| align="left" |
| align="left" |
| align="left" | XXXX is a unique query ID (string of any ASCII letters up to 16 bytes)
|-
| align="left" |
| align="left" | << STRING(ACK_XXXX, MANUAL) <<
| align="left" | Echo back an acknowledgement command was received (not yet completed)
| align="left" |
| align="left" | XXXX is the same unique query ID as the MANUAL message.
|-
| align="left" style="background:#f8f8f8;" |
| align="left" style="background:#f8f8f8;;" | << STATUS(CURRENT_STATUS, Code:0:Phase) <<
| align="left" style="background:#f8f8f8;;" | '''Code=OK:''' Confirm that the robot is transition to MANUAL mode. Phase should be "MANUAL". ''Code=DNR:'' Fails to transition. Phase should be the name of the current workphase
| align="left" style="background:#f8f8f8;;" |
| align="left" style="background:#f8f8f8;;" | DNR: Device not ready (13)
|-
| align="left" |
| align="left" |
| align="left" | Cut motor power to prevent motion of the robot base. This also eliminates causes of MR interference for insertion under live imaging.
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << STATUS(MANUAL, OK:??:??) <<
| align="left" | Reply with OK when robot is in a safe, locked state
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" |
| align="left" |
| align="left" | Insert a needle, optionally under live MR imaging. Perform intervention with the needle (biopsy or seed placement).
| align="left" |
|-
| align="left" |
| align="left" |
| align="left" |
| align="left" | Retract the needle
| align="left" |
|-
| align="left" | Ask to unlock the robot and confirm needle is retracted
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" |
| align="left" |
| align="left" | The operator presses "Unlock"
| align="left" |
|-
| align="left" |
| align="left" |
| align="left" |
| align="left" |
| align="left" | Return to the TARGETING phase (Slicer sends STRING(ACK_XXXXX, TARGETING) )
|-
| colspan=5 align="center" style="background:#f0f0f0;" | All workhpases
|-
| align="left" | The operator presses "Stop" button
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | >> STRING(CMD_XXXX, STOP) >>
| align="left" |
| align="left" |
| align="left" | XXXX is a unique query ID (string of any ASCII letters up to 16 bytes)
|-
| align="left" |
| align="left" | << STRING(ACK_XXXX, STOP) <<
| align="left" | Acknowledge receiving targeting command
| align="left" |
| align="left" | XXXX is the same unique query ID as the STOP message.
|-
| align="left" style="background:#f8f8f8;" |
| align="left" style="background:#f8f8f8;;" | << STATUS(CURRENT_STATUS, Code:0:Phase) <<
| align="left" style="background:#f8f8f8;;" | '''Code=OK:''' Confirm that the robot is transition to STOP mode. Phase should be "STOP". ''Code=DNR:'' Fails to transition. Phase should be the name of the current workphase
| align="left" style="background:#f8f8f8;;" |
| align="left" style="background:#f8f8f8;;" | DNR: Device not ready (13)
|-
| align="left" |
| align="left" |
| align="left" | The robot stops all motion. Stays in current state/workphase.
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << STATUS(STOP, OK:??:??) <<
| align="left" | Reply with OK when robot stopped safely.
| align="left" |
| align="left" |
|-
| colspan=5 align="center" style="background:#f0f0f0;" | All workhpases
|-
| align="left" | The operator presses "Emergency" button
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | >> STRING(CMD_XXXX, EMERGENCY) >>
| align="left" |
| align="left" |
| align="left" | XXXX is a unique query ID (string of any ASCII letters up to 16 bytes)
|-
| align="left" |
| align="left" | << STRING(ACK_XXXX, EMERGENCY) <<
| align="left" | Acknowledge receiving targeting command
| align="left" |
| align="left" | XXXX is the same unique query ID as the STOP message.
|-
| align="left" style="background:#f8f8f8;" |
| align="left" style="background:#f8f8f8;;" | << STATUS(CURRENT_STATUS, Code:0:Phase) <<
| align="left" style="background:#f8f8f8;;" | '''Code=OK:''' Confirm that the robot is transition to EMERGENCY mode. Phase should be "EMERGENCY". ''Code=DNR:'' Fails to transition. Phase should be the name of the current workphase
| align="left" style="background:#f8f8f8;;" |
| align="left" style="background:#f8f8f8;;" | DNR: Device not ready (13)
|-
| align="left" |
| align="left" |
| align="left" | The robot stops all motion and disables/locks motors. Switches to Emergency state/workphase. ?? IS THIS THE DESIRED ACTION
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << STATUS(EMERGENCY, Emergency:??:??) <<
| align="left" | Reply with OK when robot stopped safely.
| align="left" |
| align="left" |
|-
| colspan=5 align="center" style="background:#f0f0f0;" | All workhpases
|-
| align="left" | Request current robot pose (or target or calibration transforms)
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | >> GET_TRANSFORM(CURRENT_POSITION) >>
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" |
| align="left" | The robot transmits current pose ("CURRENT_POSITION") through IGTLink upon request. This also works for requesting "TARGET_POSITION" and "CALIBRATION" transforms stored in robot controller.
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << TRANSFORM(CURRENT_POSITION, Current robot pose matrix in RAS coordinates) <<
| align="left" |
| align="left" |
| align="left" |
|-
| colspan=5 align="center" style="background:#f0f0f0;" | All workhpases
|-
| align="left" | Request the robot status/workphase
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | >> GET_STATUS(CURRENT_STATUS) >> ?? CONFIRM COMMAND STRUCTURE FOR STATUS REQUEST
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" |
| align="left" | Sends current state/workphase. ?? SHOULD IT SEND OTHER INFO TOO
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << STATUS(CURRENT_STATUS, Code:0:Status) <<
| align="left" | Send status code. Status should be the name of the current status e.g. "TARGETING". Code is OK, when the robot is successfully determines its workphase. Otherwise, Code should be configuration error (10)
| align="left" |
| align="left" |
|-
| colspan=5 align="center" style="background:#f0f0f0;" | All workhpases
|-
| align="left" |
| align="left" |
| align="left" | Robot controller sends errors or notifications through IGTLink. Transmitted asynchronously with error text in message body. To be used with limit events, hardware failures, invalid commands, etc.
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << STATUS(ERROR, Code:??:Error name) <<
| align="left" | | align="left" | Send status code. [http://openigtlink.org/protocols/v2_status.html error list]
| align="left" |
| align="left" |
|}

<font color=red>NOTE: Suggested modification -- Agreed on 9/5/13</font>

Although MOVE_TO_TARGET workphase is currently part of TARGETING, Nirav suggested to make MOVE_TO_TARGET phase an independent workhpase. If we agree, the MOVE_TO_TARGET workphase should be defined as follows:

