NAMIC Wiki - User contributions [en]

2017 Winter Project Week/Organizations

2017-01-13T16:30:00Z

Lauren:

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

</gallery>

==Key Investigators==

* Beatriz Paniagua, Kitware
* Lauren O'Donnell, BWH
* Isaiah Norton, BWH
* Fan Zhang, BWH
* Gregory Sharp, MGH
* Louise Oram, The Intervention Centre-Oslo University Hospital

==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;"
|

* Increase visibility of Slicer* {Projects, Topics, Organizations, Flavors, Solutions} and their training material, webpages, etc., from slicer.org
* Build community
* Increase impact of slicer.org website by showing impressive Slicer* information
|

* Meet and discuss
* Initial mockup of landing page
* Discussion of favorite quotes
** Quality is the enemy of speed

|

* We crashed a CSAIL conference room and used their whiteboard to plot and plan Thursday
* We drafted lists of the following:
** REQUIREMENTS to be a Slicer Solution/Project/Organization
*** open-source repo, specialized functionality, and live project with a contact person responsible for answering user questions
** INFORMATION needed for inclusion on the proposed webpage
*** very short description, icon, institute, Slicer* name, main webpage link, tutorials webpage link
**Brainstorming for NAME of what these should be called
*** Slicer Topics, Projects, Toolkits, Organizations, Bundles, Tools, Flavors, Environments, Solutions
*** Tentative interest in Solutions
* Made a mockup of slicer.org top-level page (see image)
* Discussed including pointers to Slicer Solutions from the training page
|}

==Background and References==

2017 Winter Project Week/Organizations

2017-01-13T16:18:20Z

Lauren:

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

</gallery>

==Key Investigators==

* Beatriz Paniagua, Kitware
* Lauren O'Donnell, BWH
* Isaiah Norton, BWH
* Fan Zhang, BWH
* Gregory Sharp, MGH
* Louise Oram, The Intervention Centre-Oslo University Hospital

==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;"
|

* Increase visibility of Slicer* {Projects, Topics, Organizations, Flavors, Solutions} and their training material, webpages, etc., from slicer.org
* Build community
* Increase impact of slicer.org website by showing impressive Slicer* information
|

* Meet and discuss
* Initial mockup of landing page
* Discussion of favorite quotes
** Quality is the enemy of speed

|

* We crashed a CSAIL conference room and used their whiteboard to plot and plan Thursday
* We drafted lists of the following:
** REQUIREMENTS to be a Slicer Solution/Project/Organization
*** open-source repo, specialized functionality, and live project with a contact person responsible for answering user questions
** INFORMATION needed for inclusion on the proposed webpage
*** very short description, icon, institute, Slicer* name, main webpage link, tutorials webpage link
**Brainstorming for NAME of what these should be called
*** Slicer Topics, Projects, Toolkits, Organizations, Bundles, Tools, Flavors, Environments, Solutions
*** Tentative interest in Solutions
|}

==Background and References==

2017 Winter Project Week/Organizations

2017-01-13T16:17:35Z

Lauren: /* Key Investigators */

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

</gallery>

==Key Investigators==

* Beatriz Paniagua, Kitware
* Lauren O'Donnell, BWH
* Isaiah Norton, BWH
* Fan Zhang, BWH
* Gregory Sharp, MGH
* Louise Oram, The Intervention Centre-Oslo University Hospital

==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;"
|

* Increase visibility of Slicer* {Projects, Topics, Organizations, Flavors, Solutions} and their training material, webpages, etc., from slicer.org
* Build community
* Increase impact of slicer.org website by showing impressive Slicer* information
|

* Meet and discuss
* Initial mockup of landing page
* Discussion of favorite quotes
** Quality is the enemy of speed

|

* We crashed a CSAIL conference room and used their whiteboard to plot and plan Thursday
* We drafted lists of the following:
** requirements to be a Slicer Solution/Project/Organization
*** open-source repo, specialized functionality, and live project with a contact person responsible for answering user questions
** information needed for inclusion on the proposed webpage
*** very short description, icon, institute, Slicer* name, main webpage link, tutorials webpage link
**Brainstorming for name of what these should be called
*** Slicer Topics, Projects, Toolkits, Organizations, Bundles, Tools, Flavors, Environments, Solutions
*** Tentative interest in Solutions
|}

==Background and References==

2017 Winter Project Week/Organizations

2017-01-12T22:18:17Z

Lauren:

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

</gallery>

==Key Investigators==


==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;"
|

* Increase visibility of Slicer* {Projects, Topics, Organizations, Flavors, Solutions} and their training material, webpages, etc., from slicer.org
* Build community
* Increase impact of slicer.org website by showing impressive Slicer* information
|

* Meet and discuss
* Initial mockup of landing page
* Discussion of favorite quotes
** Quality is the enemy of speed

|

* We crashed a CSAIL conference room and used their whiteboard to plot and plan Thursday
* We drafted lists of the following:
** requirements to be a Slicer Solution/Project/Organization
*** open-source repo, specialized functionality, and live project with a contact person responsible for answering user questions
** information needed for inclusion on the proposed webpage
*** very short description, icon, institute, Slicer* name, main webpage link, tutorials webpage link
**Brainstorming for name of what these should be called
*** Slicer Topics, Projects, Toolkits, Organizations, Bundles, Tools, Flavors, Environments, Solutions
*** Tentative interest in Solutions
|}

==Background and References==

File:Whiteboardoflife.jpg

2017-01-12T22:17:44Z

Lauren:

File:2017-01-12 16.39.44 (1).jpg

2017-01-12T22:16:08Z

Lauren:

2017 Winter Project Week/Organizations

2017-01-12T22:15:04Z

Lauren:

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

</gallery>

==Key Investigators==


==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;"
|

* Increase visibility of Slicer* {Projects, Topics, Organizations, Flavors, Solutions} and their training material, webpages, etc., from slicer.org
* Build community
* Increase impact of slicer.org website by showing impressive Slicer* information
|

* Meet and discuss
* Initial mockup of landing page
* Discussion of favorite quotes
** Quality is the enemy of speed

|

* We crashed a CSAIL conference room and used their whiteboard to plot and plan Thursday
* We drafted lists of the following:
** requirements to be a Slicer Solution/Project/Organization
*** open-source repo, specialized functionality, and live project with a contact person responsible for answering user questions
** information needed for inclusion on the proposed webpage
*** very short description, icon, institute, Slicer* name, main webpage link, tutorials webpage link
**Brainstorming for name of what these should be called
*** Slicer Topics, Projects, Toolkits, Organizations, Bundles, Tools, Flavors, Environments, Solutions
*** Tentative interest in Solutions
|}

==Background and References==

2017 Winter Project Week/Organizations

2017-01-12T22:11:56Z

Lauren: /* Project Description */

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

</gallery>

==Key Investigators==


==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;"
|

* Increase visibility of Slicer* {Projects, Topics, Organizations, Flavors, Solutions} and their training material, webpages, etc., from slicer.org
* Build community
* Increase impact of slicer.org website by showing impressive Slicer* information
|

* Meet and discuss
* Initial mockup of landing page
|

* We crashed a CSAIL conference room and used their whiteboard to plot and plan Thursday
* We drafted lists of the following:
** requirements to be a Slicer Solution/Project/Organization
*** open-source repo, specialized functionality, and live project with a contact person responsible for answering user questions
** information needed for inclusion on the proposed webpage
*** very short description, icon, institute, Slicer* name, main webpage link, tutorials webpage link
**Brainstorming for name of what these should be called
*** Slicer Topics, Projects, Toolkits, Organizations, Bundles, Tools, Flavors, Environments, Solutions
*** Tentative interest in Solutions
|}

==Background and References==

2017 Winter Project Week/Organizations

2017-01-12T22:11:06Z

Lauren:

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

</gallery>

==Key Investigators==


==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;"
|

* Increase visibility of Slicer* {Projects, Topics, Organizations, Flavors, Solutions} and their training material, webpages, etc., from slicer.org
* Build community
* Increase impact of slicer.org website by showing impressive Slicer* information
|

*
|

* We crashed a CSAIL conference room and used their whiteboard to plot and plan Thursday
* We drafted lists of the following:
** requirements to be a Slicer Solution/Project/Organization
*** open-source repo, specialized functionality, and live project with a contact person responsible for answering user questions
** information needed for inclusion on the proposed webpage
*** very short description, icon, institute, Slicer* name, main webpage link, tutorials webpage link
**Brainstorming for name of what these should be called
*** Slicer Topics, Projects, Toolkits, Organizations, Bundles, Tools, Flavors, Environments, Solutions
*** Tentative interest in Solutions
|}

==Background and References==

2017 Winter Project Week

2017-01-12T22:04:17Z

Lauren:

__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)
*'''Transportation:''' Public transportation is highly encouraged, as no parking permits will be issued by MIT. For a list of local garages, please see [http://web.mit.edu/facilities/transportation/parking/visitors/public_parking.html here]
*'''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]]

== Deep Learning and GPUs ==
#[[2017 Winter Project Week/Deep Learning for Medical Image Computation| Deep Learning for Medical Image Computing]] (Tina Kapur)
#[[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Paolo Zaffino, Ziyang Wang, Guillaume Pernelle, Tina Kapur)
#[[2017 Winter Project Week/DeepInfer| DeepInfer: Open-source Deep Learning Deployment Toolkit]] (Alireza Mehrtash, Mehran Pesteie, Yang (Silvia) Yixin, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)
#[[2017 Winter Project Week/Diffusely abnormal white matter segmentation with 3d U-net| Diffusely abnormal white matter segmentation with 3d U-net]] (Mohsen Ghafoorrian, Bram Platel, Sandy Wells, Tina Kapur, Charles Guttmann)
# [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)
#[[2017 Winter Project Week/An open-source tool to classify TMJ OA condyles | An open-source tool to classify TMJ OA condyles]] (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)
#[[2017 Winter Project Week/Evaluate Deep Learning for binary cancer legion classification | Evaluate Deep Learning for binary cancer lesion classification]] (Curt Lisle)
#[[2017 Winter Project Week/Convolutional neural nets for lung cancer survival prediction | Convolutional neural nets for lung cancer survival prediction]] (Ahmed Hosny, Chintan Parmar, Roman Zeleznik, Hugo Aerts)
#[[2017 Winter Project Week/Population Based Image Imputation | Population Based Image Imputation]] (Adrian Dalca, Katie Bouman, Mert Sabuncu, Polina Golland)

