NAMIC Wiki - User contributions [en]

2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink

2016-06-25T07:56:39Z

Christian.askeland:

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

==Key Investigators==
* Christian Askeland
* Janne Beate Bakeng
* Ole Vegard Solberg
* Jon Eiesland
* Longquan Chen
* Simon Drouin

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Provide support for Tracking and Ultrasound streaming in various IGT Navigation Systems, using PLUS and the OpenIGTLink.v3 protocol as a backend.
* The systems considered so far are
** CustusX (http://custusx.org/)
** IBIS (http://ibisneuronav.org/).
** Slicer
** MITK (in spirit only)
* CustusX: Phase out IGSTK (tracking) and in-house solutions (streaming).
</div>

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

<h3>Approach, Plan</h3>
* Base work on results from [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]], and the existing PLUS/OpenIGTLink support in CustusX.
* Coordinate efforts between systems doing the same job using a client side IGTL library: https://github.com/IGSIO/OpenIGTLinkIO, forked from 3DSlicer/OpenIGTLinkIF
* CustusX items:
** Replace IGSTK-based tracking. Evaluate if PLUS has the required features.
*** Semi-automatic gui-based configuration on the CX side.
*** Modify PLUS if necessary.
*** Wrap PLUS in CustusX. End users should not need to tweak PLUS-specific xml.
** Replace in-house US-streaming solutions by the new standards.
*** Try to use PLUS as backend for the Ultrasonix scanner.
*** Write a lightweight OpenIGTLink server for proprietary scanners.
*** Framegrabber/OpenCV-based streaming based on PLUS (?).

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* CustusX now receives ultrasound over OpenIGTLink/IO from PLUS: [[Media:CustusX_with_openigtlink3.mov]].
* IBIS now received tracking data over OpenIGTLink/IO from PLUS.
* The OpenIGTLinkIO library is integrated into CustusX, IBIS and Slicer as a common layer.
* See [https://github.com/IGSIO/OpenIGTLinkIO/issues/4] for a diagram relating the various applications and libraries.
* Command protocol is implemented in IO, yet to be used for controlling PLUS remotely.
</div>

2016 Summer Project Week/Tracked Ultrasound Standardization

2016-06-25T07:54:52Z

Christian.askeland:

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

File:CustusX PLUS igtl.png

2016-06-25T07:52:25Z

Christian.askeland:

2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink

2016-06-25T06:54:36Z

Christian.askeland: /* Project Description */

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

==Key Investigators==
* Christian Askeland
* Janne Beate Bakeng
* Ole Vegard Solberg
* Jon Eiesland
* Longquan Chen
* Simon Drouin

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Provide support for Tracking and Ultrasound streaming in various IGT Navigation Systems, using PLUS and the OpenIGTLink.v3 protocol as a backend.
* The systems considered so far are
** CustusX (http://custusx.org/)
** IBIS (http://ibisneuronav.org/).
** Slicer
** MITK (in spirit only)
* CustusX: Phase out IGSTK (tracking) and in-house solutions (streaming).
</div>

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

<h3>Approach, Plan</h3>
* Base work on results from [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]], and the existing PLUS/OpenIGTLink support in CustusX.
* Coordinate efforts between systems doing the same job using a client side IGTL library: https://github.com/IGSIO/OpenIGTLinkIO, forked from 3DSlicer/OpenIGTLinkIF
* CustusX items:
** Replace IGSTK-based tracking. Evaluate if PLUS has the required features.
*** Semi-automatic gui-based configuration on the CX side.
*** Modify PLUS if necessary.
*** Wrap PLUS in CustusX. End users should not need to tweak PLUS-specific xml.
** Replace in-house US-streaming solutions by the new standards.
*** Try to use PLUS as backend for the Ultrasonix scanner.
*** Write a lightweight OpenIGTLink server for proprietary scanners.
*** Framegrabber/OpenCV-based streaming based on PLUS (?).

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* CustusX now receives ultrasound over OpenIGTLink/IO from PLUS: [[Media:CustusX_with_openigtlink3.mov]].
* IBIS now received tracking data over OpenIGTLink/IO from PLUS.
* The OpenIGTLinkIO library is integrated into CustusX, IBIS and Slicer as a common layer.
* See [https://github.com/IGSIO/OpenIGTLinkIO/issues/4] for a diagram relating the various applications and libraries.
* Command protocol is implemented in IO, yet to be used for controlling PLUS remotely.
</div>

File:CustusX with openigtlink3.mov

2016-06-25T06:35:58Z

Christian.askeland: A PLUS server streaming 2D ultrasound to CustusX over OpenIGTLink.

A PLUS server streaming 2D ultrasound to CustusX over OpenIGTLink.