{| border="1" cellpadding="5" cellspacing="0" align="center"
|-
| align="left style="background:#e0e0e0;" | ''3D Slicer (operator)''
| align="left style="background:#e0e0e0;" | ''Message''
| align="left style="background:#e0e0e0;" | ''Robot Controller''
| align="left style="background:#e0e0e0;" | ''Radiologist''
| align="left style="background:#e0e0e0;" | ''Note''
|-
| colspan=5 align="center" style="background:#f0f0f0;" | Move to Target
|-
| align="left" | The operator confirms the target position set in the controller, and press "MOVE"
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | >> STRING(CMD_XXXX, MOVE_TO_TARGET) >>
| align="left" |
| align="left" |
| align="left" | XXXX is a unique query ID (string of any ASCII letters up to 16 bytes)
|-
| align="left" |
| align="left" | << STRING(ACK_XXXX, MOVE_TO_TARGET) <<
| align="left" | Echo back an acknowledgement command was received (not yet completed)
| align="left" |
| align="left" | XXXX is the same unique query ID as the MOVE_TO_TARGET message. <font color=red>See the note below</font>
|-
| align="left" style="background:#f8f8f8;" |
| align="left" style="background:#f8f8f8;;" | << STATUS(CURRENT_STATUS, Code:0:Phase) <<
| align="left" style="background:#f8f8f8;;" | '''Code=OK:''' Confirm that the robot is transition to MOVE_TO_TARGET mode. Phase should be "MOVE_TO_TARGET". ''Code=DNR:'' Fails to transition. Phase should be the name of the current workphase
| align="left" style="background:#f8f8f8;;" |
| align="left" style="background:#f8f8f8;;" | DNR: Device not ready (13)
|-
| align="left" | Alert the clinician to hold footpedal to align the robot
| align="left" |
| align="left" |
| align="left" | Clinician engages interlock (footpedal in scanner room) to enable robot motion. Robot will only move when interlock is engaged following a move command.
| align="left" |
|-
| align="left" |
| align="left" |
| align="left" | The robot moves to the target and streams its pose during motion
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << TRANSFORM(CURRENT_POSITION, Current robot pose matrix in RAS coordinates) <<
| align="left" | Stream current robot pose in RAS coords as moving. Can also be requested (see below).
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << STATUS(MOVE_TO_TARGET, Code:??:??) <<
| align="left" | '''Code=OK:''' Robot reaches target <br> '''Code >= 3:''' Return error code when the device fails to move to the target. See [http://openigtlink.org/protocols/v2_status.html error list]
| align="left" |
| align="left" |
|-
| align="left" |
| align="left" | << TRANSFORM(CURRENT_POSITION, Current robot pose matrix in RAS coordinates) <<
| align="left" | Push out final robot pose in RAS coords as moving. (same format as previous stream - ensures last one is at final position)
| align="left" |
| align="left" |
|-
| align="left" | Display the current final robot position at the target.
| align="left" |
| align="left" |
| align="left" |
| align="left" |
|-
|}

==Quality Assurance Protocol==
Simulator software for QA will be hosted in https://github.com/ProstateBRP.
The following tests are described as pseudo code for navigation software.

===Test 1: Normal Operation Test===
<font color=red>Updated on 9/10/13</font>

# Step 1
send STRING(CMD, START_UP)
if (not receive STRING(ACK, START_UP) within 100ms) failure # Check point 1.1
if (not receive STATUS(CURRENT_STATUS, OK,0,START_UP) within 100ms) failure # Check point 1.2
if (not receive STATUS(START_UP, OK) within 10s) failure # Check point 1.3

# Step 2
send STRING(CMD, PLANNING)
if (not receive STRING(ACK, PLANNING) within 100ms) failure # Check point 2.1
if (not receive STATUS(CURRENT_STATUS, OK,0,PLANNING) within 100ms) failure # Check point 2.2

# Step 3
send STRING(CMD, CALIBRATION)
if (not receive STRING(ACK, CALIBRATION) within 100ms) failure # Check point 3.1
if (not receive STATUS(CURRENT_STATUS, OK,0,CALIBRATION) within 100ms) failure # Check point 3.2

send TRANSFORM(CLB, matrix1)
if (not receive TRANSFORM(ACK, matrix2) within 100ms) failure # Check point 3.3
if (matrix1 != matrix2) failure # Check point 3.4
if (not receive STATUS(CALIBRATION, OK) within 10s) failure #Check point 3.5

# Step 4
send STRING(CMD, TARGETING)
if (not receive STRING(ACK, TARGETING) within 100ms) failure # Check point 4.1
if (not receive STATUS(CURRENT_STATUS, OK,0,TARGETING) within 100ms) failure # Check point 4.2
if (not receive STATUS(TARGETING, OK) within 10s) failure # Check point 4.3

send TRANSFORM(TGT, matrix3)
if (not receive TRANSFORM(ACK, matrix4) within 100ms) failure # Check point 4.4
if (matrix3 != matrix4) failure # Check point 4.5
if (not receive STATUS(TARGET, OK) within 10s) failure # Check point 4.6
if (not receive TRANSFORM(TARGET, matrix5) within 20s) failure # Check point 4.7
if (matrix3 != matrix5) failure # Check point 4.8

# Step 5
send STRING(CMD, MOVE_TO_TARGET)
if (not receive STRING(ACK, MOVE_TO_TARGET) within 100ms) failure # Check point 5.1
if (not receive STATUS(CURRENT_STATUS, OK,0,TARGET) within 100ms) failure # Check point 5.2

if (not start receiving TRANSFORM(CURRENT_POSITION, matrix 6) in 10s) failure # Check point 5.3
if (not receive STATUS(MOVE_TO_TARGET, OK) within 100ms after the robot reaches the target) failure # Check point 5.4
if (not receive TRANSFORM(CURRENT_POSITION, matrix 7) within 100ms after the status message is received) failure # Check point 5.5
if (matrix 7 does not match the current position of the robot) failure # Check point 5.6

# Step 6
send STRING(CMD, MANUAL)
if (not receive STRING(ACK, MANUAL) within 100ms) failure # Check point 6.1
if (not receive STATUS(CURRENT_STATUS, OK,0,TARGET) within 100ms) failure # Check point 6.2
if (not receive STATUS(MANUAL, OK) within 10s) failure # Check point 6.3

# Step 7
send GET_TRANSFORM(CURRENT_POSITION)
if (not receive TRANSFORM(CURRENT_POSITION, matrix8) within 10s) failure # Check point 7.1
if (matrix 8 does not match the current position of the robot) failure # Check point 7.2

# Step 8
send GET_STATUS(CURRENT_STATUS)
if (not receive STATUS(XXXXX, Code:??:??) within 10s) failure # Check point 8.1

# Step 9
send STRING(CMD, STOP)
if (not receive STRING(ACK, STOP) within 100ms) failure # Check point 9.1
if (not receive STATUS(CURRENT_STATUS, OK,0,STOP) within 100ms) failure # Check point 9.2
if (not receive STATUS(STOP, OK) within 10s) failure # Check point 9.3

# Step 10
send STRING(CMD, EMERGENCY)
if (not receive STRING(ACK, EMERGENCY) within 100ms) failure # Check point 10.1
if (not receive STATUS(CURRENT_STATUS, OK,0,EMERGENCY) within 100ms) failure # Check point 10.2
if (not receive STATUS(EMERGENCY, Emergency) within 10s) failure # Check point 10.3

This is implemented in:
https://github.com/ProstateBRP/CommunicationTest/blob/master/ClientNormalOperationTest.cxx

===Test 2: Start-up without connecting the device to the robot control computer===
<font color=red>Updated on 9/10/13</font>
Check if the robot control software returns a proper error code if there is any trouble with the hardware. Before start, unplug one of the sensors or actuators from the robot control computer. The test must be repeated for all sensors and actuators.