== 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/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, 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/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)
#[[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper)
#[[2017 Winter Project Week/Electron App to add, navigate and visualize DICOM images | Electron App to add, navigate and visualize DICOM images]] (Smruti Padhy, Satrajit Ghosh, Mathias Goncalves)
#[[2017 Winter Project Week/AMI: A 3D Medical Imaging Javascript Library | AMI: A 3D Medical Imaging Javascript Library]] (Rudolph Pienaar, Jorge Luis Bernal Rusiel, Nicolas Rannou, Teodora Szasz)
#[[2017_Winter_Project_Week/MedicalVisualizerUsingParaViewWeb | Medical Visualizer using ParaViewWeb]] (Teodora Szasz)

== 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/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
#[[2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction| 3D surgical planning solution for autologous breast reconstruction]] (Michael Chae, Andras Lasso, David Garcia, Julian Smith, Warren Rozen, David Hunter-Smith)
#[[2017 Winter Project Week/Intraoperative_Functional_Visualization | Visualization Concept for Intraoperative Use of Functional Mapping Data ]] (Anna Roethe, Rebekka Lauer, Prashin Unadkat, Sarah Frisken)

==dMRI==
#[[2017 Winter Project Week/WhiteMatterAnalysis | Fiber endpoint analysis for neurosurgical planning]] (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-Fredrik Westin)
#[[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Shun Gong, Ye Wu, Isaiah Norton, Fan Zhang, Lauren J. O'Donnell)
#[[2017 Winter Project Week/DiPy_in_Slicer | WMA & 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)

==Quantitative Imaging Informatics==
#[[2017 Winter Project Week/dcmqi | dcmqi library]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper, Teodora Szasz)
#[[2017 Winter Project Week/QuantitativeReporting | DICOM QuantitativeReporting]] (Christian Herz, Andrey Fedorov, Andras Lasso, Csaba Pinter)
#[[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christophe 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)

== Shape Analysis, Segmentation ==
#[[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
#[[2017 Winter Project Week/MandibularRegression | Mandibular and maxillary Shape Regression ]] (Beatriz Paniagua, Clement Mirabel, Priscille de Dumast, James Fishbaugh, Lucia Cevidanes, Daniella Garib)
#[[2017 Winter Project Week/Slicer_VR | Slicer + VR = <3]] (Adam Rankin, Andras Lasso, Ryan D'Souza (NDI), Matthew Jolley (Children's Hospital of Philadelphia), Kitware+Slicer dev (JC,JFinet,etc...)
#[[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
#[[2017 Winter Project Week/GeodesicSegmentationandLungtumorAnalysis| Geodesic Segmentation and Lung tumor Analysis]] (Patmaa S,)
#[[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov, Alireza Mehrtash, Christian Hansen, Teodora Szasz)
#[[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)
#[[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)
#[[2017 Winter Project Week/CoronarySegmentationTool| Automatic and Manual Segmentation Tool of Coronary Artery from CTA imaging]] (Haoyin Zhou, Jayender Jagadeesan)

== Infrastructure ==
#[[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)
#[[2017 Winter Project Week/ImprovementsToSegmentEditor | Improvements to Segment Editor]] (Csaba Pinter, Andras Lasso)
#[[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
#[[2017 Winter Project Week/UpdatingCommunityForums | Updating Slicer Community Infrastructure (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)
#[[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
#[[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Pieper)
#[[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault)
#[[2017 Winter Project Week/Integrative_Intraoperative_Interface | Integrative Interface for Intraoperative Software Applications ]] (Anna Roethe, Rebekka Lauer, Prashin Unadkat, Sarah Frisken)
#[[2017 Winter Project Week/Organizations | Slicer* Community Topics, Projects, Flavors: The SLICERVERSE ]] (Beatriz Paniagua, Lauren O'Donnell, Isaiah Norton, Gregory Sharp)

==Training and Dissemination==
#[[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)
#[[2017 Winter Project Week/2017 NVIDIA Demo Contest|NVIDIA Demo Contest]] (Abdul Halabi, Abel Brown)
#[[2017 Winter Project Week/2017 Winter Project Week Surgery|Project Week Survey]] (Krisztina Fischer, Tina Kapur)
#[[2017 Winter Project Week/Next project week| Next project week: PW#25]] (Paolo Zaffino, Maria Francesca Spadea, Tina Kapur)

= '''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].

# Aman Shboul, Zaina :: Old Dominion University
# 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
# Chen, Longquan :: Surgical Planning Lab
# Dalca, Adrian :: Massachusetts Institute of Technology
# DiPrima, Tammy :: Stony Brook University
# Drouin, Simon :: Montreal Neurological Institute
# Fan, Zhipeng :: Brigham and Women's Hospital
# Fedorov, Andriy :: Brigham and Women's Hospital
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.
# Fishbaugh, James :: New York University
# Frank, Tobias :: Leibniz Universität Hannover
# Frisken, Sarah :: Brigham and Women's Hospital
# García Mato, David :: Queen´s University / Universidad Carlos III de Madrid
# Ghafoorian, Mohsen :: Brigham and Women's Hospital
# Ghosh, Satrajit :: Massachusetts Institute of Technology
# Girault, Alexis :: Kitware, Inc.
# Golland, Polina :: Massachusetts Institute of Technology
# Gollub, Randy :: Massachusetts General Hospital
# Goncalves, Mathias :: Massachusetts Institute of Technology
# Gong, Shun :: Brigham and Women's Hospital
# Guerrier de Dumast, Priscille :: University of Michigan
# Halle, Michael :: Brigham and Women's Hospital
# Harris, Gordon :: Massachusetts General Hospital
# Helba, Brian :: Kitware, Inc.
# Herz, Christian :: Brigham and Women's Hospital
# Hong, Sungmin :: New York University
# Hosny, Ahmed :: Dana-Farber
# Jagadeesan, Jayender :: Brigham and Women's Hospital
# Jarecka, Dorota :: Massachusetts Institute of Technology
# Jensen, Henrik G. :: University of Copenhagen
# Kaczmarzyk, Jakub :: Massachusetts Institute of Technology
# Kapur, Tina :: Brigham and Women's Hospital
# Kennedy, David :: UMass Medical School
# 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
# Mousavi, Parvin :: Brigham and Women's Hospital
# Nitsch, Jennifer :: University of Bremen
# Norton, Isaiah :: Brigham and Women's Hospital
# O'Donnell, Lauren :: Brigham and Women's Hospital
# Onieva, Jorge :: Brigham and Women's Hospital
# Oram, Louise :: The Intervention Centre-Oslo University Hospital
# Padhy, Smruti :: Massachusetts Institute of Technology
# Paniagua, Beatriz :: Kitware, Inc.
# Parmar, Chintan :: DFCI-Harvard Medical School
# Peled, Sharon :: Brigham and Women's Hospital
# Pienaar, Rudolph :: Boston Children's Hospital
# Pieper, Steve :: Isomics, Inc.
# Pinter, Csaba :: Queen's University
# Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School
# Prieto, Juan :: NIRAL
# 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
# Ross, James :: Brigham and Women's Hospital
# Szczepankiewicz, Filip :: Lund University
# Sharp, Gregory :: Massachusetts General Hospital
# Sridharan, Patmaa :: University of Pennsylvania-CBICA
# Szasz, Teodora :: University of Chicago
# Tokuda, Junichi :: Brigham and Women's Hospital
# Unadkat, Prashin :: Brigham and Women's Hospital
# Van Griethuysen , Joost :: Netherlands Cancer Institute
# Vidyaratne, Lasitha :: Old Dominion University
# Wang, Yaofei :: Brigham and Women's Hospital
# Wang, Ziyang :: Brigham and Women's Hospital
# Wei, Dawei :: Brigham and Women's Hospital
# Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School
# Woo, Jonghye :: Massachusetts General Hospital
# Xu, Wanxin :: Brigham and Women's Hospital
# 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, Hongtao :: Hebei General Hospital
# Zhang, Miaomiao :: Massachusetts Institute of Technology
# Zhang, Yuqian :: Brigham and Women's Hospital
# Zhou, Haoyin :: Brigham and Women's Hospital
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital

2017 Winter Project Week/Organizations

2017-01-12T22:03:17Z

Lauren: 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

2017-01-12T22:02:51Z

Lauren:

__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)
*'''Transportation:''' Public transportation is highly encouraged, as no parking permits will be issued by MIT. For a list of local garages, please see [http://web.mit.edu/facilities/transportation/parking/visitors/public_parking.html here]
*'''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]]

== Deep Learning and GPUs ==
#[[2017 Winter Project Week/Deep Learning for Medical Image Computation| Deep Learning for Medical Image Computing]] (Tina Kapur)
#[[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Paolo Zaffino, Ziyang Wang, Guillaume Pernelle, Tina Kapur)
#[[2017 Winter Project Week/DeepInfer| DeepInfer: Open-source Deep Learning Deployment Toolkit]] (Alireza Mehrtash, Mehran Pesteie, Yang (Silvia) Yixin, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)
#[[2017 Winter Project Week/Diffusely abnormal white matter segmentation with 3d U-net| Diffusely abnormal white matter segmentation with 3d U-net]] (Mohsen Ghafoorrian, Bram Platel, Sandy Wells, Tina Kapur, Charles Guttmann)
# [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)
#[[2017 Winter Project Week/An open-source tool to classify TMJ OA condyles | An open-source tool to classify TMJ OA condyles]] (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)
#[[2017 Winter Project Week/Evaluate Deep Learning for binary cancer legion classification | Evaluate Deep Learning for binary cancer lesion classification]] (Curt Lisle)
#[[2017 Winter Project Week/Convolutional neural nets for lung cancer survival prediction | Convolutional neural nets for lung cancer survival prediction]] (Ahmed Hosny, Chintan Parmar, Roman Zeleznik, Hugo Aerts)
#[[2017 Winter Project Week/Population Based Image Imputation | Population Based Image Imputation]] (Adrian Dalca, Katie Bouman, Mert Sabuncu, Polina Golland)

== 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/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, 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/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)
#[[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper)
#[[2017 Winter Project Week/Electron App to add, navigate and visualize DICOM images | Electron App to add, navigate and visualize DICOM images]] (Smruti Padhy, Satrajit Ghosh, Mathias Goncalves)
#[[2017 Winter Project Week/AMI: A 3D Medical Imaging Javascript Library | AMI: A 3D Medical Imaging Javascript Library]] (Rudolph Pienaar, Jorge Luis Bernal Rusiel, Nicolas Rannou, Teodora Szasz)
#[[2017_Winter_Project_Week/MedicalVisualizerUsingParaViewWeb | Medical Visualizer using ParaViewWeb]] (Teodora Szasz)

