NAMIC Wiki - User contributions [en]

2017 Winter Project Week/Slicer VR

2017-01-15T17:09:12Z

Rankin: /* Project Description */

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

</gallery>

==Key Investigators==
* Adam Rankin (Robarts Research Institute, Canada)
* Ryan D'Souza (Northern Digital Inc., Canada - External)
* Matthew Jolley (Children's Hospital of Philadelphia - doesn't know it yet)
* Slicer/Kitware expert (help needed)
* Slicer UI/Rendering expert (help needed)

==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;"
|

* Identify and develop plan to enable VTK for the HoloLens
** D3D11 implementation of VTK classes started/updated by Ken Martin (https://gitlab.kitware.com/ken-martin/vtk/tree/direct3d11)
|

* Discuss with other interested parties the value of HoloLens integration
|

* HoloLens deemed not worth the effort at this time
* Discussion changed to OpenVR integration as a visualization platform from Slicer
** 30% - Upgrade Slicer to VTK >= 553a8bc0dd32889cc0eef49f2462e9b7e7ae81e3 (updated OpenVR support)
*** Slicer upgrade to using OpenGL2 backend (required for OpenVR)
** 20% - Enable support for a single application to instantiate multiple factory overrides of vtkRenderer, vtkRenderWindow, etc...
*** Subclass ctkVTKRenderView, ctkVTKAbstractView with -> ctkVTKVRRenderView, ctkVTKVRAbstractView such that they instantiate vtkOpenVRRenderer, vtkOpenVRRenderWindow, etc... instead of factory overridden default
*** SuperBuild expand to include OpenVR - https://github.com/ValveSoftware/openvr.git
*** SuperBuild expand to include SDL2 - https://github.com/spurious/SDL-mirror.git
** 50% - Extend Slicer to use new OpenVR related classes
*** Create classes qMRMLVRView, qMRMLVRWidget, etc...
*** Update layout manager to support new view type
|}

==Background and References==

2017 Winter Project Week/Tracked Ultrasound Standardization

2017-01-13T16:02:15Z

Rankin:

__NOTOC__
[[Image:UltrasoundToolGuidance3dOnly.gif|right]]
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* Andras Lasso (Queen's University, Canada)
* [http://nist.mni.mcgill.ca/?page_id=369 Simon Drouin] (Montreal Neurological Institute, Canada)
* Junichi Tokuda (Brigham and Women's Hospital, Harvard Medical School, USA)
* Longquan Chen (Brigham and Women's Hospital, Harvard Medical School, USA)
* [http://www.imaging.robarts.ca/petergrp/node/113 Adam Rankin] (Robarts Research Institute, Canada)
* [http://www.sintef.no/en/all-employees/employee/?EmpID=2596 Janne Beate Bakeng] (SINTEF, Norway)

==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;"
|

* [http://www.plustoolkit.org Plus toolkit] provides access to numerous hardware devices (imaging devices, tracking devices, navigations systems, sensors, etc.) and makes it available through [http://www.openigtlink.org OpenIGTLink] protocol
* Create a common library, [http://igsio.github.io OpenIGTLinkIO] that makes communication with Plus (and OpenIGTLink-compatible devices or software) very simple:
** Ensure software interoperability
** Share software maintenance workload
** Make it easy to share new features
* Add specific features for tracked ultrasound and surgical navigation
|

* Finish implementation of remote control of PlusServerLauncher
* Implement the ultrasound control messages
* Merge IGSIO/OpenIGTLink into OpenIGTLink and close the IGSIO/OpenIGTLink repository
* Reintegrate IGSIO/OpenIGTLinkIO in OpenIGTLinkIF
* Develop a common high-level GUI to control OpenIGTLinkIO devices
|

*OpenIGTLink cleaned up and v3 merged into master
**Slicer updated to use recent version? - Junichi/Longquan
*OpenIGTLinkIO updated to use the full capacities of OpenIGTLink v3 and code base was refactored to make library more consistent
*More extensive automated tests have been added to OpenIGTLinkIO
*Implemented automated Encoding/Decoding of command messages content
*Revised protocol to communicate with tracked US devices.
*Start implementing convenience interface for US tracking using revised protocol.
|}

==Background and References==

{| class="wikitable"
! style="text-align: left; width:50%" | [[File:1-before-winter-2016.jpeg|550px]]
! style="text-align: left; width:50%" | [[File:2-winter-2016.jpeg|550px]]
|- style="vertical-align:top;"
|
[[File:3-summer-2016.jpeg|550px]]
|
[[File:4-winter-2017.jpeg|550px]]
|}

*Winter 2016 [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | project page]]
*Summer 2016 [[ 2016 Summer Project Week/Tracked Ultrasound Standardization | project page]]

2017 Winter Project Week/Tracked Ultrasound Standardization

2017-01-13T15:57:58Z

Rankin: /* Project Description */

__NOTOC__
[[Image:UltrasoundToolGuidance3dOnly.gif|right]]
<gallery>
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators=='
* Andras Lasso (Queen's University, Canada)
* [http://nist.mni.mcgill.ca/?page_id=369 Simon Drouin] (Montreal Neurological Institute, Canada)
* Junichi Tokuda (Brigham and Women's Hospital, Harvard Medical School, USA)
* Longquan Chen (Brigham and Women's Hospital, Harvard Medical School, USA)
* Adam Rankin (Robarts Research Institute, Canada)
* [http://www.sintef.no/en/all-employees/employee/?EmpID=2596 Janne Beate Bakeng] (SINTEF, Norway)

==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;"
|

* [http://www.plustoolkit.org Plus toolkit] provides access to numerous hardware devices (imaging devices, tracking devices, navigations systems, sensors, etc.) and makes it available through [http://www.openigtlink.org OpenIGTLink] protocol
* Create a common library, [http://igsio.github.io OpenIGTLinkIO] that makes communication with Plus (and OpenIGTLink-compatible devices or software) very simple:
** Ensure software interoperability
** Share software maintenance workload
** Make it easy to share new features
* Add specific features for tracked ultrasound and surgical navigation
|

* Finish implementation of remote control of PlusServerLauncher
* Implement the ultrasound control messages
* Merge IGSIO/OpenIGTLink into OpenIGTLink and close the IGSIO/OpenIGTLink repository
* Reintegrate IGSIO/OpenIGTLinkIO in OpenIGTLinkIF
* Develop a common high-level GUI to control OpenIGTLinkIO devices
|

*OpenIGTLink cleaned up and v3 merged into master
**Slicer updated to use recent version? - Junichi/Longquan
*OpenIGTLinkIO updated to use the full capacities of OpenIGTLink v3 and code base was refactored to make library more consistent
*More extensive automated tests have been added to OpenIGTLinkIO
*Implemented automated Encoding/Decoding of command messages content
*Revised protocol to communicate with tracked US devices.
*Start implementing convenience interface for US tracking using revised protocol.
|}

==Background and References==

{| class="wikitable"
! style="text-align: left; width:50%" | [[File:1-before-winter-2016.jpeg|550px]]
! style="text-align: left; width:50%" | [[File:2-winter-2016.jpeg|550px]]
|- style="vertical-align:top;"
|
[[File:3-summer-2016.jpeg|550px]]
|
[[File:4-winter-2017.jpeg|550px]]
|}

*Winter 2016 [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | project page]]
*Summer 2016 [[ 2016 Summer Project Week/Tracked Ultrasound Standardization | project page]]

2017 Winter Project Week/Slicer VR

2017-01-12T19:06:47Z

Rankin: /* Key Investigators */

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

</gallery>

==Key Investigators==
* Adam Rankin (Robarts Research Institute, Canada)
* Ryan D'Souza (Northern Digital Inc., Canada - External)
* Matthew Jolley (Children's Hospital of Philadelphia - doesn't know it yet)
* Slicer/Kitware expert (help needed)
* Slicer UI/Rendering expert (help needed)

==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;"
|

* Identify and develop plan to enable VTK for the HoloLens
** D3D11 implementation of VTK classes started/updated by Ken Martin (https://gitlab.kitware.com/ken-martin/vtk/tree/direct3d11)
|

* Discuss with other interested parties the value of HoloLens integration
|

* HoloLens deemed not worth the effort at this time
* Discussion changed to OpenVR integration as a visualization platform from Slicer
** 20% - Upgrade Slicer to VTK >= 553a8bc0dd32889cc0eef49f2462e9b7e7ae81e3 (updated OpenVR support)
*** SuperBuild expand to include OpenVR - https://github.com/ValveSoftware/openvr.git
*** SuperBuild expand to include SDL2 - https://github.com/spurious/SDL-mirror.git
** 20% - Enable support for a single application to instantiate multiple factory overrides of vtkRenderer, vtkRenderWindow, etc...
*** Subclass ctkVTKRenderView, ctkVTKAbstractView with -> ctkVTKVRRenderView, ctkVTKVRAbstractView such that they instantiate vtkOpenVRRenderer, vtkOpenVRRenderWindow, etc... instead of factory overridden default
** 60% - Extend Slicer to use new OpenVR related classes
*** Create classes qMRMLVRView, qMRMLVRWidget, etc...
*** Update layout manager to support new view type
|}

==Background and References==

2017 Winter Project Week/Slicer VR

2017-01-12T19:06:18Z

Rankin: /* Project Description */

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

</gallery>

==Key Investigators==
* Adam Rankin (Robarts Research Institute, Canada)
* Ryan D'Souza (Northern Digital Inc., Canada - External)
* Matthew Jolley (Children's Hospital of Philadelphia - doesn't know it yet)
* Slicer UI/Rendering expert (help needed)

==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;"
|

* Identify and develop plan to enable VTK for the HoloLens
** D3D11 implementation of VTK classes started/updated by Ken Martin (https://gitlab.kitware.com/ken-martin/vtk/tree/direct3d11)
|

* Discuss with other interested parties the value of HoloLens integration
|

* HoloLens deemed not worth the effort at this time
* Discussion changed to OpenVR integration as a visualization platform from Slicer
** 20% - Upgrade Slicer to VTK >= 553a8bc0dd32889cc0eef49f2462e9b7e7ae81e3 (updated OpenVR support)
*** SuperBuild expand to include OpenVR - https://github.com/ValveSoftware/openvr.git
*** SuperBuild expand to include SDL2 - https://github.com/spurious/SDL-mirror.git
** 20% - Enable support for a single application to instantiate multiple factory overrides of vtkRenderer, vtkRenderWindow, etc...
*** Subclass ctkVTKRenderView, ctkVTKAbstractView with -> ctkVTKVRRenderView, ctkVTKVRAbstractView such that they instantiate vtkOpenVRRenderer, vtkOpenVRRenderWindow, etc... instead of factory overridden default
** 60% - Extend Slicer to use new OpenVR related classes
*** Create classes qMRMLVRView, qMRMLVRWidget, etc...
*** Update layout manager to support new view type
|}

==Background and References==

2017 Winter Project Week/Slicer VR

2017-01-12T19:04:36Z

Rankin: 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..."