# Step 1
send STRING(CMD, START-UP)
if (not receive STRING(ACK, START-UP) within 100ms) failure # Check point 1.1
if (not receive STATUS(CURRENT_STATUS, OK,0,START_UP) within 100ms) failure # Check point 1.2
if (not receive STATUS(DNP) within 10s) failure # Check point 1.3

DNP: Device Not Present (code 16)

===Test 3: Calibration error test===
<font color=red>Updated on 9/10/13</font>
Check if the robot control software returns a proper error code if the calibration matrix is not valid e.g. non-orthogonal matrix.

# Step 1
send STRING(CMD, START_UP)
if (not receive STRING(ACK, START_UP) within 100ms) failure # Check point 1.1
if (not receive STATUS(CURRENT_STATUS, OK,0,START_UP) within 100ms) failure # Check point 1.2
if (not receive STATUS(START_UP, OK) within 10s) failure # Check point 1.3

# Step 2
send STRING(CMD, PLANNING)
if (not receive STRING(ACK, PLANNING) within 100ms) failure # Check point 2.1
if (not receive STATUS(CURRENT_STATUS, OK,0,PLANNING) within 100ms) failure # Check point 2.2

# Step 3
send STRING(CMD, CALIBRATION)
if (not receive STRING(ACK, CALIBRATION) within 100ms) failure # Check point 3.1
if (not receive STATUS(CURRENT_STATUS, OK,0,CALIBRATION) within 100ms) failure # Check point 3.2

send TRANSFORM(CLB, invalid_matrix)
if (not receive TRANSFORM(ACK, invalid_matrix) within 100ms) failure # Check point 3.3
if (not receive STATUS(CALIBRATION, CE) within 10s) failure # Check point 3.4

CE: Configuration error (code 10). Example of non-orthoganl 4x4 matrix is (1.0, 1.0, 1.0, 1.0; 1.0, 1.0, 1.0, 1.0; 1.0, 1.0, 1.0, 1.0; 1.0, 1.0, 1.0, 1.0)

===Test 4: Targeting without calibration test===
<font color=red>Updated on 9/10</font>
Check if the robot control software returns a proper error code if the user attempts to run targeting before sending calibration matrix

# Step 1
send STRING(CMD, START-UP)
if (not receive STRING(ACK, START-UP) within 100ms) failure # Check point 1.1
if (not receive STATUS(CURRENT_STATUS, OK,0,START-UP) within 100ms) failure # Check point 1.2
if (not receive STATUS(OK) within 10s) failure # Check point 1.3

# Step 2
send STRING(CMD, PLANNING)
if (not receive STRING(ACK, PLANNING) within 100ms) failure # Check point 2.1
if (not receive STATUS(CURRENT_STATUS, OK,0,PLANNING) within 100ms) failure # Check point 2.2

# Step 3
send STRING(CMD, CALIBRATION)
if (not receive STRING(ACK, CALIBRATION) within 100ms) failure # Check point 3.1
if (not receive STATUS(CURRENT_STATUS, OK,0,CALIBRATION) within 100ms) failure # Check point 3.2

# Step 4
send STRING(CMD, TARGETING)
if (not receive STRING(ACK, TARGETING) within 100ms) failure # Check point 4.1
if (not receive STATUS(CURRENT_STATUS, OK,0,CALIBRATION) within 100ms) failure # Check point 4.2
if (not receive STATUS(TARGETING, DNR) within 10s) failure # Check point 4.3

DNR: Device not ready (code 13)

===Test 5: Out of range test===
<font color=red>Updated on 9/10/13</font>
Check if the robot control software returns a proper error code if a target outside of its workspace is given. Assume target described by matrix3 in the image coordinate system is out of the range for the robot registered to the image coordinate system using matrix 1.

# Step 1
send STRING(CMD, START-UP)
if (not receive STRING(ACK, START-UP) within 100ms) failure # Check point #1.1
if (not receive STATUS(CURRENT_STATUS, OK,0,START-UP) within 100ms) failure # Check point 1.2
if (not receive STATUS(OK) within 10s) failure # Check point #1.3

# Step 2
send STRING(CMD, PLANNING)
if (not receive STRING(ACK, PLANNING) within 100ms) failure # Check point #2.1
if (not receive STATUS(CURRENT_STATUS, OK,0,PLANNING) within 100ms) failure # Check point 2.2

# Step 3
send STRING(CMD, CALIBRATION)
if (not receive STRING(ACK, CALIBRATION) within 100ms) failure # Check point #3.1
if (not receive STATUS(CURRENT_STATUS, OK,0,CALIBRATION) within 100ms) failure # Check point 3.2

send TRANSFORM(CLB, matrix1)
if (not receive TRANSFORM(ACK, matrix2) within 100ms) failure # Check point #3.3
if (matrix1 != matrix2) failure # Check point #3.4
if (not receive STATUS(CALIBRATION, OK) within 10s) failure # Check point #3.5

# Step 4
send STRING(CMD, TARGETING)
if (not receive STRING(ACK, TARGETING) within 100ms) failure # Check point #4.1
if (not receive STATUS(CURRENT_STATUS, OK,0,TARGETING) within 100ms) failure # Check point 4.2
if (not receive STATUS(TARGETING, OK) within 10s) failure # Check point #4.3

send TRANSFORM(TGT, matrix3)
if (not receive TRANSFORM(ACK, matrix4) within 100ms) failure # Check point #4.4
if (matrix3 != matrix4) failure # Check point #4.5
if (not receive STATUS(TARGET, CE) within 10s) failure # Check point #4.6

CE: Configuration error (code 10)

===Test 6: Stop during operation test===
<font color=red>Updated on 9/10/13</font>
Check if the robot stops when the STOP command is sent to the robot while the robot is moving.

# Step 1
send STRING(CMD, START_UP)
if (not receive STRING(ACK, START_UP) within 100ms) failure # Check point 1.1
if (not receive STATUS(CURRENT_STATUS, OK,0,START_UP) within 100ms) failure # Check point 1.2
if (not receive STATUS(START_UP, OK) within 10s) failure # Check point 1.3

# Step 2
send STRING(CMD, PLANNING)
if (not receive STRING(ACK, PLANNING) within 100ms) failure # Check point 2.1
if (not receive STATUS(CURRENT_STATUS, OK,0,PLANNING) within 100ms) failure # Check point 2.2

# Step 3
send STRING(CMD, CALIBRATION)
if (not receive STRING(ACK, CALIBRATION) within 100ms) failure # Check point 3.1
if (not receive STATUS(CURRENT_STATUS, OK,0,CALIBRATION) within 100ms) failure # Check point 3.2

send TRANSFORM(CLB, matrix1)
if (not receive TRANSFORM(ACK, matrix2) within 100ms) failure # Check point 3.3
if (matrix1 != matrix2) failure # Check point 3.4
if (not receive STATUS(CALIBRATION, OK) within 10s) failure #Check point 3.5

# Step 4
send STRING(CMD, TARGETING)
if (not receive STRING(ACK, TARGETING) within 100ms) failure # Check point 4.1
if (not receive STATUS(CURRENT_STATUS, OK,0,TARGETING) within 100ms) failure # Check point 4.2
if (not receive STATUS(TARGETING, OK) within 10s) failure # Check point 4.3

send TRANSFORM(TGT, matrix3)
if (not receive TRANSFORM(ACK, matrix4) within 100ms) failure # Check point 4.4
if (matrix3 != matrix4) failure # Check point 4.5
if (not receive STATUS(TARGET, OK) within 10s) failure # Check point 4.6
if (not receive TRANSFORM(TARGET, matrix5) within 20s) failure # Check point 4.7
if (matrix3 != matrix5) failure # Check point 4.8