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

2016-06-22T11:01:01Z

Christian.askeland: /* Participants */

= Introduction =

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

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

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

* 9-10am: Introduction of existing open-source infrastructure for building ultrasound-guided intervention systems
** [[Media:Slicelets2016.pdf|Plus/SlicerIGT/3DSlicer (Andras Lasso)]]
** CustusX
** IBIS
* 10.30am-12pm: Bring your own problem - discussion of implementation options for specific clinical procedures using open-source platforms.
** EM needle guidance in breast brachytherapy (Thomas Vaughan)
** Tracked ultrasound guided lumpectomy (Tamas Ungi)
** <add your name and clinical application here>
* Afternoon: Hands-on session for setting up prototype systems for ultrasound guidance and tool navigation.

= Registration =

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

= Participants =
* Christian Askeland
* Janne Beate Bakeng
* David Black
* Longquan Chen
* Lauren O'Donnell
* Simon Drouin
* Jon Eiesland
* Sarah Frisken
* Mónica García-Sevilla
* Verónica García-Vazquez
* Thomas Kirchner
* Bojan Kocev
* Ines Machado
* David García-Mato
* Hans Meine
* Javier Pascau
* Steve Pieper
* Csaba Pinter
* Adam Rankin
* Ole Vegard Solberg
* Yannick Suter
* Junichi Tokuda
* Tamas Ungi
* Rocío Lopez-Velasco
* Frank Lindseth
* Ingerid Reinertsen

2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink

2016-06-20T11:13:28Z

Christian.askeland:

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

==Key Investigators==
* Christian Askeland
* Janne Beate Bakeng
* Ole Vegard Solberg
* Jon Eiesland
* Longquan Chen
* Simon Drouin

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Provide support for Tracking and Ultrasound streaming in various IGT Navigation Systems, using PLUS and the OpenIGTLink.v3 protocol as a backend.
* The systems considered so far are
** CustusX (http://custusx.org/)
** IBIS (http://ibisneuronav.org/).
** Slicer
** MITK (in spirit only)
* CustusX: Phase out IGSTK (tracking) and in-house solutions (streaming).
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Base work on results from [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]], and the existing PLUS/OpenIGTLink support in CustusX.
* Coordinate efforts between systems doing the same job using a client side IGTL library: https://github.com/IGSIO/OpenIGTLinkIO, forked from 3DSlicer/OpenIGTLinkIF
* CustusX items:
** Replace IGSTK-based tracking. Evaluate if PLUS has the required features.
*** Semi-automatic gui-based configuration on the CX side.
*** Modify PLUS if necessary.
*** Wrap PLUS in CustusX. End users should not need to tweak PLUS-specific xml.
** Replace in-house US-streaming solutions by the new standards.
*** Try to use PLUS as backend for the Ultrasonix scanner.
*** Write a lightweight OpenIGTLink server for proprietary scanners.
*** Framegrabber/OpenCV-based streaming based on PLUS (?).

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

See [https://github.com/IGSIO/OpenIGTLinkIO/issues/4] for a diagram relating the various applications and libraries.

2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink

2016-06-20T11:12:40Z

Christian.askeland:

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

==Key Investigators==
* Christian Askeland
* Janne Beate Bakeng
* Ole Vegard Solberg
* Jon Eiesland
* Longquan Chen
* Simon Drouin

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Provide support for Tracking and Ultrasound streaming in various IGT Navigation Systems, using PLUS and the OpenIGTLink.v3 protocol as a backend.
* The two systems considered so far are
** CustusX (http://custusx.org/)
** IBIS (http://ibisneuronav.org/).
** Slicer
** MITK (in spirit only)
* CustusX: Phase out IGSTK (tracking) and in-house solutions (streaming).
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Base work on results from [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]], and the existing PLUS/OpenIGTLink support in CustusX.
* Coordinate efforts between systems doing the same job using a client side IGTL library: https://github.com/IGSIO/OpenIGTLinkIO, forked from 3DSlicer/OpenIGTLinkIF
* CustusX items:
** Replace IGSTK-based tracking. Evaluate if PLUS has the required features.
*** Semi-automatic gui-based configuration on the CX side.
*** Modify PLUS if necessary.
*** Wrap PLUS in CustusX. End users should not need to tweak PLUS-specific xml.
** Replace in-house US-streaming solutions by the new standards.
*** Try to use PLUS as backend for the Ultrasonix scanner.
*** Write a lightweight OpenIGTLink server for proprietary scanners.
*** Framegrabber/OpenCV-based streaming based on PLUS (?).

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

See [https://github.com/IGSIO/OpenIGTLinkIO/issues/4] for a diagram relating the various applications and libraries.