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

</gallery>

==Key Investigators==
* Adam Rankin (Robarts Research Institute, Canada)
* Ryan D'Souza (Northern Digital Inc., Canada - External)
* Matthew Jolley (Children's Hospital of Philadelphia - doesn't know it yet)
* Slicer UI/Rendering expert (help needed)

==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;"
|

* Identify and develop plan to enable VTK for the HoloLens
** D3D11 implementation of VTK classes started/updated by Ken Martin (https://gitlab.kitware.com/ken-martin/vtk/tree/direct3d11)
|

* Discuss with other interested parties the value of HoloLens integration
|

* HoloLens deemed not worth the effort at this time
* Discussion changed to OpenVR integration as a visualization platform from Slicer
** Identification of relevant steps to enable OpenVR output from Slicer
*** 20% - Upgrade Slicer to VTK >= 553a8bc0dd32889cc0eef49f2462e9b7e7ae81e3 (updated OpenVR support)
**** SuperBuild expand to include OpenVR - https://github.com/ValveSoftware/openvr.git
**** SuperBuild expand to include SDL2 - https://github.com/spurious/SDL-mirror.git
*** 20% - Enable support for a single application to instantiate multiple factory overrides of vtkRenderer, vtkRenderWindow, etc...
**** Subclass ctkVTKRenderView, ctkVTKAbstractView with -> ctkVTKVRRenderView, ctkVTKVRAbstractView such that they instantiate vtkOpenVRRenderer, vtkOpenVRRenderWindow, etc... instead of factory overridden default
*** 60% - Extend Slicer to use new OpenVR related classes
**** Create classes qMRMLVRView, qMRMLVRWidget, etc...
**** Update layout manager to support new view type
|}

==Background and References==

2017 Winter Project Week

2017-01-12T19:04:25Z

Rankin: /* Shape Analysis, Segmentation */

__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]] (Tina Kapur, Ziyang Wang, Guillaume Pernelle, Paolo Zaffino)
#[[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 Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)
#[[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)

==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)

==Background and References==


==Next project week==
#[[2017 Winter Project Week/Next project week| Next project week]] (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/Slicer HoloLens

2017-01-12T19:03:57Z

Rankin:

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

</gallery>

==Key Investigators==
* Adam Rankin (Robarts Research Institute, Canada)
* Ryan D'Souza (Northern Digital Inc., Canada - External)
* Matthew Jolley (Children's Hospital of Philadelphia - doesn't know it yet)
* Slicer UI/Rendering expert (help needed)

==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;"
|

* Identify and develop plan to enable VTK for the HoloLens
** D3D11 implementation of VTK classes started/updated by Ken Martin (https://gitlab.kitware.com/ken-martin/vtk/tree/direct3d11)
|

* Discuss with other interested parties the value of HoloLens integration
|

* HoloLens deemed not worth the effort at this time
* Discussion changed to OpenVR integration as a visualization platform from Slicer
** Identification of relevant steps to enable OpenVR output from Slicer
*** 20% - Upgrade Slicer to VTK >= 553a8bc0dd32889cc0eef49f2462e9b7e7ae81e3 (updated OpenVR support)
**** SuperBuild expand to include OpenVR - https://github.com/ValveSoftware/openvr.git
**** SuperBuild expand to include SDL2 - https://github.com/spurious/SDL-mirror.git
*** 20% - Enable support for a single application to instantiate multiple factory overrides of vtkRenderer, vtkRenderWindow, etc...
**** Subclass ctkVTKRenderView, ctkVTKAbstractView with -> ctkVTKVRRenderView, ctkVTKVRAbstractView such that they instantiate vtkOpenVRRenderer, vtkOpenVRRenderWindow, etc... instead of factory overridden default
*** 60% - Extend Slicer to use new OpenVR related classes
**** Create classes qMRMLVRView, qMRMLVRWidget, etc...
**** Update layout manager to support new view type
|}

==Background and References==

2017 Winter Project Week

2017-01-12T18:35:35Z

Rankin: /* Shape Analysis, Segmentation */

__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]] (Tina Kapur, Ziyang Wang, Guillaume Pernelle, Paolo Zaffino)
#[[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 Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)
#[[2017 Winter Project Week/Slicer_HoloLens | 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)

==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)

==Background and References==


==Next project week==
#[[2017 Winter Project Week/Next project week| Next project week]] (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/Dinner

2017-01-11T01:06:01Z

Rankin: /* RSVPs */

==Dinner Specs==

*Date and Time: Thursday, January 12, 6pm
*Location: Desi Dhaba, 401 Massachusetts Ave, Cambridge (about 10 minute walk from MIT)
*Food: Indian. Menu: Goat curry, chicken tikka masala, chana masala (vegan), saag paneer (veg), naan, rice
*Cost: $25 - CASH ONLY! To be given to Katie Mastrogiacomo (kmast@bwh) during the week. She will provide receipts.
*Drinks: tap water is included in this price. Beyond that each person pays individually for their drinks.

==RSVPs==
# Adam Rankin
# Andras Lasso
# Curt Lisle
# Tina Kapur
# Andrey Fedorov
# Csaba Pinter
# Simon Drouin
# Alireza Mehrtash
# Henrik G. Jensen
# Beatriz Paniagua
# Beatriz Paniagua's +1
# Hans Meine
# Johan Andruejol
# Katie Mastrogiacomo
# Ron Kikinis
# Zora Kikinis
# Brian Helba
# Jennifer Nitsch
# Jean-Christophe Fillion-Robin
# Anneke Meyer
# Erik Ziegler
# Francois Rheault
# Rebekka Lauer
# Janne Beate Bakeng
# Louise Oram
# Teodora Szasz
# Danielle Pace
# David Garcia
# James Fishbaugh
# Sungmin Hong
# Mohsen Ghafoorian
# Miaomiao Zhang

2017 Winter Project Week/Slicer HoloLens

2016-12-06T16:09:58Z

Rankin: 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

2016-12-06T16:01:42Z

Rankin: /* Visualization */ Adding Slicer + HoloLens projcet

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

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

=='''Logistics''' ==

*'''Dates:''' January 9-13, 2017.
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.

== 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|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]

==Conference Calls for Preparation==

Domestic conference call number: 800-501-8979 <br>
Access code: 7327389 <br>

[[media:TollFree.png|International conference call numbers]] <br>
Access code: 7327389 <br>

Weekly, Tuesdays 10am, Boston time from Nov 22, 2016 to Jan 3rd, 2017

===Tcon #4: December 6 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials

Participants
* Tina Kapur (MIT) - organizer
* Steve Pieper (Isomics/BWH)
* Beatriz, JC (Kitware)

===Tcon #3: November 29 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials
Participants
* Tina Kapur (MIT) - organizer; planning Nvidia webinars. Proposal to use Monday as a schedule for the deep learning workshop before workshop begins.
*Steve Pieper (Isomics/BWH) - NVidia update; met with Abdul at NVidia (Medical applications of deep learning). Positive meeting and Slicer might be a reference platform. NVIdia will host a Monday Afternoon session at Project Week and hold outside webinars for basic deep learning information. Considering two or three days of a few hours each for webinar. Discussion of a prize board awarded for demonstrations that Nvidia could use.
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Beatriz, Alexis, and JC (Kitware) - Slicer support and 3 other projects (1) customized childrern's medical, (1) Alex submitted volumetric meshing project in Slicer idea to the NA-MIC email list; have a discussion on Meshing; the goal is for Finite Element analsis and light imaging (2), better MATLAB integration (use Python-like interface). (3) Beatrix - shape analysis algorithms to be added to Slicer based on recently-funded grant.
*JC (Kitware) - integration of iPython and Slicer; Tina Suggested also Deep Infer framework to integrate with Slicer
*Louise Oram (Stockholm) - Specialization of Slicer for Liver surgery, possibly using SliceLet approach or other way to tailor the Slicer UI. Currently customizations need to be in the Extension catalog. Also interested in Liver vessel segmentation project and other Liver segmentation tasks. This might complement with MeVIS lab capability focused on liver. Separate modules for liver surgery that might be integrated together later.
*Frank Pricework (BWH) - General GPU programming; experiment with rehosting algorithms has has previously developed to GPU.
*Paolo, Italy - (Summer Project Week Host)
*Naboo (Old Dominion) - two possible projects, not certain yet - (1) smaller training datasets for medical images, (2) braining atlas segmentation integration with Slicer.
*Curt Lisle (KnowledgeVis) - (1) web-based transition of subset of Slicer capability, (2) Iowa Meshing Module move from 3.6 to 4.7 (with Alex from Kitware); (3) possible integration of web-based volume rendering;
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Eric Seigler - OHIS Cornerstone Lesion Tracker author; Integrating interactive segmentation into the web-based framework

Discussions
*Training deep learning networks with smaller datasets.
*Integrating of projects with Slicer & architecture will be a discussion topic during the week.
*Everybody, be sure to register on the Wiki for the workshop; come up with a title and short description of the project(s) you will work on.
*OK to send info to the NA-MIC email list

===Tcon #2: November 22 ===
*10am Boston time
*Topics: continue Deep Learning, Web-based software
*Participants (interests)
# Tina Kapur, BWH (needle detection)
# Steve Pieper, Isomics (web-based software, GPU computing)
#Mahbub, Old Dominion University (creating architectures for deep learning networks in matlab, bridge to Slicer, MICCAI challenge code into Slicer, make learning faster and with less training)
#Siddiqi, Old Dominion
#Nicole Aucoin, BWH
#Abdul, NVIDIA Business Development (potential deep learning tutorials by web conference before the event, then at the event)
#Able Brown, NVIDIA
#JC, Kitware
#Krisztina Fischer, BWH
#Andrew Beard, MGH (deep learning, parameter estimation from MRI)
#Gordon Harris, MGH
#Laurent Chauvin, ETS Montreal (CNN, GPUs)
#John Toeber, Bremen U
#Lauren O'Donnell, BWH
#Fan Zhang, BWH
#Isaiah Norton, BWH
#Wu Ye, BWH
#Erik Siegler, MGH (Slicer / ePad connection with LesionTracker; more web-based technologies; discussion of ePad custom widget that will send out connections to remote jobs., PET/CT Lymphoma workshop as extension to lesion tracker.)
#Pete Anderson (Open source tracker)
#Guillaume Pernelle, Imperial College (CNNs, LSTMs, Deep Learning, GPUs)
#Mike Halle, BWH (slicer cross-platform architecture to work for hardware-specific; proxy running cloud that can support interface, Atlas browser is an active project for web-based interface. Slicer success is primarily application-level tools. The community could benefit with architectural study.)
#Louise, Oslo, Norway (high-speed pipelining of image processing for liver resections. )
#Paolo, Catanzaro, Italy (Multiple GPU system architecture)
#Salvatore, Catanzaro, Italy
#Daniel Rubin, Stanford
#Curt Lisle, Knowledgevis (has image web-based workflow systems; Deeply interested in web transition of imaging technologies. Also interested (but not experienced) in deep learning application; particularly feature recognition; small animal imaging applications)
#Charles Guttman, BWH (has MS data, wants to use Docker-based repository. (Boutique looks like a good repository)

===Tcon #1: November 15 ===
*10am Boston time
*Emergent interest in the application of Deep Learning techniques to medical image analysis.