== 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/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
#[[2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction| 3D surgical planning solution for autologous breast reconstruction]] (Michael Chae, Andras Lasso, David Garcia, Julian Smith, Warren Rozen, David Hunter-Smith)
#[[2017 Winter Project Week/Intraoperative_Functional_Visualization | Visualization Concept for Intraoperative Use of Functional Mapping Data ]] (Anna Roethe, Rebekka Lauer, Prashin Unadkat, Sarah Frisken)

==dMRI==
#[[2017 Winter Project Week/WhiteMatterAnalysis | Fiber endpoint analysis for neurosurgical planning]] (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-Fredrik Westin)
#[[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Shun Gong, Ye Wu, Isaiah Norton, Fan Zhang, Lauren J. O'Donnell)
#[[2017 Winter Project Week/DiPy_in_Slicer | WMA & 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)

==Quantitative Imaging Informatics==
#[[2017 Winter Project Week/dcmqi | dcmqi library]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper, Teodora Szasz)
#[[2017 Winter Project Week/QuantitativeReporting | DICOM QuantitativeReporting]] (Christian Herz, Andrey Fedorov, Andras Lasso, Csaba Pinter)
#[[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christophe 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)

== Shape Analysis, Segmentation ==
#[[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
#[[2017 Winter Project Week/MandibularRegression | Mandibular and maxillary Shape Regression ]] (Beatriz Paniagua, Clement Mirabel, Priscille de Dumast, James Fishbaugh, Lucia Cevidanes, Daniella Garib)
#[[2017 Winter Project Week/Slicer_VR | Slicer + VR = <3]] (Adam Rankin, Andras Lasso, Ryan D'Souza (NDI), Matthew Jolley (Children's Hospital of Philadelphia), Kitware+Slicer dev (JC,JFinet,etc...)
#[[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
#[[2017 Winter Project Week/GeodesicSegmentationandLungtumorAnalysis| Geodesic Segmentation and Lung tumor Analysis]] (Patmaa S,)
#[[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov, Alireza Mehrtash, Christian Hansen, Teodora Szasz)
#[[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)
#[[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)
#[[2017 Winter Project Week/CoronarySegmentationTool| Automatic and Manual Segmentation Tool of Coronary Artery from CTA imaging]] (Haoyin Zhou, Jayender Jagadeesan)

== Infrastructure ==
#[[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)
#[[2017 Winter Project Week/ImprovementsToSegmentEditor | Improvements to Segment Editor]] (Csaba Pinter, Andras Lasso)
#[[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
#[[2017 Winter Project Week/UpdatingCommunityForums | Updating Slicer Community Infrastructure (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)
#[[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
#[[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Pieper)
#[[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault)
#[[2017 Winter Project Week/Integrative_Intraoperative_Interface | Integrative Interface for Intraoperative Software Applications ]] (Anna Roethe, Rebekka Lauer, Prashin Unadkat, Sarah Frisken)
#[[2017 Winter Project Week/Organizations | Slicer* Community Topics, Projects, Flavors ]] (Anna Roethe, Rebekka Lauer, Prashin Unadkat, Sarah Frisken)

==Training and Dissemination==
#[[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)
#[[2017 Winter Project Week/2017 NVIDIA Demo Contest|NVIDIA Demo Contest]] (Abdul Halabi, Abel Brown)
#[[2017 Winter Project Week/2017 Winter Project Week Surgery|Project Week Survey]] (Krisztina Fischer, Tina Kapur)
#[[2017 Winter Project Week/Next project week| Next project week: PW#25]] (Paolo Zaffino, Maria Francesca Spadea, Tina Kapur)

= '''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].

# Aman Shboul, Zaina :: Old Dominion University
# 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
# Chen, Longquan :: Surgical Planning Lab
# Dalca, Adrian :: Massachusetts Institute of Technology
# DiPrima, Tammy :: Stony Brook University
# Drouin, Simon :: Montreal Neurological Institute
# Fan, Zhipeng :: Brigham and Women's Hospital
# Fedorov, Andriy :: Brigham and Women's Hospital
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.
# Fishbaugh, James :: New York University
# Frank, Tobias :: Leibniz Universität Hannover
# Frisken, Sarah :: Brigham and Women's Hospital
# García Mato, David :: Queen´s University / Universidad Carlos III de Madrid
# Ghafoorian, Mohsen :: Brigham and Women's Hospital
# Ghosh, Satrajit :: Massachusetts Institute of Technology
# Girault, Alexis :: Kitware, Inc.
# Golland, Polina :: Massachusetts Institute of Technology
# Gollub, Randy :: Massachusetts General Hospital
# Goncalves, Mathias :: Massachusetts Institute of Technology
# Gong, Shun :: Brigham and Women's Hospital
# Guerrier de Dumast, Priscille :: University of Michigan
# Halle, Michael :: Brigham and Women's Hospital
# Harris, Gordon :: Massachusetts General Hospital
# Helba, Brian :: Kitware, Inc.
# Herz, Christian :: Brigham and Women's Hospital
# Hong, Sungmin :: New York University
# Hosny, Ahmed :: Dana-Farber
# Jagadeesan, Jayender :: Brigham and Women's Hospital
# Jarecka, Dorota :: Massachusetts Institute of Technology
# Jensen, Henrik G. :: University of Copenhagen
# Kaczmarzyk, Jakub :: Massachusetts Institute of Technology
# Kapur, Tina :: Brigham and Women's Hospital
# Kennedy, David :: UMass Medical School
# 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
# Mousavi, Parvin :: Brigham and Women's Hospital
# Nitsch, Jennifer :: University of Bremen
# Norton, Isaiah :: Brigham and Women's Hospital
# O'Donnell, Lauren :: Brigham and Women's Hospital
# Onieva, Jorge :: Brigham and Women's Hospital
# Oram, Louise :: The Intervention Centre-Oslo University Hospital
# Padhy, Smruti :: Massachusetts Institute of Technology
# Paniagua, Beatriz :: Kitware, Inc.
# Parmar, Chintan :: DFCI-Harvard Medical School
# Peled, Sharon :: Brigham and Women's Hospital
# Pienaar, Rudolph :: Boston Children's Hospital
# Pieper, Steve :: Isomics, Inc.
# Pinter, Csaba :: Queen's University
# Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School
# Prieto, Juan :: NIRAL
# 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
# Ross, James :: Brigham and Women's Hospital
# Szczepankiewicz, Filip :: Lund University
# Sharp, Gregory :: Massachusetts General Hospital
# Sridharan, Patmaa :: University of Pennsylvania-CBICA
# Szasz, Teodora :: University of Chicago
# Tokuda, Junichi :: Brigham and Women's Hospital
# Unadkat, Prashin :: Brigham and Women's Hospital
# Van Griethuysen , Joost :: Netherlands Cancer Institute
# Vidyaratne, Lasitha :: Old Dominion University
# Wang, Yaofei :: Brigham and Women's Hospital
# Wang, Ziyang :: Brigham and Women's Hospital
# Wei, Dawei :: Brigham and Women's Hospital
# Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School
# Woo, Jonghye :: Massachusetts General Hospital
# Xu, Wanxin :: Brigham and Women's Hospital
# 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, Hongtao :: Hebei General Hospital
# Zhang, Miaomiao :: Massachusetts Institute of Technology
# Zhang, Yuqian :: Brigham and Women's Hospital
# Zhou, Haoyin :: Brigham and Women's Hospital
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital

2017 Winter Project Week

2016-12-27T15:40:03Z

Lauren: /* Agenda */

2017 Winter Project Week/SlicerDMRIDocumentationAndTesting

2016-12-27T15:37:56Z

Lauren:

2017 Winter Project Week/SlicerDMRIDocumentationAndTesting

2016-12-27T15:26:29Z

Lauren:

2016 Summer Project Week/DICOM Tractography Results

2016-06-25T09:53:40Z

Lauren: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:DICOM_tracto.png
</gallery>

==Key Investigators==
* Michael Onken
* Isaiah Norton (remotely)
* Lauren O'Donnell

==Project Description==

This software project deals with saving tractography data in DICOM.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Add API to DCMTK (library called dcmtract) which allows easy creation and reading of DICOM Tractography Results objects
* Tractography Results objects have been introduced in DICOM with [ftp://medical.nema.org/medical/dicom/final/sup181_ft_TractographyResultsStorage.pdf Supplement 181] in 2015.
* From the Supplement: Tractography results are usually calculated based on magnetic resonance diffusion tractography (MR DT). A tracking algorithm produces tracks (i.e. fibers), which are collected into track sets. A track contains the set of x, y and z coordinates of each point making up the track. Depending upon the algorithm and software used, additional quantities like Fractional Anisotropy (FA) values or color etc. may be associated with the data, by track set, track or point, either to facilitate further filtering or for clinical use. Descriptive statistics of quantities like FA may be associated with the data by track set or track.
* This week we will work to discuss and finalize the API of the the library and prepare it for checkin to DCMTK
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discuss existing API and refine it if required
* Discuss naming consistency (track vs tract)
* Discuss how to handle features currently missing from the standard but supported in Slicer (should we prepare a list of conventions to be the basis for a future DICOM change proposal).
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* There is already a version of the dcmtract library in DCMTK
* Productive conversations about coordinate systems, plan for DICOM in Slicer, release next week of DICOM tracts on SlicerDMRI site
</div>
</div>

2016 Summer Project Week

2016-06-25T09:43:13Z

Lauren:

__NOTOC__

[[image:PW-Summer2016.png|300px]]
<br><br>

<font color="maroon" size="5">Please fill in the survey about project weeks today!</font>

<font size="5">
[https://hms.az1.qualtrics.com/jfe/form/SV_6gK6BFe4Ivfo9RH click here]
</font>

<br><br>

<font color="maroon" size="5">Please hold January 9-13, 2017 for Project Week#24 at MIT. </font>

<br><br>

<font color="maroon" size="5">Please hold June 16-24 for Project Week#25 in Europe. It will be either right before IPCAI (i.e June ~16-20) or right after CARS! (~June 25-29)</font>

<br><br>

<br><br>

<font color="maroon" size="5"> Please add photos from this week here: https://goo.gl/photos/Dhx6Fdei27NZe2rX9

<br><br>

</font>

=Welcome to the web page for the 23rd Project Week!=
The 23rd Project Week open source hackathon is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS) and the [http://www.ipcai.org/ IPCAI 2016] conferences in Heidelberg, Germany. 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].