# Step 5
send STRING(CMD, MOVE_TO_TARGET)
if (not receive STRING(ACK, MOVE_TO_TARGET) within 100ms) failure # Check point 5.1
if (not receive STATUS(CURRENT_STATUS, OK,0,TARGET) within 100ms) failure # Check point 5.2

if (not start receiving TRANSFORM(CURRENT_POSITION, matrix 6) in 10s) failure # Check point 5.3
if (not receive STATUS(MOVE_TO_TARGET, OK) within 100ms after the robot reaches the target) failure # Check point 5.4
if (not receive TRANSFORM(CURRENT_POSITION, matrix 7) within 100ms after the status message is received) failure # Check point 5.5
if (matrix 7 does not match the current position of the robot) failure # Check point 5.6

# Step 6
// While the robot is moving to the target
send STRING(CMD, STOP) before receiving STATUS(MOVE_TO_TARGET, OK)
if (not receive STRING(ACK, STOP) within 100ms) failure #Check point #6.1
if (not receive STATUS(CURRENT_STATUS, OK,0,STOP) within 100ms) failure # Check point 6.2
if (not receive STATUS(STOP, OK) within 200ms) failure #Check point #6.3

The test fails if the robot does not stop within 200ms after sending STRING(CMD, STOP).

===Test 7: Emergency stop during operation test===
<font color=red>Updated on 9/10/13</font>
Check if the robot stops when the EMERGENCY command is sent to the robot while the robot is moving.

# Step 1
send STRING(CMD, START_UP)
if (not receive STRING(ACK, START_UP) within 100ms) failure # Check point 1.1
if (not receive STATUS(CURRENT_STATUS, OK,0,START_UP) within 100ms) failure # Check point 1.2
if (not receive STATUS(START_UP, OK) within 10s) failure # Check point 1.3

# Step 2
send STRING(CMD, PLANNING)
if (not receive STRING(ACK, PLANNING) within 100ms) failure # Check point 2.1
if (not receive STATUS(CURRENT_STATUS, OK,0,PLANNING) within 100ms) failure # Check point 2.2

# Step 3
send STRING(CMD, CALIBRATION)
if (not receive STRING(ACK, CALIBRATION) within 100ms) failure # Check point 3.1
if (not receive STATUS(CURRENT_STATUS, OK,0,CALIBRATION) within 100ms) failure # Check point 3.2

send TRANSFORM(CLB, matrix1)
if (not receive TRANSFORM(ACK, matrix2) within 100ms) failure # Check point 3.3
if (matrix1 != matrix2) failure # Check point 3.4
if (not receive STATUS(CALIBRATION, OK) within 10s) failure #Check point 3.5

# Step 4
send STRING(CMD, TARGETING)
if (not receive STRING(ACK, TARGETING) within 100ms) failure # Check point 4.1
if (not receive STATUS(CURRENT_STATUS, OK,0,TARGETING) within 100ms) failure # Check point 4.2
if (not receive STATUS(TARGETING, OK) within 10s) failure # Check point 4.3

send TRANSFORM(TGT, matrix3)
if (not receive TRANSFORM(ACK, matrix4) within 100ms) failure # Check point 4.4
if (matrix3 != matrix4) failure # Check point 4.5
if (not receive STATUS(TARGET, OK) within 10s) failure # Check point 4.6
if (not receive TRANSFORM(TARGET, matrix5) within 20s) failure # Check point 4.7
if (matrix3 != matrix5) failure # Check point 4.8

# Step 5
send STRING(CMD, MOVE_TO_TARGET)
if (not receive STRING(ACK, MOVE_TO_TARGET) within 100ms) failure # Check point 5.1
if (not receive STATUS(CURRENT_STATUS, OK,0,TARGET) within 100ms) failure # Check point 5.2

if (not start receiving TRANSFORM(CURRENT_POSITION, matrix 6) in 10s) failure # Check point 5.3
if (not receive STATUS(MOVE_TO_TARGET, OK) within 100ms after the robot reaches the target) failure # Check point 5.4
if (not receive TRANSFORM(CURRENT_POSITION, matrix 7) within 100ms after the status message is received) failure # Check point 5.5
if (matrix 7 does not match the current position of the robot) failure # Check point 5.6

# Step 6
// While the robot is moving to the target
send STRING(CMD, EMERGENCY) before receiving STATUS(MOVE_TO_TARGET, OK)
if (not receive STRING(ACK, EMERGENCY) within 100ms) failure # Check point #6.1
if (not receive STATUS(CURRENT_STATUS, OK,0,EMERGENCY) within 100ms) failure # Check point 6.2
if (not receive STATUS(STOP, EMERGENCY) within 200ms) failure # Check point #6.3

The test fails if the robot does not completely shutdown within 200ms after sending STRING(CMD, EMERGENCY).

===Test 8: MOVE_TO_TARGET without sending target ===
<font color=red>Updated on 9/10/13</font>

# Step 1
send STRING(CMD, START_UP)
if (not receive STRING(ACK, START_UP) within 100ms) failure # Check point 1.1
if (not receive STATUS(CURRENT_STATUS, OK,0,START_UP) within 100ms) failure # Check point 1.2
if (not receive STATUS(START_UP, OK) within 10s) failure # Check point 1.3

# Step 2
send STRING(CMD, PLANNING)
if (not receive STRING(ACK, PLANNING) within 100ms) failure # Check point 2.1
if (not receive STATUS(CURRENT_STATUS, OK,0,PLANNING) within 100ms) failure # Check point 2.2

# Step 3
send STRING(CMD, CALIBRATION)
if (not receive STRING(ACK, CALIBRATION) within 100ms) failure # Check point 3.1
if (not receive STATUS(CURRENT_STATUS, OK,0,CALIBRATION) within 100ms) failure # Check point 3.2

send TRANSFORM(CLB, matrix1)
if (not receive TRANSFORM(ACK, matrix2) within 100ms) failure # Check point 3.3
if (matrix1 != matrix2) failure # Check point 3.4
if (not receive STATUS(CALIBRATION, OK) within 10s) failure #Check point 3.5

# Step 4
send STRING(CMD, TARGETING)
if (not receive STRING(ACK, TARGETING) within 100ms) failure # Check point 4.1
if (not receive STATUS(CURRENT_STATUS, OK,0,TARGETING) within 100ms) failure # Check point 4.2
if (not receive STATUS(TARGETING, OK) within 10s) failure # Check point 4.3

# Step 5
send STRING(CMD, MOVE_TO_TARGET)
if (not receive STRING(ACK, MOVE_TO_TARGET) within 100ms) failure # Check point 5.1
if (not receive STATUS(CURRENT_STATUS, OK,0,TARGET) within 100ms) failure # Check point 5.2
if (not receive STATUS(MOVE_TO_TARGET, DNR) within 100ms after the robot reaches the target) failure # Check point #5.3

===Test 9: Accidental target/move_to command during manual mode===
<font color=red>Updated on 9/10/13</font>

# Step 1
send STRING(CMD, START_UP)
if (not receive STRING(ACK, START_UP) within 100ms) failure # Check point 1.1
if (not receive STATUS(CURRENT_STATUS, OK,0,START_UP) within 100ms) failure # Check point 1.2
if (not receive STATUS(START_UP, OK) within 10s) failure # Check point 1.3