Participants and interests
*#Tina Kapur, BWH -- needle detection
*#Steve Pieper, Isomics - GPUs
*#Andras Lasso, Queens - Slicer expert
*#Frankie Preiswerk, BWH -- hybrid ultrasound and MRI, interested in NVIDIA workshop
*#JC, Kitware -- Slicer expert
*#Mike Halle, BWH -- image feature search using deep learning (w/ Sandy Wells)
*#Peter Neher, DKFZ (filling in for Marco Nolden) -- experience with deep learning with face recognition
*#Nicole Aucoin, BWH -- Slicer expert
*#Alireza Mehrtash, UBC, BWH -- deep learning for prostate interventions, extension server for deep learning for Slicer
*#Daniel Rubin deep learning
*#Krisztina Fischer -- teaching

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 9
!style="width:18%" |Tuesday, January 10
!style="width:18%" |Wednesday, January 11
!style="width:18%" |Thursday, January 12
!style="width:18%" |Friday, January 13
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#faedb6"| '''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|rowspan="2"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-10:30am'''
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|-
|bgcolor="#ffffdd"|'''10:30am-12pm:'''
|'''Talk (Sebastian Ourselin, PhD, UCL)'''
|
|
|
|Project Reporting
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1:00-5:30pm'''
|'''1:00pm-2:30pm:''' Project Presentations
|
|
|
|'''1:30-2:30pm:''' [[AMIGO_TourPW2017Winter|AMIGO Tour]]
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day <br> (Optional) [[2017_Winter_Project_Week/Dinner|Dinner on Thursday Night]]
|
|}

==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'''=

The '''Independent Activities Period (IAP) 2017 at MIT''' is scheduled for '''January 9 through February 3, 2017'''. Visit [http://web.mit.edu/iap/listings/index.html Browse Listings] to see what will be offered in this IAP.

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

== Learning and GPUs ==

== Web Technologies ==

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

== IGT ==
* [[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)

== Infrastructure ==

== DICOM ==

= '''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].

2017 Winter Project Week

2016-12-06T15:59:31Z

Rankin: /* IGT */

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

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

=='''Logistics''' ==

*'''Dates:''' January 9-13, 2017.
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.

== 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|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]

==Conference Calls for Preparation==

Domestic conference call number: 800-501-8979 <br>
Access code: 7327389 <br>

[[media:TollFree.png|International conference call numbers]] <br>
Access code: 7327389 <br>

Weekly, Tuesdays 10am, Boston time from Nov 22, 2016 -- Jan 3rd, 2017

===Tcon #4: December 6 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials

Participants
* Tina Kapur (MIT) - organizer
* Steve Pieper (Isomics/BWH)
* Beatriz, JC (Kitware)

===Tcon #3: November 29 ===
*10am Boston time
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials
Participants
* Tina Kapur (MIT) - organizer; planning Nvidia webinars. Proposal to use Monday as a schedule for the deep learning workshop before workshop begins.
*Steve Pieper (Isomics/BWH) - NVidia update; met with Abdul at NVidia (Medical applications of deep learning). Positive meeting and Slicer might be a reference platform. NVIdia will host a Monday Afternoon session at Project Week and hold outside webinars for basic deep learning information. Considering two or three days of a few hours each for webinar. Discussion of a prize board awarded for demonstrations that Nvidia could use.
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Beatriz, Alexis, and JC (Kitware) - Slicer support and 3 other projects (1) customized childrern's medical, (1) Alex submitted volumetric meshing project in Slicer idea to the NA-MIC email list; have a discussion on Meshing; the goal is for Finite Element analsis and light imaging (2), better MATLAB integration (use Python-like interface). (3) Beatrix - shape analysis algorithms to be added to Slicer based on recently-funded grant.
*JC (Kitware) - integration of iPython and Slicer; Tina Suggested also Deep Infer framework to integrate with Slicer
*Louise Oram (Stockholm) - Specialization of Slicer for Liver surgery, possibly using SliceLet approach or other way to tailor the Slicer UI. Currently customizations need to be in the Extension catalog. Also interested in Liver vessel segmentation project and other Liver segmentation tasks. This might complement with MeVIS lab capability focused on liver. Separate modules for liver surgery that might be integrated together later.
*Frank Pricework (BWH) - General GPU programming; experiment with rehosting algorithms has has previously developed to GPU.
*Paolo, Italy - (Summer Project Week Host)
*Naboo (Old Dominion) - two possible projects, not certain yet - (1) smaller training datasets for medical images, (2) braining atlas segmentation integration with Slicer.
*Curt Lisle (KnowledgeVis) - (1) web-based transition of subset of Slicer capability, (2) Iowa Meshing Module move from 3.6 to 4.7 (with Alex from Kitware); (3) possible integration of web-based volume rendering;
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation
*Eric Seigler - OHIS Cornerstone Lesion Tracker author; Integrating interactive segmentation into the web-based framework

Discussions
*Training deep learning networks with smaller datasets.
*Integrating of projects with Slicer & architecture will be a discussion topic during the week.
*Everybody, be sure to register on the Wiki for the workshop; come up with a title and short description of the project(s) you will work on.
*OK to send info to the NA-MIC email list

===Tcon #2: November 22 ===
*10am Boston time
*Topics: continue Deep Learning, Web-based software
*Participants (interests)
# Tina Kapur, BWH (needle detection)
# Steve Pieper, Isomics (web-based software, GPU computing)
#Mahbub, Old Dominion University (creating architectures for deep learning networks in matlab, bridge to Slicer, MICCAI challenge code into Slicer, make learning faster and with less training)
#Siddiqi, Old Dominion
#Nicole Aucoin, BWH
#Abdul, NVIDIA Business Development (potential deep learning tutorials by web conference before the event, then at the event)
#Able Brown, NVIDIA
#JC, Kitware
#Krisztina Fischer, BWH
#Andrew Beard, MGH (deep learning, parameter estimation from MRI)
#Gordon Harris, MGH
#Laurent Chauvin, ETS Montreal (CNN, GPUs)
#John Toeber, Bremen U
#Lauren O'Donnell, BWH
#Fan Zhang, BWH
#Isaiah Norton, BWH
#Wu Ye, BWH
#Erik Siegler, MGH (Slicer / ePad connection with LesionTracker; more web-based technologies; discussion of ePad custom widget that will send out connections to remote jobs., PET/CT Lymphoma workshop as extension to lesion tracker.)
#Pete Anderson (Open source tracker)
#Guillaume Pernelle, Imperial College (CNNs, LSTMs, Deep Learning, GPUs)
#Mike Halle, BWH (slicer cross-platform architecture to work for hardware-specific; proxy running cloud that can support interface, Atlas browser is an active project for web-based interface. Slicer success is primarily application-level tools. The community could benefit with architectural study.)
#Louise, Oslo, Norway (high-speed pipelining of image processing for liver resections. )
#Paolo, Catanzaro, Italy (Multiple GPU system architecture)
#Salvatore, Catanzaro, Italy
#Daniel Rubin, Stanford
#Curt Lisle, Knowledgevis (has image web-based workflow systems; Deeply interested in web transition of imaging technologies. Also interested (but not experienced) in deep learning application; particularly feature recognition; small animal imaging applications)
#Charles Guttman, BWH (has MS data, wants to use Docker-based repository. (Boutique looks like a good repository)

===Tcon #1: November 15 ===
*10am Boston time
*Emergent interest in the application of Deep Learning techniques to medical image analysis.

Participants and interests
*#Tina Kapur, BWH -- needle detection
*#Steve Pieper, Isomics - GPUs
*#Andras Lasso, Queens - Slicer expert
*#Frankie Preiswerk, BWH -- hybrid ultrasound and MRI, interested in NVIDIA workshop
*#JC, Kitware -- Slicer expert
*#Mike Halle, BWH -- image feature search using deep learning (w/ Sandy Wells)
*#Peter Neher, DKFZ (filling in for Marco Nolden) -- experience with deep learning with face recognition
*#Nicole Aucoin, BWH -- Slicer expert
*#Alireza Mehrtash, UBC, BWH -- deep learning for prostate interventions, extension server for deep learning for Slicer
*#Daniel Rubin deep learning
*#Krisztina Fischer -- teaching

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 9
!style="width:18%" |Tuesday, January 10
!style="width:18%" |Wednesday, January 11
!style="width:18%" |Thursday, January 12
!style="width:18%" |Friday, January 13
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#faedb6"| '''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|rowspan="2"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-10:30am'''
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|bgcolor="#88aaae"|Clinical Topics
|-
|bgcolor="#ffffdd"|'''10:30am-12pm:'''
|'''Talk (Sebastian Ourselin, PhD, UCL)'''
|
|
|
|Project Reporting
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1:00-5:30pm'''
|'''1:00pm-2:30pm:''' Project Presentations
|
|
|
|'''1:30-2:30pm:''' [[AMIGO_TourPW2017Winter|AMIGO Tour]]
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day <br> (Optional) [[2017_Winter_Project_Week/Dinner|Dinner on Thursday Night]]
|
|}

==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'''=

The '''Independent Activities Period (IAP) 2017 at MIT''' is scheduled for '''January 9 through February 3, 2017'''. Visit [http://web.mit.edu/iap/listings/index.html Browse Listings] to see what will be offered in this IAP.

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

== Learning and GPUs ==

== Web Technologies ==

== Visualization ==

== IGT ==
* [[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)

== Infrastructure ==

== DICOM ==

= '''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].

2016 Summer Project Week/OpenVR integration

2016-06-25T09:14:08Z

Rankin: /* Project Description */ Adding approach details

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

==Key Investigators==
* Adam Rankin (Robarts Research Institute)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Render Slicer to the Oculus DK2
** Integrate VTK7.1 into Slicer
** Integrate vtkOpenVR classes into Slicer
*** Extend ctkVTKAbstractView to support creation of configurable render window/interactor/etc...
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Download vtkOpenVR remote module and build with VTK: http://vtk.1045678.n5.nabble.com/attachment/5737996/0/vtkOpenVR.remote.cmake
** http://www.vtk.org/Wiki/VTK/Remote_Modules
* '''Edit downloaded remote module to strip everything related to the factory overrides'''
* Clone slicer from https://github.com/adamrankin/Slicer.git
** Switch to branch slicer_vtk71
* CMake/Build Slicer
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* [[File:Car.jpg]]
</div>
</div>

2016 Summer Project Week

2016-06-25T08:54:00Z

Rankin: /* Worldwide Ultrasound Navigation */ Adding SINTEF contributors

__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_Imaging_workflow_in_Hybrid_ORs | 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 Documentations 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

2016-06-25T08:48:18Z

Rankin: /* Worldwide Ultrasound Navigation */

__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 (PLUS library: 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 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)
* [[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_Imaging_workflow_in_Hybrid_ORs | 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 Documentations 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/OpenVR integration

2016-06-25T08:46:02Z

Rankin:

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

==Key Investigators==
* Adam Rankin (Robarts Research Institute)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Render Slicer to the Oculus DK2
** Integrate VTK7.1 into Slicer
** Integrate vtkOpenVR classes into Slicer
*** Extend ctkVTKAbstractView to support creation of configurable render window/interactor/etc...
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Hack, hack, ha-- FBI: Excuse me sir. Please step this way.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* [[File:Car.jpg]]
</div>
</div>

File:Car.jpg

2016-06-25T08:43:23Z

Rankin:

2016 Summer Project Week

2016-06-24T08:45:18Z

Rankin: Formatting

__NOTOC__

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

<font color="red" size="30">Please fill in the survey about project weeks today!</font>

<font size="28">
[https://hms.az1.qualtrics.com/jfe/form/SV_6gK6BFe4Ivfo9RH click here]
</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].