='''Agenda'''=
<font color="maroon">Please note that on '''Tuesday''' there is no organized Project Week activity due to IPCAI @ CARS</font>
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:7%" |Time
!style="width:15%" |Monday, June 20 <br> [https://goo.gl/maps/e3ZbcsM5KC82 DKFZ]
!style="width:3%" |Tuesday, June 21 <br> IPCAI
!style="width:15%" |Wednesday, June 22 <br> Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Thursday, June 23 <br> Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Friday, June 24 <br> Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Saturday, June 25 <br> Congress Hall of CARS, Room Trübnersaal
|-
|bgcolor="#ffffdd"|'''9:00am-10:00am'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="8"|
|bgcolor="#ffffff"|[[{{FULLPAGENAME}}/Workshop_on_Shared_Software_Platform_for_Ultrasound-Guided_Medical_Interventions|Workshop: Ultrasound-guided interventions software platform (all day)]]
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''10:00am-10:30am'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''10:30-12pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| 10:30am-12pm: Progress Review
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch and adjourn
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffff"| Welcome! <br> Project Introductions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="4"|
|-
|bgcolor="#ffffdd"|'''3:00pm-3:30pm'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''3:30pm-5:00pm'''
|bgcolor="#ffffff"| What does a Neurosurgeon need from technologists? (Alexandra Golby, MD)
|bgcolor="#ffffff"| [[{{FULLPAGENAME}}/Breakout Session Slicer Extensions|Breakout Session: Slicer Extensions]] (JC, Steve)
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|}

='''Projects'''=

* Note: Please use this [[2016_Summer_Project_Week_Template | template]] to create project pages

=== Worldwide Ultrasound Navigation ===
Over the last several PWs, an international group has emerged for collaborative specification and development of ultrasound-based navigation for surgical and interventional radiology applications. This group represents the leadership of ultrasound navigation technology from Queens University (PERK Lab, PLUS: Andras Lasso, Tamas Ungi, Csaba Pinter, Gabor Fichtinter), Montreal Neurologic Institute (Simon Drouin), Brigham and Women's Hospital/HMS (William Wells, Steve Pieper, Sarah Frisken), Robarts Research Institute, Western University (Terry Peters, Adam Rankin), Trondheim University and SINTEF (CustusX: Christian Askeland, Frank Lindseth).

* [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Thomas Kirchner, Janne Beate Bakeng, Ole Vegard Solberg, Jon Eiesland)
* [[2016 Summer Project Week/Guided Ultrasound Calibration | Guided Ultrasound Calibration]] (Elvis Chen, Inês Prata, Tamas Ungi)
* [[2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink | Integrating PLUS in Applications using OpenIGTLink]] (Christian Askeland, Janne Beate Bakeng, Ole Vegard Solberg, Jon Eiesland, Longquan Chen, Simon Drouin)

=== Simplified Human-Computer Interactions for Intra-Operative Usage===
This theme focuses on infrastructure for simplified human-computer interactions for intra-operative usage. This includes Guidelets, simplified graphical user interfaces that can access the same backend as 3D Slicer; as well as interfaces for virtual reality/augmented reality devices from the consumer market that are that are improving by leaps and bounds and show promise for surgical use.

* [[2016 Summer Project Week/Guidelets | Guidelets (Slicelets for IGT)]] (Tamas Ungi, Andras Lasso, Thomas Vaughan)
* [[2016 Summer Project Week/Slicelet For Ultrasound Acquisition | Slicelet for Ultrasound Acquisition]] (Sarah Frisken, Prashin Unadkat, Steve Pieper, Anna Roethe)
* [[2016 Summer Project Week/OpenVR_integration | OpenVR Integration]] (Adam Rankin, Andras Lasso)
* [[2016 Summer Project Week/VRPN Integration | VRPN Integration]] (Dženan Zukić)
* [[2016 Summer Project Week/AR with a tablet device in the surgical room | AR with a Tablet Device in the Surgical Room]] (David García, Javier Pascau)
* [[2016 Summer Project Week/Auditory Display | Auditory Display Integration]] (David Black, Sarah Frisken, Christian Hansen, Longquan Chen)

===Machine Learning for IGT===
This theme applies concepts from machine learning to image-guided therapy, including the application of convolutional neural networks for segmentation of mechanically implanted devices during surgery, and the use of Gaussian processes for estimation of uncertainty in image-fusion.

* [[2016 Summer Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Guillaume Pernelle, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea, Tina Kapur)
* [[2016 Summer Project Week/Uncertainty-aware Information Fusion | Uncertainty-aware Information Fusion for Real-time Soft Tissue Motion Estimation]] (Bojan Kocev, Sarah Frisken, Christian Hansen, William Wells)

===IGT Other===
* [[2016 Summer Project Week/SliceTracker | SliceTracker for Data Collection and Prostate Biopsy Support ]] (Christian Herz, Peter Behringer, Andrey Fedorov)
* [[2016 Summer Project Week/Intra-procedural prostate motion characterization | Prostate Motion Characterization ]] (Peter Behringer, Christian Herz, Andrey Fedorov)
* [[2016 Summer Project Week/Structural-functional measurements | Structural - Functional Relationship Measurements of Tractography Data with fMRI ]] (Yannick Suter, Lauren J. O'Donnell)
* [[2016 Summer Project Week/Sacral Neuromodulation | Sacral Neuromodulation ]] (Rocío López, Javier Pascau, Tamas Ungi)
* [[2016 Summer Project Week/Histological Brain Atlas | Tool for the construction of an integrated brain atlas based on histology and MRI to aid Deep Brain Stimulation]] (Fernando Pérez García)
* [[2016 Summer Project Week/Integrating/Using OpenIGTLink for the communications of Robotics devices | Integrating/Using OpenIGTLink for the Communications of Robotics Devices]] (Scheherazade Kraß, Longquan Chen)
* [[2016 Summer Project Week/Intraoperative Functional Guidance workflows in Neurosurgery | Intraoperative Functional Guidance Workflows in Neurosurgery]] (Prashin Unadkat, Sarah Frisken, Anna Roethe, Christian Hansen)

=== Informatics ===
This theme deals with creating data formats to enable medical image informatics. Led by the [http://qiicr.org/about.html QIICR project], the results will be made available in the DICOM for Quantitative Imaging (DCMQI) Library for sharing quantitative image-processing results in a standardized way.

* [[2016 Summer Project Week/dcmqi | DICOM for Quantitative Imaging (dcmqi) Library]] (Andrey Fedorov, Christian Herz, Marco Nolden, Hans Meine, Csaba Pinter, Steve Pieper, et al)
* [[2016 Summer Project Week/DICOM Parametric Maps | Finalizing DICOM Parametric Map Implementation in DCMTK for QIICR project]] (Michael Onken, Jan Schlamelcher, Andrey Fedorov, Christian Herz)
* [[2016 Summer Project Week/MeVisLab SEG Colors | Support Reading and Writing DICOM Tags for SEG Colors]] (Hans Meine, Andrey Fedorov)
* [[2016 Summer Project Week/Segmentation Editor and Terminology | Segmentation Editor and Terminology]] (Nicole Aucoin, Andrey Fedorov, Csaba Pinter, Andras Lasso, Marco Nolden, Christian Herz)

=== Infrastructure ===
Improvements to the core functionality of widely used open source tools is an on-going theme.

* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)
* [[2016 Summer Project Week/3D Lasso Selection | Implementation and Testing Performance of 3-D Lasso Selection within the Segmentation Editor Infrastructure ]] (Davide Punzo, Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2016 Summer Project Week/Segmentations Integration | Integration of Segmentations Infrastructure and Related Modules to Slicer Core]] (Csaba Pinter, Andras Lasso)
* [[2016 Summer Project Week/DICOM Tractography Results | Finalizing DICOM Tractography Results Implementation in DCMTK for BWH Project]] (Lauren O'Donnell, Isaiah Norton, Michael Onken)
* [[2016 Summer Project Week/Curve and Surface Creation from Fiducials|Curve and Surface Creation from Fiducials]] (Thomas Vaughan, Junichi Tokuda)
* [[2016 Summer Project WEB and 3D DICOM viewer to the rest of us]] (Koji Kobayashi, Steve Pieper)
* [[2016 Summer Project Week/CommonGL|CommonGL: GPU Rendering and Computation]] (Steve Pieper, Christian Askeland, Andra Lasso, Simon Drouin, Fernando Pérez García)

=== Tutorial===
Creation of tutorials and documentation is an on-going theme.

* [[2016 Summer Project Week/SlicerDMRIDocumentation | Tutorials and Documentation in SlicerDMRI]] (Lauren J. O'Donnell, Fan Zhang, Isaiah Norton)
* [[2016 Summer Project Week/UniversityCourse | Create the basics of a university course about medical image computing]] (Attila Nagy)
* [[2016 Summer Project Week/CameraTutorial | How to use Basler Cameras for Medical Applications]] (Peter Behringer, Santhirarajah Mathimugan, Steve Pieper)

='''Logistics'''=
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
==Location==
*'''Location:''' Heidelberg, Germany.
**'''Getting to Heidelberg:''' Most will fly into Frankfurt Main International (FRA). At the airport look for "long distance trains". There you can buy a ticket from the machine to Heidelberg Hauptbahnhof (main station), around EUR 25. It usually takes less than an hour, with a change in Mannheim to a regional train. https://www.bahn.de . If you arrive on Sunday you can take a bus from the station to the Old Town or where your hotel is. Heidelberg is pretty small, look for directions on Google Maps. If you arrive on Monday see below on how to get to DKFZ directly.
**'''Monday''' at German Cancer Research Center - DKFZ
*** Enter through the main lobby ( just north of https://goo.gl/maps/e3ZbcsM5KC82, you can't miss it, it's the tallest building on campus with a big "dkfz." on top). The meeting room is on the 8th floor (H824, "Glaskasten", "glass box"). We will leave some instructions how to get there at the reception. The meeting time in the lobby will be 8:45am for those who wish to be at the meeting room by 9am. Official activities will start at noon with lunch.
*** To get to DKFZ in the morning you can use the Google Maps link above, public transport information is available there. For people staying in the Old Town, near Bismarckplatz or coming from the station it will be most likely Bus #32, exit at stop "Chirurgische Klinik", which is the second one after crossing the Neckar river. More detailed timetables at [http://fahrplanauskunft.vrn.de/vrn/XSLT_TRIP_REQUEST2?language=en the local transportation services VRN]. If you are up early there is also a nice [https://goo.gl/maps/SRRG6x7KDNU2 walk along the river].
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
***Suggested place for meetings is the Marstall student center ([https://www.google.de/maps/place/Zeughaus-Mensa+im+Marstall/@49.4124525,8.7056926,349m/data=!3m1!1e3!4m5!3m4!1s0x0000000000000000:0x8fd41be2e27fc36e!8m2!3d49.412919!4d8.7044381 map])
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
==Preparatory Conference Calls: ==
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**Call #1 Tuesday, May 10, 3pm Boston time.
**Call #2 Tuesday, May 17, 3pm Boston time.
**Call #3 Tuesday, May 31, 9am Boston time.
**Call #4 Tuesday, Jun 7, 9am Boston time.
**Call #5 Tuesday, Jun 14, 9am Boston time.