# Step 2
send STRING(CMD, PLANNING)
if (not receive STRING(ACK, PLANNING) within 100ms) failure # Check point 2.1
if (not receive STATUS(CURRENT_STATUS, OK,0,PLANNING) within 100ms) failure # Check point 2.2

# Step 3
send STRING(CMD, CALIBRATION)
if (not receive STRING(ACK, CALIBRATION) within 100ms) failure # Check point 3.1
if (not receive STATUS(CURRENT_STATUS, OK,0,CALIBRATION) within 100ms) failure # Check point 3.2

send TRANSFORM(CLB, matrix1)
if (not receive TRANSFORM(ACK, matrix2) within 100ms) failure # Check point 3.3
if (matrix1 != matrix2) failure # Check point 3.4
if (not receive STATUS(CALIBRATION, OK) within 10s) failure #Check point 3.5

# Step 4
send STRING(CMD, TARGETING)
if (not receive STRING(ACK, TARGETING) within 100ms) failure # Check point 4.1
if (not receive STATUS(CURRENT_STATUS, OK,0,TARGETING) within 100ms) failure # Check point 4.2
if (not receive STATUS(TARGETING, OK) within 10s) failure # Check point 4.3

send TRANSFORM(TGT, matrix3)
if (not receive TRANSFORM(ACK, matrix4) within 100ms) failure # Check point 4.4
if (matrix3 != matrix4) failure # Check point 4.5
if (not receive STATUS(TARGET, OK) within 10s) failure # Check point 4.6
if (not receive TRANSFORM(TARGET, matrix5) within 20s) failure # Check point 4.7
if (matrix3 != matrix5) failure # Check point 4.8

# Step 5
send STRING(CMD, MOVE_TO_TARGET)
if (not receive STRING(ACK, MOVE_TO_TARGET) within 100ms) failure # Check point 5.1
if (not receive STATUS(CURRENT_STATUS, OK,0,TARGET) within 100ms) failure # Check point 5.2

if (not start receiving TRANSFORM(CURRENT_POSITION, matrix 6) in 10s) failure # Check point 5.3
if (not receive STATUS(MOVE_TO_TARGET, OK) within 100ms after the robot reaches the target) failure # Check point 5.4
if (not receive TRANSFORM(CURRENT_POSITION, matrix 7) within 100ms after the status message is received) failure # Check point 5.5
if (matrix 7 does not match the current position of the robot) failure # Check point 5.6

# Step 6
send STRING(CMD, MANUAL)
if (not receive STRING(ACK, MANUAL) within 100ms) failure # Check point 6.1
if (not receive STATUS(CURRENT_STATUS, OK,0,MANUAL) within 100ms) failure # Check point 6.2
if (not receive STATUS(MANUAL, OK) within 10s) failure # Check point 6.3

# Step 7
send STRING(CMD, MOVE_TO_TARGET)
if (not receive STRING(ACK, MOVE_TO_TARGET) within 100ms) failure # Check point 7.1
if (not receive STATUS(CURRENT_STATUS, OK,0,MANUAL) within 100ms) failure # Check point 6.2
if (not receive STATUS(MOVE_TO_TARGET, DNR) within 100ms after the robot reaches the target) failure # Check point 7.2

The test fails if the robot starts moving.

===Test 10: Hardware error during operation===
<font color=red>Updated on 9/10/13</font>
Unplug one of motors/encoders while the robot is moving to the target.

# Step 1
send STRING(CMD, START_UP)
if (not receive STRING(ACK, START_UP) within 100ms) failure # Check point 1.1
if (not receive STATUS(CURRENT_STATUS, OK,0,START_UP) within 100ms) failure # Check point 1.2
if (not receive STATUS(START_UP, OK) within 10s) failure # Check point 1.3

# Step 2
send STRING(CMD, PLANNING)
if (not receive STRING(ACK, PLANNING) within 100ms) failure # Check point 2.1
if (not receive STATUS(CURRENT_STATUS, OK,0,PLANNING) within 100ms) failure # Check point 2.2

# Step 3
send STRING(CMD, CALIBRATION)
if (not receive STRING(ACK, CALIBRATION) within 100ms) failure # Check point 3.1
if (not receive STATUS(CURRENT_STATUS, OK,0,CALIBRATION) within 100ms) failure # Check point 3.2

send TRANSFORM(CLB, matrix1)
if (not receive TRANSFORM(ACK, matrix2) within 100ms) failure # Check point 3.3
if (matrix1 != matrix2) failure # Check point 3.4
if (not receive STATUS(CALIBRATION, OK) within 10s) failure #Check point 3.5

# Step 4
send STRING(CMD, TARGETING)
if (not receive STRING(ACK, TARGETING) within 100ms) failure # Check point 4.1
if (not receive STATUS(CURRENT_STATUS, OK,0,TARGETING) within 100ms) failure # Check point 4.2
if (not receive STATUS(TARGETING, OK) within 10s) failure # Check point 4.3

send TRANSFORM(TGT, matrix3)
if (not receive TRANSFORM(ACK, matrix4) within 100ms) failure # Check point 4.4
if (matrix3 != matrix4) failure # Check point 4.5
if (not receive STATUS(TARGET, OK) within 10s) failure # Check point 4.6
if (not receive TRANSFORM(TARGET, matrix5) within 20s) failure # Check point 4.7
if (matrix3 != matrix5) failure # Check point 4.8

# Step 5
send STRING(CMD, MOVE_TO_TARGET)
if (not receive STRING(ACK, MOVE_TO_TARGET) within 100ms) failure # Check point 5.1
if (not receive STATUS(CURRENT_STATUS, OK,0,TARGET) within 100ms) failure # Check point 5.2

if (not start receiving TRANSFORM(CURRENT_POSITION, matrix 6) in 10s) failure # Check point 5.3

While the robot is moving to the target, unplug one of the cables for the actuators or the sensors

# Step 6
if (not receive STATUS(MOVE_TO_TARGET, 19) within 100ms) failure # Check point #6.1

Robot OpenIGTLink Communication March 2014

2014-03-19T20:57:09Z

Lchauvin: /* Diagram */

Robot OpenIGTLink Communication March 2014

2014-03-19T20:42:38Z

Lchauvin: Created page with 'The following table shows message exchange diagram for the communication between 3D Slicer (and other navigation software) and the robot in each workhpase. ==Notations== *STRING…'

2013 Summer Project Week:LabelMapStatistics

2013-06-21T14:06:54Z

Lchauvin:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Slicer4-DiceComputation-GUI.png|DiceComputation GUI
Image:DiceComputation-newFeatures.png|New features
</gallery>

==Key Investigators==
* Queen's: Csaba Pinter
* BWH: Laurent Chauvin

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

<h3>Objective</h3>
* Add more label map statistics computation to Dice module
</div>

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

<h3>Approach, Plan</h3>
* Discuss with Csaba to regroup several modules computation statistics on label maps
* New module will allow to compute Dice coefficient, distance map, etc... for several label maps and display results for easy reading
</div>

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

<h3>Progress</h3>
* Implemented label map cropping feature
* Implemented exportation of dice and statistics as csv
* Discussed with Csaba
** Merging modules will be difficult. Lot of their modules use plastimatch.
** Plan to publish plastimatch as non-module extension
** Plan to create CMake auto-download dependency
** When plastimatch will be available in auto-download, try to switch dice algorithm to plastimatch
</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer extension. Repository is here [https://github.com/lchauvin/DiceComputation]