='''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
***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.

='''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 (all day)]]
|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 | Guidelets (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]] (Prashin Unadkat, Sarah Frisken, Anna Roethe, 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, Longquan Chen)

=== 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, 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)

=== 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 (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/Breakout Session Slicer Extensions

2016-06-22T13:19:20Z

Rankin:

Google Event
* [https://plus.google.com/events/cs67o0d5sol9sjs5jkrt1371k30 Link]

Moderator: Steve Pieper

* [https://jcfr.github.io/slicer_projectweek_2016-06-22_slicerextensions_talk/#/ Summary of current status and future plans]

* Gel dosimetry slicelet [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry extension]
** Specification & design: data-flow diagram defining the workflow steps that were eventually implemented (on extension page)
** Tutorial slides and dataset (on extension page)
** [https://app.assembla.com/spaces/slicerrt/subversion/source/HEAD/trunk/GelDosimetryAnalysis Code]

2016 Summer Project Week

2016-06-16T16:03:49Z

Rankin: /* Equipment */

__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
*** 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
!style="width:15%" |Thursday, June 23 <br> Congress Hall of CARS
!style="width:15%" |Friday, June 24 <br> Congress Hall of CARS
!style="width:15%" |Saturday, June 25 <br> Congress Hall of CARS
|-
|bgcolor="#ffffdd"|'''9am-10am'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="8"|
|bgcolor="#ffffff"|[[Breakout Session/Shared Software Platform for Ultrasound-Guided Medical Interventions]] (Andras Lasso)
|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"| [[Breakout Session/Slicer Extensions]]
|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"|
|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.ipcai.org/ IPCAI 2016] conference that is hosted by 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/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, Andre Mastmeyer, Tina Kapur, Paolo Zaffino)
* [[2016 Summer Project Week/Guided Ultrasound Calibration | Guided Ultrasound Calibration]] (Elvis Chen, Inês Prata, Tamas Ungi)
* [[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/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/SliceTracker | SliceTracker for Data Collection and Prostate Biopsy Support ]] (Christian Herz, Peter Behringer, Andrey Fedorov)
* [[2016 Summer Project Week/Sacral Neuromodulation | Sacral Neuromodulation ]] (Javier Pascau, Rocío López, Tamas Ungi)
* [[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 ]] (Lauren J. O'Donnell, Yannick Suter)
* [[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)
* [[2016 Summer Project Week/Slicelet For Ultrasound Acquisition | Slicelet for Ultrasound Acquisition]] (Sarah Frisken, Prashin Unadkat, Steve Pieper)
* [[2016 Summer Project Week/Fusion of Electromagnetic and Surface Scanner Data | Fusion of Electromagnetic and Surface Scanner Data]] (Javier Pascau, Mónica García)

=== Infrastructure ===
* [[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]] (Michael Onken)

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

=== Cloud ===
* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)

=== 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)

=== Informatics ===
* [[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/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/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)

=== Tutorial===
* [[2016 Summer Project Week/CameraTutorial | How to use Basler Cameras for Medical Applications]] (Peter Behringer, Santhirarajah Mathimugan, Steve Pieper)
* [[2016 Summer Project Week/SlicerDMRIDocumentation | Tutorials and Documentations 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)

= '''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)
#Gabor Fichtinger, Queen's University, Canada
# 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:Equipment Requests

2016-06-16T16:02:55Z

Rankin: /* Equipment */

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

[[2016_Summer_Project_Week#Projects|Projects List]]

==Equipment==
* Telemed US Probe
* Magnetic tracker
* Loudspeakers
* HTC Vive

2016 Summer Project Week/OpenVR integration

2016-05-25T17:04:46Z

Rankin: /* Project Description */

2016 Summer Project Week/OpenVR integration

2016-05-25T17:02:56Z

Rankin: /* Key Investigators */

2016 Summer Project Week/Tracked Ultrasound Standardization

2016-05-25T17:01:50Z

Rankin:

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

==Key Investigators==
* Andras Lasso (Queen's University, Canada)
* Christian Askeland (SINTEF, Norway)
* Simon Drouin (Montreal Neurological Institute, Canada)
* Junichi Tokuda (Brigham and Women's Hospital, Harvard Medical School, USA)
* Longquan Chen (Brigham and Women's Hospital, Harvard Medical School, USA)
* Adam Rankin (Robarts Research Institute, Canada)
* Thomas Kirchner (German Cancer Research Center, Germany)

==Background==
* NAMIC Winter 2016 [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | project page]]

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Formalize and complete OpenIGTLink v3 specification
* Complete OpenIGTLink v3 implementation
** Add support for metadata fields in v3 messages
* Finalize implementation of OpenIGTLink v3 in PLUS
* Finalize implementation of OpenIGTLink v3 in OpenIGTLink
* Finalize implementation of OpenIGTLink v3 in OpenIGTLinkRemote (SlicerIGT)
* Finalize separation of internals in OpenIGTLinkIF to enable re-use
* Maintain backwards compatibility
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2016 Summer Project Week/Tracked Ultrasound Standardization

2016-05-25T16:58:26Z

Rankin: Adding author information

2016 Summer Project Week

2016-05-25T16:58:10Z

Rankin: /* IGT */

2016 Summer Project Week

2016-05-25T16:55:25Z

Rankin: /* Registrants */

2016 Summer Project Week

2016-05-25T16:54:46Z

Rankin: /* Registrants */

2016 Summer Project Week

2016-05-25T16:54:02Z

Rankin: /* IGT */

2016 Summer Project Week

2016-05-25T16:36:57Z

Rankin: /* Registrants */

2016 Summer Project Week

2016-05-25T16:32:24Z

Rankin:

2016 Summer Project Week

2016-05-25T16:31:37Z

Rankin: /* Equipment */

2016 Summer Project Week

2016-05-25T16:31:13Z

Rankin: /* Augmented Reality */

2016 Summer Project Week

2016-05-25T16:31:00Z

Rankin: /* Augmented Reality */

2016 Summer Project Week/OpenVR integration

2016-05-25T16:30:47Z

Rankin: Created page with "__NOTOC__ <gallery> Image:PW-Summer2016.png|Projects List </gallery> ==Key Investigators== * * ==Project Description== <div style="ma..."

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

==Key Investigators==
*
*

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2016 Summer Project Week/Tracked Ultrasound Standardization

2016-05-25T16:30:31Z

Rankin: Created page with "__NOTOC__ <gallery> Image:PW-Summer2016.png|Projects List </gallery> ==Key Investigators== * * ==Project Description== <div style="ma..."

2016 Summer Project Week:Equipment Requests

2016-05-25T16:30:09Z

Rankin:

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

[[2016_Summer_Project_Week#Projects|Projects List]]

==Equipment==
* Telemed US Probe
* Magnetic tracker

2016 Summer Project Week:Equipment Requests

2016-05-25T16:29:11Z

Rankin: Created page with "300px ==Equipment== * Telemed US Probe * Magnetic tracker"

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

==Equipment==
* Telemed US Probe
* Magnetic tracker

2016 Summer Project Week

2016-05-25T16:28:30Z

Rankin: /* Equipment */

2016 Summer Project Week/Guided Ultrasound Calibration

2016-05-25T16:27:00Z

Rankin: Created page with "__NOTOC__ <gallery> Image:PW-Summer2016.png|Projects List </gallery> ==Key Investigators== * Elvis Chen (Robarts Research Institute) * A..."

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

==Key Investigators==
* Elvis Chen (Robarts Research Institute)
* Adam Rankin (Robarts Research Institute)

==Background==
* IJCARS Paper: http://link.springer.com/article/10.1007/s11548-016-1390-7
==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2016 Summer Project Week

2016-05-25T16:25:22Z

Rankin: /* IGT */

2016 Summer Project Week

2016-05-25T16:24:59Z

Rankin: /* IGT */ Adding tracked ultrasound standardization project

2016 Summer Project Week

2016-05-25T16:05:07Z

Rankin: /* Projects */ Forgot link structure for last project

2016 Summer Project Week

2016-05-25T16:04:26Z

Rankin: /* Projects */ Restructuring into categories

2016 Winter Project Week/Projects/TrackedUltrasoundStandardization

2016-01-08T18:40:57Z

Rankin: /* OpenIGTLink Revisions */

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

==Key Investigators==
[[Image:UltrasoundToolGuidance3dOnly.gif|right]]
* Andras Lasso, Tamas Ungi (PerkLab, Queen's University)
* Christian Askeland, Ingerid Reinertsen, Ole Vegard Solberg (CustusX, IGT research, SINTEF)
* Simon Drouin (Mcgill University, Montreal, Canada)
* Junichi Tokuda (BWH)
* Steve Pieper (Isomics)
* Adam Rankin (VASST Laboratory, Western University, Canada)
* Thomas Kirchner, Janek Gröhl (MITK, DKFZ, Heidelberg, Germany)

==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;"
|
* Establish a common software platform for tracked ultrasound and image-guided interventions by converging existing IGT toolkits:
** [http://www.slicer.org 3D Slicer], [http://www.slicerigt.org SlicerIGT extension]
** [http://www.plustoolkit.org Plus toolkit]
** [http://custusx.org/ CustusX]
** [http://www.bic.mni.mcgill.ca/~sdrouin/Ibis IBIS]
** [http://www.imaging.robarts.ca/petergrp/Technology Echelon]
** [http://mitk.org/wiki/IGT MITK-IGT]
|
* Pre-Project Week online meetings and emails
** Notes below
** SINTEF design document [https://github.com/SINTEFMedtek/CustusX/wiki/OpenIGTLink-US-messaging-proposal]
* Coordination with the CommonTK effort
* Survey of current implementations and use cases
* Development of long-term development practices to encourage collaboration
|
* IGSIO [https://github.com/igsio]
* Preparation meeting minutes [[2016_Winter_Project_Week:TrackedUltrasoundStandardization/PreparationMeetings|[0]]]
* Live meeting minutes [https://docs.google.com/document/d/1jOHkFQJ5-GPyT3b9XHBJ5rnVkNOQQ2Q6G6evTfnl-CU/edit?usp=sharing]
|}

== OpenIGTLink Revisions ==
v3 proposal document [http://openigtlink.org/protocols/v3_proposal.html]
=== Tracked ultrasound OpenIGTLink client ===
* Move out part of OpenIGTLinkIF
* Only use OpenIGTLink and VTK

====Commands====
=====SetDeviceParameters=====
<b>Message</b>
<Command>
<Parameter Name=”Depth” Value=”45” />
<Parameter Name=”Gain” Value=”35” />
</Command>

<b>Response 1</b>
<Command>
<Result>SetDeviceParameters: success</Result>
<Parameter Name=”Depth” Value=”45” />
<Parameter Name=”Gain” Value=”35” />
...
</Command>

<b>Response 2</b>
<Command>
<Result>SetDeviceParameters: failure</Result> 
</Command>

=====GetDeviceParameters=====
<b>Message</b>
<Command>
<Parameter Name=”Depth” />
<Parameter Name=”Gain” />
...
</Command>

<b>Response</b>
<Command>
<Result>GetDeviceParameters: success</Result>
<Parameter Name=”Depth” Value=”45” />
<Parameter Name=”Gain” Value=”35” />
...
</Command>

=====SubscribeDeviceParameters=====
This will cause the server to send a GetDeviceParameters reply every time any of the subscribed parameters change.