=='''Equipment'''==
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)
*[[2016_Summer_Project_Week:Equipment_Requests|Specialized equipment that people would like to have]] '''Updated June 16 2016'''

= '''Registrants''' =

'''REGISTRATION:''' Please add your name to this list if you are definitely planning to attend. If you are not already on it, please add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]. We need to know the number of people at DKFZ, so if you are there on Monday, please add "(Mon)" next to your name. Official registration for the event is through the CARS conference at http://www.cars-int.org/cars_2016/registration.html -- which you can do now or onsite.

# Tina Kapur, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA (Mon)
# Ron Kikinis, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA and University of Bremen / Fraunhofer MEVIS, Germany (Mon)
# Dženan Zukić, Kitware, USA
# Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal. (Mon)
# Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School (Mon)
# Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Steve Pieper, Isomics, Inc., USA (Mon)
# Nicole Aucoin, Brigham and Women's Hospital (Mon)
# Simon Drouin, Montreal Neurological Institute (Mon)
# Thomas Kirchner, German Cancer Research Center (Mon)
# Elvis Chen, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Adam Rankin, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Christian Askeland, SINTEF, Norway (Mon)
# Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany (Mon)
# Longquan Chen, BWH/HMS, Boston, USA (Mon)
# Davide Punzo, Kapteyn Astronomical Institute, Netherlands (Mon)
# Lauren O'Donnell, BWH/HMS (Mon)
# Yannick Suter, BWH/HMS (Mon)
# Junichi Tokuda, BWH/HMS (Mon)
# Sarah Frisken, BWH/HMS (Mon)
# Prashin Unadkat, BWH/HMS
# Anna Roethe, Charite, Berlin
# Michael Onken, Open Connections, Germany (Mon)
#Jan Schlamelcher, Open Connections/OFFIS, Germany
# Janne Beate Bakeng, SINTEF, Norway
# Ole Vegard Solberg, SINTEF, Norway
# Jon Eiesland, SINTEF, Norway
# Tamas Ungi, Queen's University, Canada (Mon)
# Andras Lasso, Queen's University, Canada (Mon)
# Csaba Pinter, Queen's University, Canada (Mon)
# Thomas Vaughan, Queen's University, Canada (Mon)
# Javier Pascau, Universidad Carlos III de Madrid, Spain (Mon)
# Verónica García-Vazquez, Universidad Carlos III de Madrid, Spain (Mon)
# Mónica García-Sevilla, Universidad Carlos III de Madrid, Spain (Mon)
# David García-Mato, Universidad Carlos III de Madrid, Spain (Mon)
# Rocío López-Velazco, Universidad Carlos III de Madrid, Spain (Mon)
# Raúl San José, BWH/HMS, Boston
# Pietro Nardeli, BWH/HMS, Boston
# Andrey Fedorov, BWH/HMS, Boston (Mon, Wed, Thu)
# Christian Herz, BWH/HMS, Boston (Mon)
# Frank Lindseth, NTNU/SINTEF, Norway
# Peter Behringer, Basler AG, Germany
# Santhirarajah Mathimugan, Basler AG, Germany
# Koji Kobayashi, Vocsis Corporation, Japan
# David Black, University of Bremen / Fraunhofer MEVIS, Germany (Mon)
#William Wells, BWH/HMS (Mon)
# Attila Nagy, University of Szeged, Hungary (Mon)
# Bojan Kocev, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Sara Fernández Vidal, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Fernando Pérez García, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Marco Nolden, [http://mbi.dkfz-heidelberg.de Medical and Biological Informatics, German Cancer Research Center] (Mon)
# Christian Hansen, [http://isgwww.cs.uni-magdeburg.de/cas/ University of Magdeburg], Germany (Mon)
# Julian Hettig, [http://isgwww.cs.uni-magdeburg.de/cas/ University of Magdeburg], Germany (Mon)
# Jorge Onieva, BWH/HMS, Boston
# Caspar Goch, German Cancer Research Center (Mon)

'''Please don't forget to add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].'''

2016 Summer Project Week/SlicerDMRIDocumentation

2016-06-25T09:12:50Z

Lauren:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:AG1624_AF_left_fMRI_lines_new.png
</gallery>

==Key Investigators==
* Lauren J. O'Donnell
* Fan Zhang (remotely)
* Isaiah Norton (remotely)
* Sonia Pujol

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improve and extend tutorials and documentation that explain how to use the modules in SlicerDMRI: https://github.com/SlicerDMRI/SlicerDMRI
* Assess and improve within-module documentation for modules in SlicerDMRI
* Improve website for SlicerDMRI
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Assess state of documentation and GUI organization status
* Begin to improve docs
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial inventory of modules and state of documentation was created
* Initial test update of help documentation: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DiffusionTensorScalarMeasurements
* Assessment of UI organization and issues; brainstorming of possible name changes
* Plan for future progress in help documentation, possible youtube video(s)
</div>
</div>

2016 Summer Project Week/SlicerDMRIDocumentation

2016-06-24T12:45:46Z

Lauren:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:AG1624_AF_left_fMRI_lines_new.png
</gallery>

==Key Investigators==
* Lauren J. O'Donnell
* Fan Zhang (remotely)
* Isaiah Norton (remotely)
* Sonia Pujol

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improve and extend tutorials and documentation that explain how to use the modules in SlicerDMRI: https://github.com/SlicerDMRI/SlicerDMRI
* Assess and improve within-module documentation for modules in SlicerDMRI
* Improve website for SlicerDMRI
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Assess state of documentation and GUI organization status
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial inventory of modules and state of documentation was created
* Initial update of help documentation: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DiffusionTensorScalarMeasurements
* Assessment of UI organization and issues; brainstorming of possible name changes
</div>
</div>

2016 Summer Project Week/Workshop on Shared Software Platform for Ultrasound-Guided Medical Interventions

2016-06-22T08:31:54Z

Lauren:

= Introduction =

Several groups have developed ultrasound-guided intervention systems in the last two decades but until recently these groups have worked mostly in parallel, independently from each other. The Image Guided Systems Inter-Operability (IGSIO) group was founded in 2016 January after lengthy discussions regarding the standardization of tracked ultrasound communication to work towards improving the interoperability between industrial products and research software platforms. See more information about this effort at http://igsio.github.io/.

The goal of this workshop is to promote the concept and practice of a shared software platform for ultrasound-guided interventions. Participants will learn, in practice, to build clinical applications using software platform tools.

= Tentative agenda (keep checking this page for more details) =

* 9-10am: Introduction of existing open-source infrastructure for building ultrasound-guided intervention systems
** Plus/SlicerIGT/3DSlicer (Andras Lasso)
** CustusX
** IBIS
* 10.30am-12pm: Bring your own problem - discussion of implementation options for specific clinical procedures using open-source platforms.
** EM needle guidance in breast brachytherapy (Thomas Vaughan)
** Tracked ultrasound guided lumpectomy (Tamas Ungi)
** <add your name and clinical application here>
* Afternoon: Hands-on session for setting up prototype systems for ultrasound guidance and tool navigation.

= Registration =

No registration is required, just add your name to the participant list below or send an email to Andras Lasso (lasso@queensu.ca).

= Participants =
* Christian Askeland
* Janne Beate Bakeng
* Longquan Chen
* Simon Drouin
* Jon Eiesland
* Thomas Kirchner
* Adam Rankin
* Ole Vegard Solberg
* Junichi Tokuda
* Sarah Frisken
* Bojan Kocev
* Ines Machado
* Tamas Ungi
* David Black
* Lauren O'Donnell

2016 Summer Project Week/SlicerDMRIDocumentation

2016-06-20T12:59:44Z

Lauren:

2016 Summer Project Week/Structural-functional measurements

2016-06-20T11:18:26Z

Lauren: /* Key Investigators */

==Key Investigators==
* Yannick Suter
* Lauren J. O'Donnell

==Project Description==
[[File:AF_left_fMRI_lines.png|thumb|center|upright=2.0|Left AF tracts with putative Broca and Wernicke's areas (yellow) with T2 image in the background. ]]
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Tractography data and language fMRI activations are available for 10 neurosurgical patients and in the connectome dataset. We are evaluating different distance measurements between the fMRI activations and fiber tracts to find structural-functional relationships.
* Evaluate different structural-functional measurements (e.g. tract enpoints in fMRI activations / tracts passing through / within a distance threshold).
* Find tracts that are related to language across patients.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Before Project Week:
** Run distance measurement for patient data with language fMRI activations
* During Project Week:
** Evaluate distance measurements
** Find suitable statistics to evaluate measurements.
** Improve distance measurement (e.g. line interpolation)
** Find fiber tracts that are related to language across patients
** If this works well, apply this method to some patients from the connectome dataset.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Distance measurements with different methods for patient data are available
</div>
</div>

2016 Summer Project Week

2016-06-20T11:18:01Z

Lauren: put Yannick first on list since it's his project

__NOTOC__

[[image:PW-Summer2016.png|300px]]
<br><br>
=Welcome to the web page for the 23rd Project Week!=
The 23rd Project Week open source hackathon is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS) and the [http://www.ipcai.org/ IPCAI 2016] conferences in Heidelberg, Germany. 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:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
*'''Location:''' Heidelberg, Germany.
**'''Getting to Heidelberg:''' Most will fly into Frankfurt Main International (FRA). At the airport look for "long distance trains". There you can buy a ticket from the machine to Heidelberg Hauptbahnhof (main station), around EUR 25. It usually takes less than an hour, with a change in Mannheim to a regional train. https://www.bahn.de . If you arrive on Sunday you can take a bus from the station to the Old Town or where your hotel is. Heidelberg is pretty small, look for directions on Google Maps. If you arrive on Monday see below on how to get to DKFZ directly.
**'''Monday''' at German Cancer Research Center - DKFZ
*** Enter through the main lobby ( just north of https://goo.gl/maps/e3ZbcsM5KC82, you can't miss it, it's the tallest building on campus with a big "dkfz." on top). The meeting room is on the 8th floor (H824, "Glaskasten", "glass box"). We will leave some instructions how to get there at the reception. The meeting time in the lobby will be 8:45am for those who wish to be at the meeting room by 9am. Official activities will start at noon with lunch.
*** To get to DKFZ in the morning you can use the Google Maps link above, public transport information is available there. For people staying in the Old Town, near Bismarckplatz or coming from the station it will be most likely Bus #32, exit at stop "Chirurgische Klinik", which is the second one after crossing the Neckar river. More detailed timetables at [http://fahrplanauskunft.vrn.de/vrn/XSLT_TRIP_REQUEST2?language=en the local transportation services VRN]. If you are up early there is also a nice [https://goo.gl/maps/SRRG6x7KDNU2 walk along the river].
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
*Preparatory Conference Calls:
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**Call #1 Tuesday, May 10, 3pm Boston time.
**Call #2 Tuesday, May 17, 3pm Boston time.
**Call #3 Tuesday, May 31, 9am Boston time.
**Call #4 Tuesday, Jun 7, 9am Boston time.
**Call #5 Tuesday, Jun 14, 9am Boston time.