==References==

File:DiceComputation-newFeatures.png

2013-06-21T14:06:03Z

Lchauvin:

2013 Summer Project Week:LabelMapStatistics

2013-06-21T13:50:09Z

Lchauvin: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Slicer4-DiceComputation-GUI.png|DiceComputation GUI
</gallery>

==Key Investigators==
* Queen's: Csaba Pinter
* BWH: Laurent Chauvin

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

<h3>Objective</h3>
* Add more label map statistics computation to Dice module
</div>

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

<h3>Approach, Plan</h3>
* Discuss with Csaba to regroup several modules computation statistics on label maps
* New module will allow to compute Dice coefficient, distance map, etc... for several label maps and display results for easy reading
</div>

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

<h3>Progress</h3>
* Implemented label map cropping feature
* Implemented exportation of dice and statistics as csv
* Discussed with Csaba
** Merging modules will be difficult. Lot of their modules use plastimatch.
** Plan to publish plastimatch as non-module extension
** Plan to create CMake auto-download dependency
** When plastimatch will be available in auto-download, try to switch dice algorithm to plastimatch
</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer extension. Repository is here [https://github.com/lchauvin/DiceComputation]

==References==

2013 Summer Project Week:Liver Trajectory Management

2013-06-21T13:46:45Z

Lchauvin: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Slicer4-PathPlanner-GUI.png|PathPlanner GUI
Image:Slicer4-VisuaLine-GUI.png|VisuaLine GUI
Image:Slicer4-VolumeResliceDriver-GUI.png|VolumeResliceDriver GUI
Image:OpenTrajectoryManager-Planning.png|OpenTrajectoryManager planning panel
Image:OpenTrajectoryManager-Visualization.png|OpenTrajectoryManager visualization panel
</gallery>

==Key Investigators==
* BWH: Laurent Chauvin, Junichi Tokuda

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

<h3>Objective</h3>
* Discuss missing features with people in the community
* Discuss packaging as part of [http://slicerigt.github.io SlicerIGT]
</div>

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

<h3>Approach, Plan</h3>
Currently we have three separate modules:
*[https://github.com/SlicerIGT/PathPlanner PathPlanner]
*[https://github.com/SlicerIGT/VisuaLine VisuaLine]
*[https://github.com/SlicerIGT/VolumeResliceDriver VolumeResliceDriver] (part of SlicerIGT package)
In this week we will
* Create a single package that combines frequently-used functions in the PathPlanner, VisuaLine and VolumeResliceDriver modules.
* We will keep the previously-developed three modules for advanced users.
* Discuss with people interested in this/these modules to implement new features (if requested)
</div>

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

<h3>Progress</h3>
* Created new version of PathPlanner, now regrouping planning, visualization and reslicing
* Discussed with Tamas in order to integrate it to SlicerIGT extension package
** Need to restructure module in order to have the logic (and MRMLNode) available from other module
** Move reslicing part to VolumeResliceDriver and call the logic of VolumeResliceDriver to reslice with ruler
** Implement OpenIGTLink trajectory support
* Will be submit as extension soon (temporary name: OpenTrajectoryManager), waiting to be restructured and included in SlicerIGT
</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer Extension. The repository will be created at [https://github.com/SlicerIGT].

==References==

2013 Summer Project Week:Liver Trajectory Management

2013-06-21T13:45:30Z

Lchauvin: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Slicer4-PathPlanner-GUI.png|PathPlanner GUI
Image:Slicer4-VisuaLine-GUI.png|VisuaLine GUI
Image:Slicer4-VolumeResliceDriver-GUI.png|VolumeResliceDriver GUI
Image:OpenTrajectoryManager-Planning.png|OpenTrajectoryManager planning panel
Image:OpenTrajectoryManager-Visualization.png|OpenTrajectoryManager visualization panel
</gallery>

==Key Investigators==
* BWH: Laurent Chauvin, Junichi Tokuda

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

<h3>Objective</h3>
* Discuss missing features with people in the community
* Discuss packaging as part of [http://slicerigt.github.io SlicerIGT]
</div>

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

<h3>Approach, Plan</h3>
Currently we have three separate modules:
*[https://github.com/SlicerIGT/PathPlanner PathPlanner]
*[https://github.com/SlicerIGT/VisuaLine VisuaLine]
*[https://github.com/SlicerIGT/VolumeResliceDriver VolumeResliceDriver] (part of SlicerIGT package)
In this week we will
* Create a single package that combines frequently-used functions in the PathPlanner, VisuaLine and VolumeResliceDriver modules.
* We will keep the previously-developed three modules for advanced users.
* Discuss with people interested in this/these modules to implement new features (if requested)
</div>

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

<h3>Progress</h3>
* Created new version of PathPlanner, now regrouping planning, visualization and reslicing
* Discussed with Tamas in order to integrate it to SlicerIGT extension package
** Need to restructure module in order to have the logic (and MRMLNode) available from other module
** Move reslicing part to VolumeResliceDriver and call the logic of VolumeResliceDriver to reslice with ruler
** Implement OpenIGTLink trajectory support
* Will be submit as extension soon (temporary name: OpenTrajectoryManager)
</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer Extension. The repository will be created at [https://github.com/SlicerIGT].

==References==

2013 Summer Project Week:Liver Trajectory Management

2013-06-21T13:44:36Z

Lchauvin:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Slicer4-PathPlanner-GUI.png|PathPlanner GUI
Image:Slicer4-VisuaLine-GUI.png|VisuaLine GUI
Image:Slicer4-VolumeResliceDriver-GUI.png|VolumeResliceDriver GUI
Image:OpenTrajectoryManager-Planning.png|OpenTrajectoryManager planning panel
Image:OpenTrajectoryManager-Visualization.png|OpenTrajectoryManager visualization panel
</gallery>

==Key Investigators==
* BWH: Laurent Chauvin, Junichi Tokuda

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

<h3>Objective</h3>
* Discuss missing features with people in the community
* Discuss packaging as part of [http://slicerigt.github.io SlicerIGT]
</div>

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

<h3>Approach, Plan</h3>
Currently we have three separate modules:
*[https://github.com/SlicerIGT/PathPlanner PathPlanner]
*[https://github.com/SlicerIGT/VisuaLine VisuaLine]
*[https://github.com/SlicerIGT/VolumeResliceDriver VolumeResliceDriver] (part of SlicerIGT package)
In this week we will
* Create a single package that combines frequently-used functions in the PathPlanner, VisuaLine and VolumeResliceDriver modules.
* We will keep the previously-developed three modules for advanced users.
* Discuss with people interested in this/these modules to implement new features (if requested)
</div>

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

<h3>Progress</h3>
* Created new version of PathPlanner, now regrouping planning, visualization and reslicing
* Discussed with Tamas in order to integrate it to SlicerIGT extension package
** Need to restructure module in order to have the logic (and MRMLNode) available from other module
** Move reslicing part to VolumeResliceDriver and call the logic of VolumeResliceDriver to reslice with ruler
** Implement OpenIGTLink trajectory support
* Submit it as extension (temporary name: OpenTrajectoryManager)
</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer Extension. The repository will be created at [https://github.com/SlicerIGT].