<b>Message</b>
<Command>
<Parameter Name=”Depth” Subscribe=”TRUE” />
<Parameter Name=”Gain” Subscribe=”FALSE” />
...
</Command>

<b>Response</b>
<Command>
<Result>SubscribeDeviceParameters: success</Result>
<Parameter Name=”Depth” Subscribed="TRUE" />
<Parameter Name=”Gain” Subscribed="FALSE" />
...
</Command>

=====GetCapabilities=====
SINTEF will specify and implement.

<b>Message</b>
<Command></Command>

<b>Response</b>
<Command>
<Result>GetCapabilities: success</Result>
<UltrasoundCapabilities>
<Probes>
<Probe name="L14-5/38"/>
<Probe name="C5-2/42"/>
</Probes>
<ImagingModes>
<ImagingMode Name=”b-mode+angio”>B-Mode,Angio</ImagingMode>
</ImagingModes>
<Streams>
<Stream name="B-Mode">
<Parameters>
<Parameter name="depth" min="5" max="220" step="5"/>
</Parameters>
</Stream>
<Stream name="Angio">
<Parameters>
<Parameter name="depth" min="5" max="220" step="5"/>
</Parameters>
</Stream>
</Streams>
<Presets>
<Preset name="Vascular small object B+Angio">
<Probe Name=”L14-5/38” />
<Parameter Name=”Depth” Value=”50” />
</Preset>
</Presets>
</UltrasoundCapabilities>
</Command>
===Tracking===
Tracked ultrasound communication will use the TDATA message.

Use 1 bit of the Reserved byte to indicate valid/invalid status

Use metadata attributes for tool status information:

====Attributes====
<ToolStatus>
<Tool Id=”Reference” Status=”WARNING” Description=”Marker 1 on tool X is damaged” />
</ToolStatus>

* Status
** "OK"
** "WARNING"
** "ERROR"
* Description: human-readable string

===Meta Data===
====Header V1====
Bytes
0 2 14 34 42 50 58
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
| V | TYPE | DEVICE_NAME | TIME_STAMP | BODY_SIZE | CRC64 |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

====Header V2====
<nowiki>#</nowiki>Bytes HEADER_FIELD
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
0 V 2 TYPE 14 DEV_NAME 34 TS 42 BODY_SIZE 50 CRC64 58 EXT_HEADER_SIZE 60 METADATA_SIZE 64 MSG_ID 68 RV 72 CONTENT… | METADATA… |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
* V = VERSION
* DEV_NAME = DEVICE_NAME
* RV = RESERVED

=====EXT_HEADER=====
v1 header (58 bytes) + new header (EXT_HEADER_SIZE bytes)

=====CONTENT (=v1 body)=====
BODY_SIZE - EXT_HEADER_SIZE - METADATA_SIZE

=====METADATA=====
<nowiki>#</nowiki>Bytes HEADER_FIELD
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
|INDEX_COUNT (uint16) | KEY_SIZE (uint16) | VALUE_ENCODING (uint16) | VALUE_SIZE (uint32) | … | KEY | VALUE | … |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

=====VALUE_ENCODING=====
As specified at http://www.iana.org/assignments/character-sets/character-sets.xhtml

=====BODY=====
Contains extended header data, message content, and metadata.

==US over OpenIGTLink==
===Parameters===
<b>Read-write</b>
* Depth (mm): (“40”, “45”, “50”, …)
* ImagingMode (string): (“bmode”, “bmode+rf”, “bmode+angio”, “rf+angio”, ...)
* Probe (string): probe name (“L14-5/38”)
* Frequency (MHz)
* DynRange (db)
* Gain (%)
* Power (%)
* Zoom (%)
* SoundVelocity (m/s)
* TGC (space-separated string, each entry -1.0 to 1.0)
* AcquisitionState (string): “FREEZE” or “RUN”

<b>Read-only</b>
* ClipRectangleOrigin="27 27"
* ClipRectangleSize="766 562"
* FanAnglesDeg=”-30 30” (for 3D: FanAnglesDeg=”-30 30 -15 15”)
* FanOriginPixel=”240 10”
* FanRadiusStartPixel=”30”
* FanRadiusStopPixel=”500”
* Encoding: how to interpret values ("BRIGHTNESS", "RF_REAL", "RF_IQ_LINE", "RF_I_LINE_Q_LINE", "RGB_COLOR")

== Implementation plan ==
=== Tasks ===
* Clean up the vtkMRMLIGTLConnectorNode to be logic, MRML and Slicer free
* Creating a new converter base class which does not depend on MRML
* Implementation of the new Command Message
=== Github Fork ===
* OpenIGTLinkIF fork [https://github.com/drouin-simon/OpenIGTLinkIF]
* OpenIGTLink fork [https://github.com/lassoan/OpenIGTLink]
=== PLUS ===
* Interson probe settings [https://www.assembla.com/spaces/plus/tickets/869-interson-probe-settings-/details]
* Interson class cleanup [https://www.assembla.com/spaces/plus/tickets/897-clean-up-interson-video-source-code/details]
* Get/Set TGC support for US devices [https://www.assembla.com/spaces/plus/tickets/1056-add-tgc-support-to-ultrasonix-interface/details]
* Get transform over OpenIGTLink [https://www.assembla.com/spaces/plus/tickets/1054-add-get_transform-command-to-plus-server-to-support-querying-of-transforms/details]
* Sonix transition to imaging parameters [https://www.assembla.com/spaces/plus/tickets/1058-convert-sonixvideo-source-to-use-new-imaging-parameters-design/details]

=== CustusX ===
* Example CustusX class [https://github.com/SINTEFMedtek/CustusX/blob/master/source/resource/OpenIGTLinkUtilities/cxIGTLinkConversionImage.h]

==Presentations==
* [[Media:NAMIC - IGT - Adam Rankin.pptx|Adam Rankin, Robarts Research Institute]]
* [[Media:PerkLabTrackedUs.pdf|Andras Lasso, PerkLab, Queen's University]]
* [[Media:MITKTrackedProbes.pdf|Thomas Kirchner, CAI group, German Cancer Research Center]]

2016 Winter Project Week/Projects/TrackedUltrasoundStandardization

2016-01-08T18:37:29Z

Rankin: /* Parameters */

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

==Key Investigators==
[[Image:UltrasoundToolGuidance3dOnly.gif|right]]
* Andras Lasso, Tamas Ungi (PerkLab, Queen's University)
* Christian Askeland, Ingerid Reinertsen, Ole Vegard Solberg (CustusX, IGT research, SINTEF)
* Simon Drouin (Mcgill University, Montreal, Canada)
* Junichi Tokuda (BWH)
* Steve Pieper (Isomics)
* Adam Rankin (VASST Laboratory, Western University, Canada)
* Thomas Kirchner, Janek Gröhl (MITK, DKFZ, Heidelberg, Germany)

==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;"
|
* Establish a common software platform for tracked ultrasound and image-guided interventions by converging existing IGT toolkits:
** [http://www.slicer.org 3D Slicer], [http://www.slicerigt.org SlicerIGT extension]
** [http://www.plustoolkit.org Plus toolkit]
** [http://custusx.org/ CustusX]
** [http://www.bic.mni.mcgill.ca/~sdrouin/Ibis IBIS]
** [http://www.imaging.robarts.ca/petergrp/Technology Echelon]
** [http://mitk.org/wiki/IGT MITK-IGT]
|
* Pre-Project Week online meetings and emails
** Notes below
** SINTEF design document [https://github.com/SINTEFMedtek/CustusX/wiki/OpenIGTLink-US-messaging-proposal]
* Coordination with the CommonTK effort
* Survey of current implementations and use cases
* Development of long-term development practices to encourage collaboration
|
* IGSIO [https://github.com/igsio]
* Preparation meeting minutes [[2016_Winter_Project_Week:TrackedUltrasoundStandardization/PreparationMeetings|[0]]]
* Live meeting minutes [https://docs.google.com/document/d/1jOHkFQJ5-GPyT3b9XHBJ5rnVkNOQQ2Q6G6evTfnl-CU/edit?usp=sharing]
|}

== OpenIGTLink Revisions ==
=== Tracked ultrasound OpenIGTLink client ===
* Move out part of OpenIGTLinkIF
* Only use OpenIGTLink and VTK

====Commands====
=====SetDeviceParameters=====
<b>Message</b>
<Command>
<Parameter Name=”Depth” Value=”45” />
<Parameter Name=”Gain” Value=”35” />
</Command>

<b>Response 1</b>
<Command>
<Result>SetDeviceParameters: success</Result>
<Parameter Name=”Depth” Value=”45” />
<Parameter Name=”Gain” Value=”35” />
...
</Command>

<b>Response 2</b>
<Command>
<Result>SetDeviceParameters: failure</Result> 
</Command>

=====GetDeviceParameters=====
<b>Message</b>
<Command>
<Parameter Name=”Depth” />
<Parameter Name=”Gain” />
...
</Command>

<b>Response</b>
<Command>
<Result>GetDeviceParameters: success</Result>
<Parameter Name=”Depth” Value=”45” />
<Parameter Name=”Gain” Value=”35” />
...
</Command>

=====SubscribeDeviceParameters=====
This will cause the server to send a GetDeviceParameters reply every time any of the subscribed parameters change.

<b>Message</b>
<Command>
<Parameter Name=”Depth” Subscribe=”TRUE” />
<Parameter Name=”Gain” Subscribe=”FALSE” />
...
</Command>

<b>Response</b>
<Command>
<Result>SubscribeDeviceParameters: success</Result>
<Parameter Name=”Depth” Subscribed="TRUE" />
<Parameter Name=”Gain” Subscribed="FALSE" />
...
</Command>

=====GetCapabilities=====
SINTEF will specify and implement.