='''Agenda'''=
<font color="maroon">Please note that on '''Tuesday''' there is no organized Project Week activity due to IPCAI @ CARS</font>
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:7%" |Time
!style="width:15%" |Monday, June 20 <br> [https://goo.gl/maps/e3ZbcsM5KC82 DKFZ]
!style="width:3%" |Tuesday, June 21 <br> IPCAI
!style="width:15%" |Wednesday, June 22 <br> Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Thursday, June 23 <br> Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Friday, June 24 <br> Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Saturday, June 25 <br> Congress Hall of CARS, Room Trübnersaal
|-
|bgcolor="#ffffdd"|'''9am-10am'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="8"|
|bgcolor="#ffffff"|[[{{FULLPAGENAME}}/Workshop_on_Shared_Software_Platform_for_Ultrasound-Guided_Medical_Interventions|Workshop: Ultrasound-guided interventions software platform]]
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''10:00am-10:30am'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''10:30-12pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch and adjourn
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffff"| Welcome! <br> Project Introductions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="4"|
|-
|bgcolor="#ffffdd"|'''3:00pm-3:30pm'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''3:30pm-5:00pm'''
|bgcolor="#ffffff"| What does a Neurosurgeon need from technologists? (Alexandra Golby, MD)
|bgcolor="#ffffff"| [[{{FULLPAGENAME}}/Breakout Session Slicer Extensions|Breakout Session: Slicer Extensions]] (JC, Steve)
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|}

='''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 researchers from around the world and is led by [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD]. 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], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

An introduction and summary of all previous Project Events is available [[Project_Events|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

The 23rd Project Week is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS).

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

='''Equipment'''=
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)
*[[2016_Summer_Project_Week:Equipment_Requests|Specialized equipment that people would like to have]] '''Updated June 16 2016'''

='''Projects'''=
* Use this [[2016_Summer_Project_Week_Template | template]] for project pages

=== IGT ===
* [[2016 Summer Project Week/Guidelets | Guildelets (Slicelets for IGT)]] (Tamas Ungi, Andras Lasso, Thomas Vaughan)
* [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Thomas Kirchner, Janne Beate Bakeng)
* [[2016 Summer Project Week/Guided Ultrasound Calibration | Guided Ultrasound Calibration]] (Elvis Chen, Inês Prata, Tamas Ungi)
* [[2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink | Integrating PLUS in Applications using OpenIGTLink]] (Christian Askeland, Janne Beate Bakeng, Ole Vegard Solberg, Jon Eiesland, Longquan Chen, Simon Drouin)
* [[2016 Summer Project Week/Slicelet For Ultrasound Acquisition | Slicelet for Ultrasound Acquisition]] (Sarah Frisken, Prashin Unadkat, Steve Pieper, Anna Roethe)
* [[2016 Summer Project Week/Structural-functional measurements | Structural - Functional Relationship Measurements of Tractography Data with fMRI ]] (Yannick Suter, Lauren J. O'Donnell)
* [[2016 Summer Project Week/SliceTracker | SliceTracker for Data Collection and Prostate Biopsy Support ]] (Christian Herz, Peter Behringer, Andrey Fedorov)
* [[2016 Summer Project Week/Intra-procedural prostate motion characterization | Prostate Motion Characterization ]] (Peter Behringer, Christian Herz, Andrey Fedorov)
* [[2016 Summer Project Week/Sacral Neuromodulation | Sacral Neuromodulation ]] (Rocío López, Javier Pascau, Tamas Ungi)
* [[2016 Summer Project Week/Fusion of Electromagnetic and Surface Scanner Data | Fusion of Electromagnetic and Surface Scanner Data]] (Mónica García, Javier Pascau)
* [[2016 Summer Project Week/Integrating/Using OpenIGTLink for the communications of Robotics devices | Integrating/Using OpenIGTLink for the Communications of Robotics Devices]] (Scheherazade Kraß, Longquan Chen)
* [[2016 Summer Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Guillaume Pernelle, Tina Kapur, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea)
* [[2016 Summer Project Week/Uncertainty-aware Information Fusion | Uncertainty-aware Information Fusion for Real-time Soft Tissue Motion Estimation]] (Bojan Kocev, Sarah Frisken, William Wells, Christian Hansen)
* [[2016 Summer Project Week/Intraoperative Imaging workflow in Hybrid ORs | Intraoperative Imaging in Hybrid ORs]] (Sarah Frisken, Anna Roethe, Prashin Unadkat, Christian Hansen)
* [[2016 Summer Project Week/Curve and Surface Creation from Fiducials|Curve and Surface Creation from Fiducials]] (Thomas Vaughan, Junichi Tokuda)

=== Infrastructure ===
* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)
* [[2016 Summer Project Week/3D Lasso Selection | Implementation and Testing Performance of 3-D Lasso Selection within the Segmentation Editor Infrastructure ]] (Davide Punzo, Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2016 Summer Project Week/Segmentations Integration | Integration of Segmentations Infrastructure and Related Modules to Slicer Core]] (Csaba Pinter, Andras Lasso)
* [[2016 Summer Project Week/DICOM Tractography Results | Finalizing DICOM Tractography Results Implementation in DCMTK for BWH Project]] (Lauren O'Donnell, Isaiah Norton, Michael Onken)
* [[2016 Summer Project Week/Feedback for Project Week | Measuring the Impact of Project Weeks]] (Tina Kapur)
* [[2016 Summer Project WEB and 3D DICOM viewer to the rest of us]] (Koji Kobayashi)

=== Augmented Reality ===
* [[2016 Summer Project Week/OpenVR_integration | OpenVR Integration]] (Adam Rankin, Andras Lasso)
* [[2016 Summer Project Week/VRPN Integration | VRPN Integration]] (Dženan Zukić)
* [[2016 Summer Project Week/AR with a tablet device in the surgical room | AR with a Tablet Device in the Surgical Room]] (David García, Javier Pascau)
* [[2016 Summer Project Week/Auditory Display | Auditory Display Integration]] (David Black, Sarah Frisken, Christian Hansen)

=== Informatics ===
* [[2016 Summer Project Week/dcmqi | DICOM for Quantitative Imaging (dcmqi) Library]] (Andrey Fedorov, Christian Herz, Marco Nolden, Hans Meine, Csaba Pinter, Steve Pieper, et al)
* [[2016 Summer Project Week/DICOM Parametric Maps | Finalizing DICOM Parametric Map Implementation in DCMTK for QIICR project]] (Michael Onken, Jan Schlamelcher, Andrey Fedorov, Christian Herz)
* [[2016 Summer Project Week/MeVisLab SEG Colors | Support Reading and Writing DICOM Tags for SEG Colors]] (Hans Meine)
* [[2016 Summer Project Week/Segmentation Editor and Terminology | Segmentation Editor and Terminology]] (Nicole Aucoin, Andrey Fedorov, Csaba Pinter, Andras Lasso)

=== Atlas construction ===
* [[2016 Summer Project Week/Histological Brain Atlas | Tool for the construction of an integrated brain atlas based on histology and MRI]] (Fernando Pérez García)

=== Tutorial===
* [[2016 Summer Project Week/SlicerDMRIDocumentation | Tutorials and Documentations in SlicerDMRI]] (Lauren J. O'Donnell, Fan Zhang, Isaiah Norton)
* [[2016 Summer Project Week/CameraTutorial | How to use Basler Cameras for Medical Applications]] (Peter Behringer, Santhirarajah Mathimugan, Steve Pieper)
* [[2016 Summer Project Week/UniversityCourse | Create the basics of a university course about medical image computing]] (Attila Nagy)

= '''Registrants''' =

'''REGISTRATION:''' Please add your name to this list if you are definitely planning to attend. If you are not already on it, please add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]. We need to know the number of people at DKFZ, so if you are there on Monday, please add "(Mon)" next to your name. Official registration for the event is through the CARS conference at http://www.cars-int.org/cars_2016/registration.html -- which you can do now or onsite.

# Tina Kapur, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA (Mon)
# Ron Kikinis, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA and University of Bremen / Fraunhofer MEVIS, Germany (Mon)
# Dženan Zukić, Kitware, USA
# Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal. (Mon)
# Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School (Mon)
# Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Steve Pieper, Isomics, Inc., USA (Mon)
# Nicole Aucoin, Brigham and Women's Hospital (Mon)
# Simon Drouin, Montreal Neurological Institute (Mon)
# Thomas Kirchner, German Cancer Research Center (Mon)
# Elvis Chen, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Adam Rankin, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Christian Askeland, SINTEF, Norway (Mon)
# Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany
# Longquan Chen, BWH/HMS, Boston, USA (Mon)
# Davide Punzo, Kapteyn Astronomical Institute, Netherlands (Mon)
# Lauren O'Donnell, BWH/HMS
# Yannick Suter, BWH/HMS (Mon)
# Junichi Tokuda, BWH/HMS (Mon)
# Sarah Frisken, BWH/HMS (Mon)
# Prashin Unadkat, BWH/HMS
# Anna Roethe, Charite, Berlin
# Michael Onken, Open Connections, Germany (Mon)
#Jan Schlamelcher, Open Connections/OFFIS, Germany
# Janne Beate Bakeng, SINTEF, Norway
# Ole Vegard Solberg, SINTEF, Norway
# Jon Eiesland, SINTEF, Norway
# Tamas Ungi, Queen's University, Canada (Mon)
# Andras Lasso, Queen's University, Canada (Mon)
# Csaba Pinter, Queen's University, Canada (Mon)
# Thomas Vaughan, Queen's University, Canada (Mon)
# Javier Pascau, Universidad Carlos III de Madrid, Spain (Mon)
# Verónica García-Vazquez, Universidad Carlos III de Madrid, Spain (Mon)
# Mónica García-Sevilla, Universidad Carlos III de Madrid, Spain (Mon)
# David García-Mato, Universidad Carlos III de Madrid, Spain (Mon)
# Rocío López-Velazco, Universidad Carlos III de Madrid, Spain (Mon)
# Raúl San José, BWH/HMS, Boston
# Pietro Nardeli, BWH/HMS, Boston
# Andrey Fedorov, BWH/HMS, Boston (Mon, Wed, Thu)
# Christian Herz, BWH/HMS, Boston (Mon)
# Frank Lindseth, NTNU/SINTEF, Norway
# Peter Behringer, Basler AG, Germany
# Santhirarajah Mathimugan, Basler AG, Germany
# Koji Kobayashi, Vocsis Corporation, Japan
# David Black, University of Bremen / Fraunhofer MEVIS, Germany (Mon)
#William Wells, BWH/HMS (Mon)
# Attila Nagy, University of Szeged, Hungary (Mon)
# Bojan Kocev, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Sara Fernández Vidal, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Fernando Pérez García, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Marco Nolden, [http://mbi.dkfz-heidelberg.de Medical and Biological Informatics, German Cancer Research Center] (Mon)
# Christian Hansen, [http://isgwww.cs.uni-magdeburg.de/cas/ University of Magdeburg], Germany (Mon)
# Julian Hettig, [http://isgwww.cs.uni-magdeburg.de/cas/ University of Magdeburg], Germany

'''Please don't forget to add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].'''