==References==

2013 Summer Project Week:Liver Trajectory Management

2013-06-21T13:44:05Z

Lchauvin:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Slicer4-PathPlanner-GUI.png|PathPlanner GUI
Image:Slicer4-VisuaLine-GUI.png|VisuaLine GUI
Image:Slicer4-VolumeResliceDriver-GUI.png|VolumeResliceDriver GUI
Image:OpenTrajectoryManager-Planning.png
Image:OpenTrajectoryManager-Visualization.png
</gallery>

==Key Investigators==
* BWH: Laurent Chauvin, Junichi Tokuda

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

<h3>Objective</h3>
* Discuss missing features with people in the community
* Discuss packaging as part of [http://slicerigt.github.io SlicerIGT]
</div>

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

<h3>Approach, Plan</h3>
Currently we have three separate modules:
*[https://github.com/SlicerIGT/PathPlanner PathPlanner]
*[https://github.com/SlicerIGT/VisuaLine VisuaLine]
*[https://github.com/SlicerIGT/VolumeResliceDriver VolumeResliceDriver] (part of SlicerIGT package)
In this week we will
* Create a single package that combines frequently-used functions in the PathPlanner, VisuaLine and VolumeResliceDriver modules.
* We will keep the previously-developed three modules for advanced users.
* Discuss with people interested in this/these modules to implement new features (if requested)
</div>

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

<h3>Progress</h3>
* Created new version of PathPlanner, now regrouping planning, visualization and reslicing
* Discussed with Tamas in order to integrate it to SlicerIGT extension package
** Need to restructure module in order to have the logic (and MRMLNode) available from other module
** Move reslicing part to VolumeResliceDriver and call the logic of VolumeResliceDriver to reslice with ruler
** Implement OpenIGTLink trajectory support
* Submit it as extension (temporary name: OpenTrajectoryManager)
</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer Extension. The repository will be created at [https://github.com/SlicerIGT].

==References==

File:OpenTrajectoryManager-Visualization.png

2013-06-21T13:43:15Z

Lchauvin:

File:OpenTrajectoryManager-Planning.png

2013-06-21T13:42:41Z

Lchauvin:

2013 Summer Project Week

2013-06-21T13:29:01Z

Lchauvin: /* IGT and Device Integration with Slicer */

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

<gallery widths="800px" heights="300px" perrow="1" caption="Lunch in the Amphitheater at Stata, June 20 2013">
Image:Lunch at Project week IMG 0367.JPG|Shade was a popular commodity
</gallery>

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] (Steve Pieper) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans Johnson, Brad Lowekamp)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|
'''9:30-10:30am''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina Kapur)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
'''12pm''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|[http://www.na-mic.org/Wiki/index.php/File:NamicToAmphi.png Lunch in Outdoor Amphitheather!]
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-262]]
|
|<br>----------------------------------------<br>'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Projects''' ==

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

==Some Stats==
73 Projects, 104 Attendees. First time attendees 25.

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


7 projects

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


5 projects

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


8 projects

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


8 projects

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


12 projects

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


3 projects

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


16 projects

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

14 projects

== '''Background''' ==

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 25th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], [http://www.cimit.org CIMIT], and OCAIRO. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

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

== '''Logistics''' ==

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

== '''Preparation''' ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. Participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 13: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

== '''Registrants''' ==

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

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

2013 Summer Project Week:Liver Trajectory Management

2013-06-20T17:21:39Z

Lchauvin: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Slicer4-PathPlanner-GUI.png|PathPlanner GUI
Image:Slicer4-VisuaLine-GUI.png|VisuaLine GUI
Image:Slicer4-VolumeResliceDriver-GUI.png|VolumeResliceDriver GUI
</gallery>

==Key Investigators==
* BWH: Laurent Chauvin, Junichi Tokuda

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

<h3>Objective</h3>
* Discuss missing features with people in the community
* Discuss packaging as part of [http://slicerigt.github.io SlicerIGT]
</div>

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

<h3>Approach, Plan</h3>
Currently we have three separate modules:
*[https://github.com/SlicerIGT/PathPlanner PathPlanner]
*[https://github.com/SlicerIGT/VisuaLine VisuaLine]
*[https://github.com/SlicerIGT/VolumeResliceDriver VolumeResliceDriver] (part of SlicerIGT package)
In this week we will
* Create a single package that combines frequently-used functions in the PathPlanner, VisuaLine and VolumeResliceDriver modules.
* We will keep the previously-developed three modules for advanced users.
* Discuss with people interested in this/these modules to implement new features (if requested)
</div>

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

<h3>Progress</h3>
* Created new version of PathPlanner, now regrouping planning, visualization and reslicing
* Discussed with Tamas in order to integrate it to SlicerIGT extension package
** Need to restructure module in order to have the logic (and MRMLNode) available from other module
** Move reslicing part to VolumeResliceDriver and call the logic of VolumeResliceDriver to reslice with ruler
** Implement OpenIGTLink trajectory support
</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer Extension. The repository will be created at [https://github.com/SlicerIGT].

==References==

2013 Project Week Breakout Session: IGT

2013-06-20T15:08:01Z

Lchauvin:

[[2013_Summer_Project_Week#Agenda|Back to Summer project week Agenda]]

==Discussion Topics==

#First hour - Neurosurgery (10am-11am)
## How to integrate tracked ultrasound calibration in a sterile OR workflow (Tamas, Isaiah, Tina, Alex)
## Ultrasound to ultrasound registration update (Daniel, Matt)
## NAC/NCIGT Collaboration: Intra-procedural image analysis and CaseHub (Steve, Jim)
#Second hour - Prostate (11am-12pm)
## MR-Ultrasound registration update (Demian)
## brainstorm plans for RF data analysis (Jason)
## discuss plans for MR-informed-ultrasound biopsy in AMIGO (Tina, Andriy, Sandy, Clare)
## "Replay" capability for procedures run with Slicer. The questions is basically the capacity of Slicer4 with Plus to enable us to replay real time guidance (minimum of 20Hz for 30 minutes). If No, can Plus platform be extended? (Kirby)
##What would be a useful ultrasound guided surgery phantom? (AAPM working group) (Kirby)
#Third hour? 1-2pm? Technical
## How should be modules organized under IGT? - Is there a need for a collective SlicerIGT extension? (Tamas)
## New features of PLUS 2.0 available from Slicer (Adam/Andras)
## OpenIGTLink update (Junichi)
## ultrasound needle tracking/detection update (Alireza)
## PathPlanner update (Laurent)

2013 Summer Project Week:LabelMapStatistics

2013-06-17T16:21:57Z

Lchauvin:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Slicer4-DiceComputation-GUI.png|DiceComputation GUI
</gallery>

==Key Investigators==
* Queen's: Csaba Pinter
* BWH: Laurent Chauvin

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

<h3>Objective</h3>
* Add more label map statistics computation to Dice module
</div>

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

<h3>Approach, Plan</h3>
* Discuss with Csaba to regroup several modules computation statistics on label maps
* New module will allow to compute Dice coefficient, distance map, etc... for several label maps and display results for easy reading
</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer extension. Repository is here [https://github.com/lchauvin/DiceComputation]

==References==

2013 Summer Project Week:Liver Trajectory Management

2013-06-17T16:19:32Z

Lchauvin:

File:Slicer4-VolumeResliceDriver-GUI.png

2013-06-17T16:19:04Z

Lchauvin:

File:Slicer4-VisuaLine-GUI.png

2013-06-17T16:15:46Z

Lchauvin:

File:Slicer4-PathPlanner-GUI.png

2013-06-17T16:14:53Z

Lchauvin:

2013 Summer Project Week:LabelMapStatistics

2013-06-17T16:12:35Z

Lchauvin:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Slicer4-DiceComputation-GUI.png|DiceComputation GUI
</gallery>

==Key Investigators==
* Queen's: Csaba Pinter
* BWH: Laurent Chauvin

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

<h3>Objective</h3>
* Add more label map statistics computation to Dice module
</div>

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

<h3>Approach, Plan</h3>
* Discuss with Csaba to regroup several modules computation statistics on label maps
* New module will allow to compute Dice coefficient, distance map, etc... for several label maps and display results for easy reading
</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##<b>Extension -- loadable</b>
#Other (Please specify)

==References==

2013 Summer Project Week:LabelMapStatistics

2013-06-17T16:11:15Z

Lchauvin:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:Slicer4-DiceComputation-GUI.png|DiceComputation GUI
</gallery>

==Key Investigators==
* Queen's: Csaba Pinter
* BWH: Laurent Chauvin

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

<h3>Objective</h3>
* Add more label map statistics computation to Dice module
</div>

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

<h3>Approach, Plan</h3>
* Discuss with Csaba to regroup several modules computation statistics on label maps
* New module will allow to compute Dice coefficient, distance map, etc... for several label maps and display results for easy reading
</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==

File:Slicer4-DiceComputation-GUI.png

2013-06-17T16:10:41Z

Lchauvin:

2013 Summer Project Week

2013-06-17T04:09:29Z

Lchauvin: /* IGT and Device Integration with Slicer */

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

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] (Steve Pieper) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans Johnson, Brad Lowekamp)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina Kapur)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|<br>----------------------------------------<br>'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Projects''' ==

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

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

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

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

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

===IGT and Device Integration with Slicer===
* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering for Neurosurgery]] (Lauren O'Donnell)
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Stephen Aylward, Isaiah Norton, Tamas Ungi)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:LabelMapStatistics| Label map statistics]] (Laurent Chauvin, Csaba Pinter)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
* [[2013_Summer_Project_Week:3D_prostate_segmentation_of_Ultrasound_image| Segmentation of Prostate Gland from 3D US for Prostate Interventions]] (Xu Li, Andriy Fedorov, Tina Kapur, William Wells)

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

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

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

== '''Background''' ==

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 25th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], [http://www.cimit.org CIMIT], and OCAIRO. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

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

== '''Logistics''' ==

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

== '''Preparation''' ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. Participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 13: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

== '''Registrants''' ==

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

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

2013 Summer Project Week:LabelMapStatistics

2013-06-17T04:09:09Z

Lchauvin: Created page with '__NOTOC__ <gallery> Image:PW-MIT2013.png|Projects List </gallery> ==Key Investigators== * Queen's: Csaba Pinter * BWH: Laurent Chauvin <di…'

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Queen's: Csaba Pinter
* BWH: Laurent Chauvin

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

<h3>Objective</h3>
* Add more label map statistics computation to Dice module
</div>

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

<h3>Approach, Plan</h3>
* Discuss with Csaba to regroup several modules computation statistics on label maps
* New module will allow to compute Dice coefficient, distance map, etc... for several label maps and display results for easy reading
</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==

2013 Summer Project Week

2013-06-17T04:06:14Z

Lchauvin: /* IGT and Device Integration with Slicer */

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

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] (Steve Pieper) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans Johnson, Brad Lowekamp)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina Kapur)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|<br>----------------------------------------<br>'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Projects''' ==

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

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

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

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

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

===IGT and Device Integration with Slicer===
* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering for Neurosurgery]] (Lauren O'Donnell)
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Stephen Aylward, Isaiah Norton, Tamas Ungi)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:LabelMapStatistics| Label map statistics]] (Laurent Chauvin)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
* [[2013_Summer_Project_Week:3D_prostate_segmentation_of_Ultrasound_image| Segmentation of Prostate Gland from 3D US for Prostate Interventions]] (Xu Li, Andriy Fedorov, Tina Kapur, William Wells)

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

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

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

== '''Background''' ==

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 25th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], [http://www.cimit.org CIMIT], and OCAIRO. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

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

== '''Logistics''' ==

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

== '''Preparation''' ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. Participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 13: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

== '''Registrants''' ==

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

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

2013 Summer Project Week:4DUltrasound

2013-06-17T04:03:41Z

Lchauvin: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Queen's: Tamas Ungi
* BWH: Laurent Chauvin, Junichi Tokuda

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

<h3>Objective</h3>
* Discuss and implement 3D Ultrasound scanner communication with Slicer
* Create a simulator if needed
</div>

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

<h3>Approach, Plan</h3>
* Create scanner simulator using OpenIGTLink (in collaboration with Tamas)
* Display 4D data on Slicer
* Analyze performances
</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==

2013 Summer Project Week:4DUltrasound

2013-06-17T04:03:17Z

Lchauvin:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Queen's: Tamas Ungi
* BWH: Laurent Chauvin, Junichi Tokuda

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

<h3>Objective</h3>
* Discuss and implement 3D Ultrasound scanner communication with Slicer
* Create a simulator if needed
</div>

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

<h3>Approach, Plan</h3>
* Create scanner simulator using OpenIGTLink
* Display 4D data on Slicer
* Analyze performances
</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==

2013 Summer Project Week:Liver Trajectory Management

2013-06-17T04:02:13Z

Lchauvin:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Laurent Chauvin, Junichi Tokuda

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

<h3>Objective</h3>
* Present existing extensions: PathPlanner and VisuaLine
* Discuss about bugs or missing features
* Discuss about packaging (one extension including several modules, include in SlicerIGT, ...)
</div>

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

<h3>Approach, Plan</h3>
* Present extensions currently available
* Create a extension regrouping PathPlanner and VisuaLine
* Discuss with people interested in this/these modules to implement new features (if requested)
</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==

2013 Summer Project Week:4DUltrasound

2013-05-28T14:52:42Z

Lchauvin:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Queen's: Tamas Ungi
* BWH: Laurent Chauvin, Junichi Tokuda

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

<h3>Objective</h3>
* Discuss and implement 3D Ultrasound scanner communication with Slicer
* Create a simulator if needed
</div>

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

<h3>Approach, Plan</h3>

</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==

2013 Summer Project Week:Liver Trajectory Management

2013-05-28T14:50:15Z

Lchauvin:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Laurent Chauvin, Junichi Tokuda

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

<h3>Objective</h3>
* Present existing extensions: PathPlanner and VisuaLine
* Discuss about bugs or missing features
* Discuss about packaging (one extension including several modules, include in SlicerIGT, ...)
</div>

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

<h3>Approach, Plan</h3>

</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==

2013 Summer Project Week:4DUltrasound

2013-05-24T18:09:49Z

Lchauvin: Created page with '__NOTOC__ <gallery> Image:PW-MIT2013.png|Projects List </gallery> ==Key Investigators== * SNR: Laurent Chauvin, Junichi Tokuda <div style=…'

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* SNR: Laurent Chauvin, Junichi Tokuda

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

<h3>Objective</h3>

</div>

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

<h3>Approach, Plan</h3>

</div>

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

<h3>Progress</h3>

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==