<b>Message</b>
<Command></Command>

<b>Response</b>
<Command>
<Result>GetCapabilities: success</Result>
<UltrasoundCapabilities>
<Probes>
<Probe name="L14-5/38"/>
<Probe name="C5-2/42"/>
</Probes>
<ImagingModes>
<ImagingMode Name=”b-mode+angio”>B-Mode,Angio</ImagingMode>
</ImagingModes>
<Streams>
<Stream name="B-Mode">
<Parameters>
<Parameter name="depth" min="5" max="220" step="5"/>
</Parameters>
</Stream>
<Stream name="Angio">
<Parameters>
<Parameter name="depth" min="5" max="220" step="5"/>
</Parameters>
</Stream>
</Streams>
<Presets>
<Preset name="Vascular small object B+Angio">
<Probe Name=”L14-5/38” />
<Parameter Name=”Depth” Value=”50” />
</Preset>
</Presets>
</UltrasoundCapabilities>
</Command>
===Tracking===
Tracked ultrasound communication will use the TDATA message.

Use 1 bit of the Reserved byte to indicate valid/invalid status

Use metadata attributes for tool status information:

====Attributes====
<ToolStatus>
<Tool Id=”Reference” Status=”WARNING” Description=”Marker 1 on tool X is damaged” />
</ToolStatus>

* Status
** "OK"
** "WARNING"
** "ERROR"
* Description: human-readable string

===Meta Data===
====Header V1====
Bytes
0 2 14 34 42 50 58
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
| V | TYPE | DEVICE_NAME | TIME_STAMP | BODY_SIZE | CRC64 |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

====Header V2====
<nowiki>#</nowiki>Bytes HEADER_FIELD
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
0 V 2 TYPE 14 DEV_NAME 34 TS 42 BODY_SIZE 50 CRC64 58 EXT_HEADER_SIZE 60 METADATA_SIZE 64 MSG_ID 68 RV 72 CONTENT… | METADATA… |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
* V = VERSION
* DEV_NAME = DEVICE_NAME
* RV = RESERVED

=====EXT_HEADER=====
v1 header (58 bytes) + new header (EXT_HEADER_SIZE bytes)

=====CONTENT (=v1 body)=====
BODY_SIZE - EXT_HEADER_SIZE - METADATA_SIZE

=====METADATA=====
<nowiki>#</nowiki>Bytes HEADER_FIELD
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
|INDEX_COUNT (uint16) | KEY_SIZE (uint16) | VALUE_ENCODING (uint16) | VALUE_SIZE (uint32) | … | KEY | VALUE | … |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

=====VALUE_ENCODING=====
As specified at http://www.iana.org/assignments/character-sets/character-sets.xhtml

=====BODY=====
Contains extended header data, message content, and metadata.

==US over OpenIGTLink==
===Parameters===
<b>Read-write</b>
* Depth (mm): (“40”, “45”, “50”, …)
* ImagingMode (string): (“bmode”, “bmode+rf”, “bmode+angio”, “rf+angio”, ...)
* Probe (string): probe name (“L14-5/38”)
* Frequency (MHz)
* DynRange (db)
* Gain (%)
* Power (%)
* Zoom (%)
* SoundVelocity (m/s)
* TGC (space-separated string, each entry -1.0 to 1.0)
* AcquisitionState (string): “FREEZE” or “RUN”

<b>Read-only</b>
* ClipRectangleOrigin="27 27"
* ClipRectangleSize="766 562"
* FanAnglesDeg=”-30 30” (for 3D: FanAnglesDeg=”-30 30 -15 15”)
* FanOriginPixel=”240 10”
* FanRadiusStartPixel=”30”
* FanRadiusStopPixel=”500”
* Encoding: how to interpret values ("BRIGHTNESS", "RF_REAL", "RF_IQ_LINE", "RF_I_LINE_Q_LINE", "RGB_COLOR")

== Implementation plan ==
=== Tasks ===
* Clean up the vtkMRMLIGTLConnectorNode to be logic, MRML and Slicer free
* Creating a new converter base class which does not depend on MRML
* Implementation of the new Command Message
=== Github Fork ===
* OpenIGTLinkIF fork [https://github.com/drouin-simon/OpenIGTLinkIF]
* OpenIGTLink fork [https://github.com/lassoan/OpenIGTLink]
=== PLUS ===
* Interson probe settings [https://www.assembla.com/spaces/plus/tickets/869-interson-probe-settings-/details]
* Interson class cleanup [https://www.assembla.com/spaces/plus/tickets/897-clean-up-interson-video-source-code/details]
* Get/Set TGC support for US devices [https://www.assembla.com/spaces/plus/tickets/1056-add-tgc-support-to-ultrasonix-interface/details]
* Get transform over OpenIGTLink [https://www.assembla.com/spaces/plus/tickets/1054-add-get_transform-command-to-plus-server-to-support-querying-of-transforms/details]
* Sonix transition to imaging parameters [https://www.assembla.com/spaces/plus/tickets/1058-convert-sonixvideo-source-to-use-new-imaging-parameters-design/details]

=== CustusX ===
* Example CustusX class [https://github.com/SINTEFMedtek/CustusX/blob/master/source/resource/OpenIGTLinkUtilities/cxIGTLinkConversionImage.h]

==Presentations==
* [[Media:NAMIC - IGT - Adam Rankin.pptx|Adam Rankin, Robarts Research Institute]]
* [[Media:PerkLabTrackedUs.pdf|Andras Lasso, PerkLab, Queen's University]]
* [[Media:MITKTrackedProbes.pdf|Thomas Kirchner, CAI group, German Cancer Research Center]]

2016 Winter Project Week/Projects/TrackedUltrasoundStandardization

2016-01-08T15:49:02Z

Rankin: /* PLUS */ adding sonix video rework ticket

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

==Key Investigators==
[[Image:UltrasoundToolGuidance3dOnly.gif|right]]
* Andras Lasso, Tamas Ungi (PerkLab, Queen's University)
* Christian Askeland, Ingerid Reinertsen, Ole Vegard Solberg (CustusX, IGT research, SINTEF)
* Simon Drouin (Mcgill University, Montreal, Canada)
* Junichi Tokuda (BWH)
* Steve Pieper (Isomics)
* Adam Rankin (VASST Laboratory, Western University, Canada)
* Thomas Kirchner, Janek Gröhl (MITK, DKFZ, Heidelberg, Germany)

==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;"
|
* Establish a common software platform for tracked ultrasound and image-guided interventions by converging existing IGT toolkits:
** [http://www.slicer.org 3D Slicer], [http://www.slicerigt.org SlicerIGT extension]
** [http://www.plustoolkit.org Plus toolkit]
** [http://custusx.org/ CustusX]
** [http://www.bic.mni.mcgill.ca/~sdrouin/Ibis IBIS]
** [http://www.imaging.robarts.ca/petergrp/Technology Echelon]
** [http://mitk.org/wiki/IGT MITK-IGT]
|
* Pre-Project Week online meetings and emails
** Notes below
** SINTEF design document [https://github.com/SINTEFMedtek/CustusX/wiki/OpenIGTLink-US-messaging-proposal]
* Coordination with the CommonTK effort
* Survey of current implementations and use cases
* Development of long-term development practices to encourage collaboration
|
* IGSIO [https://github.com/igsio]
* Preparation meeting minutes [[2016_Winter_Project_Week:TrackedUltrasoundStandardization/PreparationMeetings|[0]]]
* Live meeting minutes [https://docs.google.com/document/d/1jOHkFQJ5-GPyT3b9XHBJ5rnVkNOQQ2Q6G6evTfnl-CU/edit?usp=sharing]
|}

== OpenIGTLink Revisions ==
=== Tracked ultrasound OpenIGTLink client ===
* Move out part of OpenIGTLinkIF
* Only use OpenIGTLink and VTK

====Commands====
=====SetDeviceParameters=====
<b>Message</b>
<Command>
<Parameter Name=”Depth” Value=”45” />
<Parameter Name=”Gain” Value=”35” />
</Command>

<b>Response 1</b>
<Command>
<Result>SetDeviceParameters: success</Result>
<Parameter Name=”Depth” Value=”45” />
<Parameter Name=”Gain” Value=”35” />
...
</Command>

<b>Response 2</b>
<Command>
<Result>SetDeviceParameters: failure</Result> 
</Command>

=====GetDeviceParameters=====
<b>Message</b>
<Command>
<Parameter Name=”Depth” />
<Parameter Name=”Gain” />
...
</Command>

<b>Response</b>
<Command>
<Result>GetDeviceParameters: success</Result>
<Parameter Name=”Depth” Value=”45” />
<Parameter Name=”Gain” Value=”35” />
...
</Command>

=====SubscribeDeviceParameters=====
This will cause the server to send a GetDeviceParameters reply every time any of the subscribed parameters change.

<b>Message</b>
<Command>
<Parameter Name=”Depth” Subscribe=”TRUE” />
<Parameter Name=”Gain” Subscribe=”FALSE” />
...
</Command>

<b>Response</b>
<Command>
<Result>SubscribeDeviceParameters: success</Result>
<Parameter Name=”Depth” Subscribed="TRUE" />
<Parameter Name=”Gain” Subscribed="FALSE" />
...
</Command>

=====GetCapabilities=====
SINTEF will specify and implement.

<b>Message</b>
<Command></Command>

<b>Response</b>
<Command>
<Result>GetCapabilities: success</Result>
<UltrasoundCapabilities>
<Probes>
<Probe name="L14-5/38"/>
<Probe name="C5-2/42"/>
</Probes>
<ImagingModes>
<ImagingMode Name=”b-mode+angio”>B-Mode,Angio</ImagingMode>
</ImagingModes>
<Streams>
<Stream name="B-Mode">
<Parameters>
<Parameter name="depth" min="5" max="220" step="5"/>
</Parameters>
</Stream>
<Stream name="Angio">
<Parameters>
<Parameter name="depth" min="5" max="220" step="5"/>
</Parameters>
</Stream>
</Streams>
<Presets>
<Preset name="Vascular small object B+Angio">
<Probe Name=”L14-5/38” />
<Parameter Name=”Depth” Value=”50” />
</Preset>
</Presets>
</UltrasoundCapabilities>
</Command>
===Tracking===
Tracked ultrasound communication will use the TDATA message.