2016 Summer Project Week/SlicerDMRIDocumentation

2016-06-20T11:14:49Z

Lauren:

2016 Summer Project Week/SlicerDMRIDocumentation

2016-06-20T11:10:23Z

Lauren:

File:AG1624 AF left fMRI lines new.png

2016-06-20T11:09:56Z

Lauren:

2016 Summer Project Week/DICOM Tractography Results

2016-06-20T11:07:23Z

Lauren:

File:DICOM tracto.png

2016-06-20T11:07:18Z

Lauren: Lauren uploaded a new version of File:DICOM tracto.png

File:DICOM tracto.png

2016-06-20T11:06:11Z

Lauren:

2016 Winter Project Week/Projects/BatchImageAnalysis

2016-01-08T15:54:48Z

Lauren:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]

</gallery>

[[File:LungCT-3DSIFT.png|200px|thumb|left|3D SIFT Lung Features]]

==Key Investigators==


* Kalli Retzepi (MGH)
* Yangming Ou (MGH)
* Matt Toews (ETS)
* Lilla Zollei (MGH)
* Lauren O'Donnell (BWH)
* Steve Pieper (BWH)
* Sandy Wells (BWH)
* Randy Gollub (MGH)

==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;"
|

* Run feature detection code over a collection of medical images pulled from PACS
* Investigate a collection of ADC maps of neonates (diffusion MR)
* Patients labeled with age and health status (normal, mildly abnormal, severely abnormal)
* Use 3D SIFT code to see if health status can be detected in images
* (if time) try text analysis of radiology reports
|

* Use deidentified cohort of neonate images collected from MGH
* Install data and software on AWS, try StarCluster
* Explore visualization options
* (if time) integrate image features with analysis of radiology report text
|


Algorithm

* feature extraction (20 seconds per image)

* Feature matching O(log N) indexing (< 1 second per image)

* 3D SIFT-Rank code (Windows, Linux, Max) and read me
http://www.matthewtoews.com/fba/featExtract1.5.zip

Result
Baseline HIE classification rate: 73%, leave-one-out moderate vs normal.

Data
231 subjects, Apparent Diffusion Coefficient (ADC) images.

|}

==Features Extracted in ADC MRI Volume ==

http://wiki.na-mic.org/Wiki/images/b/b2/Image_%282%29.png

2016 Winter Project Week/Breakout Sessions/SlicerExtensions Birds of a Feather

2016-01-05T15:56:08Z

Lauren:

=Slicer Extensions=
==Moderator ==
Steve Pieper

== Goal ==

This will be a "birds of a feather" session for current and potential developers of Slicer extensions to share ideas and experiences. Among other things, we will discuss what the right boundaries are between Slicer Core and Extensions, the types of needs there are across current/future Extensions, and whether we should have a hierarchy of dependencies between Extensions.

==Attendees==
All interested extension developers are encouraged to attend. The following people are active extension developers and are encouraged to participate.

[http://www.na-mic.org/Wiki/images/6/63/SlicerRT_Extension_Pinter.pptx Csaba Pinter], Andras Lasso, Raul San Jose Estepar, Jorge Onieva, [http://www.na-mic.org/Wiki/images/0/0c/SlicerExtensions_CMFteam.pdf Beatriz Paniagua], Andrey Fedorov, Eric Moult, Lauren O'Donnell, Isaiah Norton, Greg Sharp, Erich Bremer

== Preparation ==

Extension developers should be prepared to discuss their development plans, particularly if they have any requirements for the Slicer core that can be used to prioritize discussions for the Thursday afternoon discussion of development in the Slicer core.

[http://www.na-mic.org/Wiki/index.php/File:SlicerDMRIU01.pdf SlicerDMRIU01]

2016 Winter Project Week/Breakout Sessions/SlicerExtensions Birds of a Feather

2016-01-05T15:41:16Z

Lauren:

File:SlicerDMRIU01.pdf

2016-01-05T15:39:35Z

Lauren:

2016 Winter Project Week/Breakout Sessions/DiffusionMRI

2015-12-28T13:48:54Z

Lauren: start off with who this is for

This breakout is for users and developers of diffusion MRI tools in Slicer. We will discuss this year's goals for improvements to Slicer diffusion MRI under the new NIH NCI ITCR grant "Open Source Diffusion MRI Technology for Brain Cancer Research."

We will be very happy to receive input from the user community and from existing and new collaborators.

This year's goals are:
* refactoring of SlicerDMRI
* creation of SlicerDMRI extension
* open-source library for tractography DICOM
* open-source library for tractography file formats to/from DICOM
* increased documentation coverage and tutorials
* creation of releasable dMRI test data in a variety of scanner DICOM formats
* creation of nightly tests for modules in SlicerDMRI
* improved infrastructure for multishell dMRI
* addition of new modules from BWH LMI

2016 Winter Project Week/Breakout Sessions/DiffusionMRI

2015-12-19T14:57:26Z

Lauren: filled in this page for DMRI and for TINA

We will discuss this year's goals for improvements to Slicer diffusion MRI infrastructure and capabilities under the new NIH NCI ITCR grant "Open Source Diffusion MRI Technology for Brain Cancer Research."

We will be very happy to receive input from the user community and from existing and new collaborators.

This year's goals are:
* refactoring of SlicerDMRI
* creation of SlicerDMRI extension
* open-source library for tractography DICOM
* open-source library for tractography file formats to/from DICOM
* increased documentation coverage and tutorials
* creation of releasable dMRI test data in a variety of scanner DICOM formats
* creation of nightly tests for modules in SlicerDMRI
* improved infrastructure for multishell dMRI
* addition of new modules from BWH LMI

Cortex Clustering

2015-01-09T16:40:52Z

Lauren:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
Image:cluster_exp.png
Image:InitialAcrossSubjectsJan2015Cortex.jpg
</gallery>

==Key Investigators==
Lauren O'Donnell, Sandy Wells

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Perform early experiments in cortex point clustering based on diffusion tractography
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Work on code to enable across-subjects clustering and test this
* Analyze the proposed model
* Perform preliminary experiments
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Discussed method
* Implemented and tested initial across-subjects clustering code. Corresponding points are identified across subjects based on their connectivity.
* Next step is to analyze meaning and utility of this approach with further experiments.
</div>
</div>

File:InitialAcrossSubjectsJan2015Cortex.jpg

2015-01-09T16:39:23Z

Lauren:

Cortex Clustering

2015-01-09T16:27:53Z

Lauren: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
Image:cluster_exp.png

</gallery>

==Key Investigators==
Lauren O'Donnell, Sandy Wells

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Perform early experiments in cortex point clustering based on diffusion tractography
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Work on code to enable across-subjects clustering and test this
* Analyze the proposed model
* Perform preliminary experiments
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Discussed method
* Implemented and tested initial across-subjects clustering code
</div>
</div>

Slicer Tract Analysis

2015-01-09T16:27:05Z

Lauren: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Alex Yarmarkovich, Lauren O'Donnell, JC

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To finalize tract hierarchy and measurement framework in Slicer
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Compile second round of beta user feedback before Project Week
* Plan what to address during project week and file bug reports as needed
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Beta user feedback incorporated
* Fixed bugs and added features regarding output of measures to excel-readable text files
* Found bugs in some measure computation
* Found/reported issues with hierarchy multiple node adding, which Alex and JC looked into
* Created page for organization of this ongoing work: http://wiki.slicer.org/slicerWiki/index.php/Documentation/Labs/FiberTractMeasurementAndVisualization
</div>
</div>

Slicer Tract Analysis

2015-01-09T16:26:21Z

Lauren: /* Key Investigators */

Slicer Tract Analysis

2015-01-09T16:26:09Z

Lauren: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Alex Yarmarkovich, Lauren O'Donnell

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To finalize tract hierarchy and measurement framework in Slicer
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Compile second round of beta user feedback before Project Week
* Plan what to address during project week and file bug reports as needed
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Beta user feedback incorporated
* Fixed bugs and added features regarding output of measures to excel-readable text files
* Found bugs in some measure computation
* Found/reported issues with hierarchy multiple node adding, which Alex and JC looked into
</div>
</div>

2015 Winter Project Week

2015-01-05T23:34:00Z

Lauren: /* Agenda */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

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

[[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 events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 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]

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| <br><font color="#9966cc"></font>
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
| Neurosurgical Ultrasound Breakout
|
| [[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
| style="background:#dbf3ff; color:#522200"| [http://ferenc.jolesz.muchloved.com/frame.aspx? A tribute to Ferenc Jolesz] <br> [[2015_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|
| <font color="#44AA88">''(Olympus B)''</font>
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] <br><font color="#44AA88">''(Amethyst 1)'' <br> 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
* [[User:Yli|Quantitative Evaluation of Digitally Registered Pre and Post op DTI by 3D ROI Segmentation]] (Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)
* [[New Distance|A new modified Frechet distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)
* [[ProstateNavigation workflow | Workflow for prostate navigation and its components]] (Peter Behringer, Andriy Fedorov)
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[Needle Finder Tutorial | Needle Finder Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*[[VR Radiology | Application of consumer virtual reality devices in creating environments for diagnostic radiology]] (Franklin King, Steve Pieper)
*[[Distribution modeling | Summary statistics versus distributions: evaluating improved ability to detect clinical differences using DTI]] (Anuja Sharma, Guido Gerig)
*[[Valve Replacement | Aortic valve replacement using tracked 3D ultrasound]] (Adam Rankin)
*[[2015_Winter_Project_Week:CommunicationProtocolForOpticalTrackingWithSurfaceScan| Communication Protocol for Optical Tracking with Surface Scan]] (Junichi Tokuda, Sangyong Kim, ByungHyun Cho, Brian Nini, Nobuhiko Hata)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