Use 1 bit of the Reserved byte to indicate valid/invalid status

Use metadata attributes for tool status information:

====Attributes====
<ToolStatus>
<Tool Id=”Reference” Status=”WARNING” Description=”Marker 1 on tool X is damaged” />
</ToolStatus>

* Status
** "OK"
** "WARNING"
** "ERROR"
* Description: human-readable string

===Meta Data===
====Header V1====
Bytes
0 2 14 34 42 50 58
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
| V | TYPE | DEVICE_NAME | TIME_STAMP | BODY_SIZE | CRC64 |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

====Header V2====
<nowiki>#</nowiki>Bytes HEADER_FIELD
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
0 V 2 TYPE 14 DEV_NAME 34 TS 42 BODY_SIZE 50 CRC64 58 EXT_HEADER_SIZE 60 METADATA_SIZE 64 MSG_ID 68 RV 72 CONTENT… | METADATA… |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
* V = VERSION
* DEV_NAME = DEVICE_NAME
* RV = RESERVED

=====EXT_HEADER=====
v1 header (58 bytes) + new header (EXT_HEADER_SIZE bytes)

=====CONTENT (=v1 body)=====
BODY_SIZE - EXT_HEADER_SIZE - METADATA_SIZE

=====METADATA=====
<nowiki>#</nowiki>Bytes HEADER_FIELD
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
|INDEX_COUNT (uint16) | KEY_SIZE (uint16) | VALUE_ENCODING (uint16) | VALUE_SIZE (uint32) | … | KEY | VALUE | … |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

=====VALUE_ENCODING=====
As specified at http://www.iana.org/assignments/character-sets/character-sets.xhtml

=====BODY=====
Contains extended header data, message content, and metadata.

==US over OpenIGTLink==
===Parameters===
<b>Read-write</b>
* Depth (mm): (“40”, “45”, “50”, …)
* ImagingMode (string): (“bmode”, “bmode+rf”, “bmode+angio”, “rf+angio”, ...)
* Probe (string): probe name (“L14-5/38”)
* Frequency (MHz)
* DynRange (db)
* Gain (%)
* Power (%)
* Zoom (%)
* SoundVelocity (m/s)
* TGC (float[], -1.0 to 1.0)
* AcquisitionState (string): “FREEZE” or “RUN”

<b>Read-only</b>
* ClipRectangleOrigin="27 27"
* ClipRectangleSize="766 562"
* FanAnglesDeg=”-30 30” (for 3D: FanAnglesDeg=”-30 30 -15 15”)
* FanOriginPixel=”240 10”
* FanRadiusStartPixel=”30”
* FanRadiusStopPixel=”500”
* Encoding: how to interpret values ("BRIGHTNESS", "RF_REAL", "RF_IQ_LINE", "RF_I_LINE_Q_LINE", "RGB_COLOR")

== Implementation plan ==
=== Tasks ===
* Clean up the vtkMRMLIGTLConnectorNode to be logic, MRML and Slicer free
* Creating a new converter base class which does not depend on MRML
* Implementation of the new Command Message
=== Github Fork ===
* OpenIGTLinkIF fork [https://github.com/drouin-simon/OpenIGTLinkIF]
* OpenIGTLink fork [https://github.com/lassoan/OpenIGTLink]
=== PLUS ===
* Interson probe settings [https://www.assembla.com/spaces/plus/tickets/869-interson-probe-settings-/details]
* Interson class cleanup [https://www.assembla.com/spaces/plus/tickets/897-clean-up-interson-video-source-code/details]
* Get/Set TGC support for US devices [https://www.assembla.com/spaces/plus/tickets/1056-add-tgc-support-to-ultrasonix-interface/details]
* Get transform over OpenIGTLink [https://www.assembla.com/spaces/plus/tickets/1054-add-get_transform-command-to-plus-server-to-support-querying-of-transforms/details]
* Sonix transition to imaging parameters [https://www.assembla.com/spaces/plus/tickets/1058-convert-sonixvideo-source-to-use-new-imaging-parameters-design/details]

=== CustusX ===
* Example CustusX class [https://github.com/SINTEFMedtek/CustusX/blob/master/source/resource/OpenIGTLinkUtilities/cxIGTLinkConversionImage.h]

==Presentations==
* [[Media:NAMIC - IGT - Adam Rankin.pptx|Adam Rankin, Robarts Research Institute]]
* [[Media:PerkLabTrackedUs.pdf|Andras Lasso, PerkLab, Queen's University]]
* [[Media:MITKTrackedProbes.pdf|Thomas Kirchner, CAI group, German Cancer Research Center]]

2016 Winter Project Week/Projects/TrackedUltrasoundStandardization

2016-01-08T15:04:01Z

Rankin: Formatting

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

==Key Investigators==
[[Image:UltrasoundToolGuidance3dOnly.gif|right]]
* Andras Lasso, Tamas Ungi (PerkLab, Queen's University)
* Christian Askeland, Ingerid Reinertsen, Ole Vegard Solberg (CustusX, IGT research, SINTEF)
* Simon Drouin (Mcgill University, Montreal, Canada)
* Junichi Tokuda (BWH)
* Steve Pieper (Isomics)
* Adam Rankin (VASST Laboratory, Western University, Canada)
* Thomas Kirchner, Janek Gröhl (MITK, DKFZ, Heidelberg, Germany)

==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;"
|
* Establish a common software platform for tracked ultrasound and image-guided interventions by converging existing IGT toolkits:
** [http://www.slicer.org 3D Slicer], [http://www.slicerigt.org SlicerIGT extension]
** [http://www.plustoolkit.org Plus toolkit]
** [http://custusx.org/ CustusX]
** [http://www.bic.mni.mcgill.ca/~sdrouin/Ibis IBIS]
** [http://www.imaging.robarts.ca/petergrp/Technology Echelon]
** [http://mitk.org/wiki/IGT MITK-IGT]
|
* Pre-Project Week online meetings and emails
** Notes below
** SINTEF design document [https://github.com/SINTEFMedtek/CustusX/wiki/OpenIGTLink-US-messaging-proposal]
* Coordination with the CommonTK effort
* Survey of current implementations and use cases
* Development of long-term development practices to encourage collaboration
|
* IGSIO [https://github.com/igsio]
* Preparation meeting minutes [[2016_Winter_Project_Week:TrackedUltrasoundStandardization/PreparationMeetings|[0]]]
* Live meeting minutes [https://docs.google.com/document/d/1jOHkFQJ5-GPyT3b9XHBJ5rnVkNOQQ2Q6G6evTfnl-CU/edit?usp=sharing]
|}

== OpenIGTLink Revisions ==
=== Tracked ultrasound OpenIGTLink client ===
* Move out part of OpenIGTLinkIF
* Only use OpenIGTLink and VTK

====Commands====
=====SetDeviceParameters=====
<b>Message</b>
<Command>
<Parameter Name=”Depth” Value=”45” />
<Parameter Name=”Gain” Value=”35” />
</Command>

<b>Response 1</b>
<Command>
<Result>SetDeviceParameters: success</Result>
<Parameter Name=”Depth” Value=”45” />
<Parameter Name=”Gain” Value=”35” />
...
</Command>

<b>Response 2</b>
<Command>
<Result>SetDeviceParameters: failure</Result> 
</Command>

=====GetDeviceParameters=====
<b>Message</b>
<Command>
<Parameter Name=”Depth” />
<Parameter Name=”Gain” />
...
</Command>

<b>Response</b>
<Command>
<Result>GetDeviceParameters: success</Result>
<Parameter Name=”Depth” Value=”45” />
<Parameter Name=”Gain” Value=”35” />
...
</Command>

=====SubscribeDeviceParameters=====
This will cause the server to send a GetDeviceParameters reply every time any of the subscribed parameters change.

<b>Message</b>
<Command>
<Parameter Name=”Depth” Subscribe=”TRUE” />
<Parameter Name=”Gain” Subscribe=”FALSE” />
...
</Command>

<b>Response</b>
<Command>
<Result>SubscribeDeviceParameters: success</Result>
<Parameter Name=”Depth” Subscribed="TRUE" />
<Parameter Name=”Gain” Subscribed="FALSE" />
...
</Command>

=====GetCapabilities=====
SINTEF will specify and implement.

<b>Message</b>
<Command></Command>

<b>Response</b>
<Command>
<Result>GetCapabilities: success</Result>
<UltrasoundCapabilities>
<Probes>
<Probe name="L14-5/38"/>
<Probe name="C5-2/42"/>
</Probes>
<ImagingModes>
<ImagingMode Name=”b-mode+angio”>B-Mode,Angio</ImagingMode>
</ImagingModes>
<Streams>
<Stream name="B-Mode">
<Parameters>
<Parameter name="depth" min="5" max="220" step="5"/>
</Parameters>
</Stream>
<Stream name="Angio">
<Parameters>
<Parameter name="depth" min="5" max="220" step="5"/>
</Parameters>
</Stream>
</Streams>
<Presets>
<Preset name="Vascular small object B+Angio">
<Probe Name=”L14-5/38” />
<Parameter Name=”Depth” Value=”50” />
</Preset>
</Presets>
</UltrasoundCapabilities>
</Command>
===Tracking===
Tracked ultrasound communication will use the TDATA message.

Use 1 bit of the Reserved byte to indicate valid/invalid status

Use metadata attributes for tool status information:

====Attributes====
<ToolStatus>
<Tool Id=”Reference” Status=”WARNING” Description=”Marker 1 on tool X is damaged” />
</ToolStatus>

* Status
** "OK"
** "WARNING"
** "ERROR"
* Description: human-readable string

===Meta Data===
====Header V1====
Bytes
0 2 14 34 42 50 58
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
| V | TYPE | DEVICE_NAME | TIME_STAMP | BODY_SIZE | CRC64 |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

====Header V2====
<nowiki>#</nowiki>Bytes HEADER_FIELD
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
0 V 2 TYPE 14 DEV_NAME 34 TS 42 BODY_SIZE 50 CRC64 58 EXT_HEADER_SIZE 60 METADATA_SIZE 64 MSG_ID 68 RV 72 CONTENT… | METADATA… |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
* V = VERSION
* DEV_NAME = DEVICE_NAME
* RV = RESERVED

=====EXT_HEADER=====
v1 header (58 bytes) + new header (EXT_HEADER_SIZE bytes)

=====CONTENT (=v1 body)=====
BODY_SIZE - EXT_HEADER_SIZE - METADATA_SIZE

=====METADATA=====
<nowiki>#</nowiki>Bytes HEADER_FIELD
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
|INDEX_COUNT (uint16) | KEY_SIZE (uint16) | VALUE_ENCODING (uint16) | VALUE_SIZE (uint32) | … | KEY | VALUE | … |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

=====VALUE_ENCODING=====
As specified at http://www.iana.org/assignments/character-sets/character-sets.xhtml

=====BODY=====
Contains extended header data, message content, and metadata.

==US over OpenIGTLink==
===Parameters===
<b>Read-write</b>
* Depth (mm): (“40”, “45”, “50”, …)
* ImagingMode (string): (“bmode”, “bmode+rf”, “bmode+angio”, “rf+angio”, ...)
* Probe (string): probe name (“L14-5/38”)
* Frequency (MHz)
* DynRange (db)
* Gain (%)
* Power (%)
* Zoom (%)
* SoundVelocity (m/s)
* TGC (float[], -1.0 to 1.0)
* AcquisitionState (string): “FREEZE” or “RUN”

<b>Read-only</b>
* ClipRectangleOrigin="27 27"
* ClipRectangleSize="766 562"
* FanAnglesDeg=”-30 30” (for 3D: FanAnglesDeg=”-30 30 -15 15”)
* FanOriginPixel=”240 10”
* FanRadiusStartPixel=”30”
* FanRadiusStopPixel=”500”
* Encoding: how to interpret values ("BRIGHTNESS", "RF_REAL", "RF_IQ_LINE", "RF_I_LINE_Q_LINE", "RGB_COLOR")

== Implementation plan ==
=== Tasks ===
* Clean up the vtkMRMLIGTLConnectorNode to be logic, MRML and Slicer free
* Creating a new converter base class which does not depend on MRML
* Implementation of the new Command Message
=== Github Fork ===
* OpenIGTLinkIF fork [https://github.com/drouin-simon/OpenIGTLinkIF]
* OpenIGTLink fork [https://github.com/lassoan/OpenIGTLink]
=== PLUS ===
* Interson probe settings [https://www.assembla.com/spaces/plus/tickets/869-interson-probe-settings-/details]
* Interson class cleanup [https://www.assembla.com/spaces/plus/tickets/897-clean-up-interson-video-source-code/details]
* Get/Set TGC support for US devices [https://www.assembla.com/spaces/plus/tickets/1056-add-tgc-support-to-ultrasonix-interface/details]
* Get transform over OpenIGTLink [https://www.assembla.com/spaces/plus/tickets/1054-add-get_transform-command-to-plus-server-to-support-querying-of-transforms/details]
=== CustusX ===
* Example CustusX class [https://github.com/SINTEFMedtek/CustusX/blob/master/source/resource/OpenIGTLinkUtilities/cxIGTLinkConversionImage.h]

==Presentations==
* [[Media:NAMIC - IGT - Adam Rankin.pptx|Adam Rankin, Robarts Research Institute]]
* [[Media:PerkLabTrackedUs.pdf|Andras Lasso, PerkLab, Queen's University]]
* [[Media:MITKTrackedProbes.pdf|Thomas Kirchner, CAI group, German Cancer Research Center]]

2016 Winter Project Week/Projects/TrackedUltrasoundStandardization

2016-01-08T14:56:45Z

Rankin: Adding complete contents of google doc

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

==Key Investigators==
[[Image:UltrasoundToolGuidance3dOnly.gif|right]]
* Andras Lasso, Tamas Ungi (PerkLab, Queen's University)
* Christian Askeland, Ingerid Reinertsen, Ole Vegard Solberg (CustusX, IGT research, SINTEF)
* Simon Drouin (Mcgill University, Montreal, Canada)
* Junichi Tokuda (BWH)
* Steve Pieper (Isomics)
* Adam Rankin (VASST Laboratory, Western University, Canada)
* Thomas Kirchner, Janek Gröhl (MITK, DKFZ, Heidelberg, Germany)

==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;"
|
* Establish a common software platform for tracked ultrasound and image-guided interventions by converging existing IGT toolkits:
** [http://www.slicer.org 3D Slicer], [http://www.slicerigt.org SlicerIGT extension]
** [http://www.plustoolkit.org Plus toolkit]
** [http://custusx.org/ CustusX]
** [http://www.bic.mni.mcgill.ca/~sdrouin/Ibis IBIS]
** [http://www.imaging.robarts.ca/petergrp/Technology Echelon]
** [http://mitk.org/wiki/IGT MITK-IGT]
|
* Pre-Project Week online meetings and emails
** Notes below
** [https://github.com/SINTEFMedtek/CustusX/wiki/OpenIGTLink-US-messaging-proposal Design document from SINTEF]
* Coordination with the CommonTK effort
* Survey of current implementations and use cases
* Development of long-term development practices to encourage collaboration
|
* [[2016_Winter_Project_Week:TrackedUltrasoundStandardization/PreparationMeetings|Minutes of preparation meetings]]
* [https://docs.google.com/document/d/1jOHkFQJ5-GPyT3b9XHBJ5rnVkNOQQ2Q6G6evTfnl-CU/edit?usp=sharing Live meeting minutes]
|}

== OpenIGTLink Revisions ==
=== Tracked ultrasound OpenIGTLink client ===
* Move out part of OpenIGTLinkIF
* Only use OpenIGTLink and VTK

====Commands====
=====SetDeviceParameters=====
<b>Message</b>
<Command>
<Parameter Name=”Depth” Value=”45” />
<Parameter Name=”Gain” Value=”35” />
</Command>

<b>Response 1</b>
<Command>
<Result>SetDeviceParameters: success</Result>
<Parameter Name=”Depth” Value=”45” />
<Parameter Name=”Gain” Value=”35” />
...
</Command>

<b>Response 2</b>
<Command>
<Result>SetDeviceParameters: failure</Result> 
</Command>

=====GetDeviceParameters=====
<b>Message</b>
<Command>
<Parameter Name=”Depth” />
<Parameter Name=”Gain” />
...
</Command>

<b>Response</b>
<Command>
<Result>GetDeviceParameters: success</Result>
<Parameter Name=”Depth” Value=”45” />
<Parameter Name=”Gain” Value=”35” />
...
</Command>

=====SubscribeDeviceParameters=====
This will cause the server to send a GetDeviceParameters reply every time any of the subscribed parameters change.

<b>Message</b>
<Command>
<Parameter Name=”Depth” Subscribe=”TRUE” />
<Parameter Name=”Gain” Subscribe=”FALSE” />
...
</Command>

<b>Response</b>
<Command>
<Result>SubscribeDeviceParameters: success</Result>
<Parameter Name=”Depth” Subscribed="TRUE" />
<Parameter Name=”Gain” Subscribed="FALSE" />
...
</Command>

=====GetCapabilities=====
SINTEF will specify and implement.

<b>Message</b>
<Command></Command>

<b>Response</b>
<Command>
<Result>GetCapabilities: success</Result>
<UltrasoundCapabilities>
<Probes>
<Probe name="L14-5/38"/>
<Probe name="C5-2/42"/>
</Probes>
<ImagingModes>
<ImagingMode Name=”b-mode+angio”>B-Mode,Angio</ImagingMode>
</ImagingModes>
<Streams>
<Stream name="B-Mode">
<Parameters>
<Parameter name="depth" min="5" max="220" step="5"/>
</Parameters>
</Stream>
<Stream name="Angio">
<Parameters>
<Parameter name="depth" min="5" max="220" step="5"/>
</Parameters>
</Stream>
</Streams>
<Presets>
<Preset name="Vascular small object B+Angio">
<Probe Name=”L14-5/38” />
<Parameter Name=”Depth” Value=”50” />
</Preset>
</Presets>
</UltrasoundCapabilities>
</Command>
===Tracking===
Tracked ultrasound communication will use the TDATA message.

Use 1 bit of the Reserved byte to indicate valid/invalid status

Use metadata attributes for tool status information:

====Attributes====
<ToolStatus>
<Tool Id=”Reference” Status=”WARNING” Description=”Marker 1 on tool X is damaged” />
</ToolStatus>

* Status
** "OK"
** "WARNING"
** "ERROR"
* Description: human-readable string

===Meta Data===
====Header V1====
Bytes
0 2 14 34 42 50 58
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
| V | TYPE | DEVICE_NAME | TIME_STAMP | BODY_SIZE | CRC64 |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

====Header V2====
<nowiki>#</nowiki>Bytes HEADER_FIELD
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
0 V 2 TYPE 14 DEV_NAME 34 TS 42 BODY_SIZE 50 CRC64 58 EXT_HEADER_SIZE 60 METADATA_SIZE 64 MSG_ID 68 RV 72 CONTENT… | METADATA… |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
* V = VERSION
* DEV_NAME = DEVICE_NAME
* RV = RESERVED

=====EXT_HEADER=====
v1 header (58 bytes) + new header (EXT_HEADER_SIZE bytes)

=====CONTENT (=v1 body)=====
BODY_SIZE - EXT_HEADER_SIZE - METADATA_SIZE

=====METADATA=====
<nowiki>#</nowiki>Bytes HEADER_FIELD
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
|INDEX_COUNT (uint16) | KEY_SIZE (uint16) | VALUE_ENCODING (uint16) | VALUE_SIZE (uint32) | … | KEY | VALUE | … |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

=====VALUE_ENCODING=====
As specified at http://www.iana.org/assignments/character-sets/character-sets.xhtml

=====BODY=====
Contains extended header data, message content, and metadata.

==US over OpenIGTLink==
===Parameters===
<b>Read-write</b>
* Depth (mm): (“40”, “45”, “50”, …)
* ImagingMode (string): (“bmode”, “bmode+rf”, “bmode+angio”, “rf+angio”, ...)
* Probe (string): probe name (“L14-5/38”)
* Frequency (MHz)
* DynRange (db)
* Gain (%)
* Power (%)
* Zoom (%)
* SoundVelocity (m/s)
* TGC (float[], -1.0 to 1.0)
* AcquisitionState (string): “FREEZE” or “RUN”

<b>Read-only</b>
* ClipRectangleOrigin="27 27"
* ClipRectangleSize="766 562"
* FanAnglesDeg=”-30 30” (for 3D: FanAnglesDeg=”-30 30 -15 15”)
* FanOriginPixel=”240 10”
* FanRadiusStartPixel=”30”
* FanRadiusStopPixel=”500”
* Encoding: how to interpret values ("BRIGHTNESS", "RF_REAL", "RF_IQ_LINE", "RF_I_LINE_Q_LINE", "RGB_COLOR")

== Implementation plan ==
=== Tasks ===
* Clean up the vtkMRMLIGTLConnectorNode to be logic, MRML and Slicer free
* Creating a new converter base class which does not depend on MRML
* Implementation of the new Command Message
=== Github Fork ===
* OpenIGTLinkIF fork [https://github.com/drouin-simon/OpenIGTLinkIF]
* OpenIGTLink fork [https://github.com/lassoan/OpenIGTLink]
=== PLUS ===
* Interson probe settings [https://www.assembla.com/spaces/plus/tickets/869-interson-probe-settings-/details]
* Interson class cleanup [https://www.assembla.com/spaces/plus/tickets/897-clean-up-interson-video-source-code/details]
* Get/Set TGC support for US devices [https://www.assembla.com/spaces/plus/tickets/1056-add-tgc-support-to-ultrasonix-interface/details]
* Get transform over OpenIGTLink [https://www.assembla.com/spaces/plus/tickets/1054-add-get_transform-command-to-plus-server-to-support-querying-of-transforms/details]
=== CustusX ===
* Example CustusX class [https://github.com/SINTEFMedtek/CustusX/blob/master/source/resource/OpenIGTLinkUtilities/cxIGTLinkConversionImage.h]

==Presentations==
* [[Media:NAMIC - IGT - Adam Rankin.pptx|Adam Rankin, Robarts Research Institute]]
* [[Media:PerkLabTrackedUs.pdf|Andras Lasso, PerkLab, Queen's University]]
* [[Media:MITKTrackedProbes.pdf|Thomas Kirchner, CAI group, German Cancer Research Center]]