==CTE==
* [[Slicer_Tract_Analysis | Measurement and visualization using white matter hierarchies in Slicer]] (Alexander Yarmarkovich, Lauren O'Donnell)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Fissure Enhancement | Supervised fissure enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)
== Lung ==
*[[ Small lung nodule differential diagnosis using 3D Slicer | Small lung nodule differential diagnosis using 3D Slicer]] (Li Ming, Jay Jagadeesan)

==[http://qiicr.org QIICR]==
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* [[2015_Winter_Project_Week:_DICOM_representation_of_QIICR_Iowa_DBP_data|Representation of Iowa QIN data using DICOM]] (Andrey, Christian Bauer, Steve Pieper)
* [[Whole Body PET/CT Reference Region segmentation]] (Christian Bauer)
* [[2015_Winter_Project_Week:Bolus_Arrival_Time_Estimation_in_PK_Modelling|Bolus Arrival Time (BAT) Estimation in PK Modelling]] (Alireza Mehrtash, Andriy Fedorov, Jim Miller)
* [[2015_Winter_Project_Week:DICOM_Module_Improvements|DICOM Module Improvements]] (Alireza Mehrtash, Andriy Fedorov, Ron Kikinis, Steve Pieper)
* [[2015_Winter_Project_Week:Slice_View_Annotations|Slice View Annotations]] (Alireza Mehrtash, Andriy Fedorov, Steve Pieper)

==Feature Extraction==
* [[3D_SIFT_VIEW| 3D SIFT Feature Visualization in Slicer]] (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)
* [[Cortex_Clustering| Experimental tract-based cortical clustering ]] (Lauren O'Donnell, William Wells)

==Slicer4 Extensions==
* [[PET Tumor Segmentation]] (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* Improved model display (Francois Boudin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Bradley Lowenkamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)
* [[2015_Winter_Project_Week:RemoveITKv3Compatibility|Remove ITKv3 Compatibility for 64-bit image support]] (Bradley Lowekamp, Hans Johnson?, ?)
* [[2015_Winter_Project_Week:VersorTransforms|ITK Composed Versor Transforms]] (Bradley Lowekamp, Hans Johnson?, ?)

== '''Registrants''' ==

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

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

Cortex Clustering

2015-01-05T21:47:57Z

Lauren: /* Project Description */

Cortex Clustering

2015-01-05T21:46:37Z

Lauren:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
Image:cluster_exp.png

</gallery>

==Key Investigators==
Lauren O'Donnell, Sandy Wells

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Perform early experiments in cortex point clustering
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Work on code to enable across-subjects clustering and test this
* Analyze the proposed model
* Perform preliminary experiments
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

File:Cluster exp.png

2015-01-05T21:46:22Z

Lauren:

Cortex Clustering

2015-01-05T20:41:32Z

Lauren: Created page with '__NOTOC__ <gallery> Image:PW-2015SLC.png|Projects List </gallery> ==Key Investigators== Lauren O'Donnell, Sandy Wells ==Project Descriptio…'

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Lauren O'Donnell, Sandy Wells

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Perform early experiments in cortex point clustering
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Work on code to enable across-subjects clustering and test this
* Analyze the proposed model
* Perform preliminary experiments
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2015 Winter Project Week

2015-01-05T20:38:30Z

Lauren: /* Feature Extraction */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

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

[[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 events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 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]

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| <br><font color="#9966cc"></font>
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
|
|
| [[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
| style="background:#dbf3ff; color:#522200"| [http://ferenc.jolesz.muchloved.com/frame.aspx? A tribute to Ferenc Jolesz] <br> [[2015_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|
| <font color="#44AA88">''(Olympus B)''</font>
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] <br><font color="#44AA88">''(Amethyst 1)'' <br> 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
* [[2015_Winter_Project_Week:_Registration_of_preop_and_intraop_DTI_to_correlate_parameters_with_postop_prognosis|Registration of pre-op and intra-op DTI to correlate parameters with post-op prognosis]] (Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)
* [[New Distance|A new modified Frechet distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)
* [[ProstateNavigation workflow | Workflow for prostate navigation and its components]] (Peter Behringer, Andriy Fedorov)
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[Needle Finder Tutorial | Needle Finder Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*[[VR Radiology | Application of consumer virtual reality devices in creating environments for diagnostic radiology]] (Franklin King, Steve Pieper)
*[[Distribution modeling | Summary statistics versus distributions: evaluating improved ability to detect clinical differences using DTI]] (Anuja Sharma, Guido Gerig)
*[[Valve Replacement | Aortic valve replacement using tracked 3D ultrasound]] (Adam Rankin)
*[[2015_Winter_Project_Week:CommunicationProtocolForOpticalTrackingWithSurfaceScan| Communication Protocol for Optical Tracking with Surface Scan]] (Junichi Tokuda, Sangyong Kim, ByungHyun Cho, Brian Nini, Nobuhiko Hata)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

==CTE==
* [[Slicer_Tract_Analysis | Measurement and visualization using white matter hierarchies in Slicer]] (Alexander Yarmarkovich, Lauren O'Donnell)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Fissure Enhancement | Supervised fissure enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)
== Lung ==
*[[ Small lung nodule differential diagnosis using 3D Slicer | Small lung nodule differential diagnosis using 3D Slicer]] (Li Ming, Jay Jagadeesan)

==[http://qiicr.org QIICR]==
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* [[2015_Winter_Project_Week:_DICOM_representation_of_QIICR_Iowa_DBP_data|Representation of Iowa QIN data using DICOM]] (Andrey, Christian Bauer, Steve Pieper)
* [[Whole Body PET/CT Reference Region segmentation]] (Christian Bauer)
* [[2015_Winter_Project_Week:Bolus_Arrival_Time_Estimation_in_PK_Modelling|Bolus Arrival Time (BAT) Estimation in PK Modelling]] (Alireza Mehrtash, Andriy Fedorov, Jim Miller)
* [[2015_Winter_Project_Week:DICOM_Module_Improvements|DICOM Module Improvements]] (Alireza Mehrtash, Andriy Fedorov, Ron Kikinis, Steve Pieper)
* [[2015_Winter_Project_Week:Slice_View_Annotations|Slice View Annotations]] (Alireza Mehrtash, Andriy Fedorov, Steve Pieper)

==Feature Extraction==
* [[3D_SIFT_VIEW| 3D SIFT Feature Visualization in Slicer]] (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)
* [[Cortex_Clustering| Experimental tract-based cortical clustering ]] (Lauren O'Donnell, William Wells)

==Slicer4 Extensions==
* [[PET Tumor Segmentation]] (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* Improved model display (Francois Boudin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Bradley Lowenkamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter, ?)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)
* [[2015_Winter_Project_Week:RemoveITKv3Compatibility|Remove ITKv3 Compatibility for 64-bit image support]] (Bradley Lowekamp, Hans Johnson?, ?)
* [[2015_Winter_Project_Week:VersorTransforms|ITK Composed Versor Transforms]] (Bradley Lowekamp, Hans Johnson?, ?)

== '''Registrants''' ==

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

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

Slicer Tract Analysis

2015-01-05T20:31:55Z

Lauren:

2015 Winter Project Week

2015-01-05T18:08:04Z

Lauren: /* CTE */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

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

[[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 events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 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]

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| <br><font color="#9966cc"></font>
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
|
|
| [[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
| style="background:#dbf3ff; color:#522200"| [http://ferenc.jolesz.muchloved.com/frame.aspx? A tribute to Ferenc Jolesz] <br> [[2015_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|
| <font color="#44AA88">''(Olympus B)''</font>
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] <br><font color="#44AA88">''(Amethyst 1)'' <br> 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
* [[2015_Winter_Project_Week:_Registration_of_preop_and_intraop_DTI_to_correlate_parameters_with_postop_prognosis|Registration of pre-op and intra-op DTI to correlate parameters with post-op prognosis]] (Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)
* [[New Distance|A new modified Frechet distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)
* [[ProstateSegmentation | Prostate segmentation and biopsy]] (Peter Behringer, Andriy Fedorov)
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[Needle Finder Tutorial | Needle Finder Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*[[VR Radiology | Application of consumer virtual reality devices in creating environments for diagnostic radiology]] (Franklin King, Steve Pieper)
*[[Distribution modeling | Summary statistics versus distributions: evaluating improved ability to detect clinical differences using DTI]] (Anuja Sharma, Guido Gerig)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

==CTE==
* [[Slicer_Tract_Analysis | Measurement and visualization using white matter hierarchies in Slicer]] (Alexander Yarmarkovich, Lauren O'Donnell)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Fissure Enhancement | Supervised fissure enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)
== Lung ==
*[[ Small lung nodule differential diagnosis using 3D Slicer | Small lung nodule differential diagnosis using 3D Slicer]] (Li Ming, Jay Jagadeesan)

==[http://qiicr.org QIICR]==
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* [[2015_Winter_Project_Week:_DICOM_representation_of_QIICR_Iowa_DBP_data|Representation of Iowa QIN data using DICOM]] (Andrey, Christian Bauer, Steve Pieper)
* [[Whole Body PET/CT Reference Region segmentation]] (Christian Bauer)
* [[2015_Winter_Project_Week:Bolus_Arrival_Time_Estimation_in_PK_Modelling|Bolus Arrival Time (BAT) Estimation in PK Modelling]] (Alireza Mehrtash, Andriy Fedorov, Jim Miller)
* [[2015_Winter_Project_Week:DICOM_Module_Improvements|DICOM Module Improvements]] (Alireza Mehrtash, Andriy Fedorov, Ron Kikinis, Steve Pieper)
* [[2015_Winter_Project_Week:Slice_View_Annotations|Slice View Annotations]] (Alireza Mehrtash, Andriy Fedorov, Steve Pieper)

==Feature Extraction==
* [[3D_SIFT_VIEW| 3D SIFT Feature Visualization in Slicer]] (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)

==Slicer4 Extensions==
* [[PET Tumor Segmentation]] (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* Improved model display (Francois Boudin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Bradley Lowenkamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter, ?)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)
* [[2015_Winter_Project_Week:RemoveITKv3Compatibility|Remove ITKv3 Compatibility for 64-bit image support]] (Bradley Lowekamp, Hans Johnson?, ?)
* [[2015_Winter_Project_Week:VersorTransforms|ITK Composed Versor Transforms]] (Bradley Lowekamp, Hans Johnson?, ?)

== '''Registrants''' ==

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

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

Slicer Tract Analysis

2015-01-05T18:07:38Z

Lauren: Created page with '__NOTOC__ <gallery> Image:PW-2015SLC.png|Projects List </gallery> ==Key Investigators== Alex Yarmarkovich, Lauren O'Donnell ==Project Desc…'