2016 Summer Project Week

2016-06-20T10:52:05Z

Christian.askeland: removed lonquans project

__NOTOC__

[[image:PW-Summer2016.png|300px]]
<br><br>
=Welcome to the web page for the 23rd Project Week!=
The 23rd Project Week open source hackathon is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS) and the [http://www.ipcai.org/ IPCAI 2016] conferences in Heidelberg, Germany. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

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

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

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

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws researchers from around the world and is led by [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD]. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

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

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

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

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

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

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

=== IGT ===
* [[2016 Summer Project Week/Guidelets | Guildelets (Slicelets for IGT)]] (Tamas Ungi, Andras Lasso, Thomas Vaughan)
* [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Thomas Kirchner, Janne Beate Bakeng)
* [[2016 Summer Project Week/Guided Ultrasound Calibration | Guided Ultrasound Calibration]] (Elvis Chen, Inês Prata, Tamas Ungi)
* [[2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink | Integrating PLUS in Applications using OpenIGTLink]] (Christian Askeland, Janne Beate Bakeng, Ole Vegard Solberg, Jon Eiesland, Longquan Chen, Simon Drouin)
* [[2016 Summer Project Week/Slicelet For Ultrasound Acquisition | Slicelet for Ultrasound Acquisition]] (Sarah Frisken, Prashin Unadkat, Steve Pieper, Anna Roethe)
* [[2016 Summer Project Week/Structural-functional measurements | Structural - Functional Relationship Measurements of Tractography Data with fMRI ]] (Lauren J. O'Donnell, Yannick Suter)
* [[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/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Guillaume Pernelle, Tina Kapur, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea)
* [[2016 Summer Project Week/Uncertainty-aware Information Fusion | Uncertainty-aware Information Fusion for Real-time Soft Tissue Motion Estimation]] (Bojan Kocev, Sarah Frisken, William Wells, Christian Hansen)
* [[2016 Summer Project Week/Intraoperative Imaging workflow in Hybrid ORs | Intraoperative Imaging in Hybrid ORs]] (Sarah Frisken, Anna Roethe, Prashin Unadkat, Christian Hansen)
* [[2016 Summer Project Week/Curve and Surface Creation from Fiducials]] (Thomas Vaughan)

=== 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]] (Michael Onken)
* [[2016 Summer Project Week/Feedback for Project Week | Measuring the Impact of Project Weeks]] (Tina Kapur)
* [[2016 Summer Project WEB and 3D DICOM viewer to the rest of us]] (Koji Kobayashi)

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

=== Informatics ===
* [[2016 Summer Project Week/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, Andras Lasso)

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

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

= '''Registrants''' =

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

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

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

2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink

2016-06-06T18:05:46Z

Christian.askeland:

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

==Key Investigators==
* Christian Askeland
* Janne Beate Bakeng
* Ole Vegard Solberg
* Jon Eiesland
* Longquan Chen
* Simon Drouin

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Provide support for Tracking and Ultrasound streaming in various IGT Navigation Systems, using PLUS and the OpenIGTLink.v3 protocol as a backend.
* The two systems considered so far are
** CustusX (http://custusx.org/)
** IBIS (http://ibisneuronav.org/).
* CustusX: Phase out IGSTK (tracking) and in-house solutions (streaming).
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Base work on results from [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]], and the existing PLUS/OpenIGTLink support in CustusX.
* Coordinate efforts between systems doing the same job using a client side IGTL library: https://github.com/IGSIO/OpenIGTLinkIO, forked from 3DSlicer/OpenIGTLinkIF
* CustusX items:
** Replace IGSTK-based tracking. Evaluate if PLUS has the required features.
*** Semi-automatic gui-based configuration on the CX side.
*** Modify PLUS if necessary.
*** Wrap PLUS in CustusX. End users should not need to tweak PLUS-specific xml.
** Replace in-house US-streaming solutions by the new standards.
*** Try to use PLUS as backend for the Ultrasonix scanner.
*** Write a lightweight OpenIGTLink server for proprietary scanners.
*** Framegrabber/OpenCV-based streaming based on PLUS (?).

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

See [https://github.com/IGSIO/OpenIGTLinkIO/issues/4] for a diagram relating the various applications and libraries.

2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink

2016-06-02T06:15:29Z

Christian.askeland: /* Project Description */

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

==Key Investigators==
* Christian Askeland
* Janne Beate Bakeng
* Ole Vegard Solberg
* Jon Eiesland
* Longquan Chen
* Simon Drouin

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Provide support for Tracking and Ultrasound streaming in various IGT Navigation Systems, using PLUS and the OpenIGTLink.v3 protocol as a backend.
* The two systems considered so far are
** CustusX (http://custusx.org/)
** IBIS (http://ibisneuronav.org/).
* CustusX: Phase out IGSTK (tracking) and in-house solutions (streaming).
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Base work on results from [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]], and the existing PLUS/OpenIGTLink support in CustusX.
* Coordinate efforts between systems doing the same job using a client side IGTL library: https://github.com/IGSIO/OpenIGTLinkIO, forked from 3DSlicer/OpenIGTLinkIF
* CustusX items:
** Replace IGSTK-based tracking. Evaluate if PLUS has the required features.
*** Semi-automatic gui-based configuration on the CX side.
*** Modify PLUS if necessary.
*** Wrap PLUS in CustusX. End users should not need to tweak PLUS-specific xml.
** Replace in-house US-streaming solutions by the new standards.
*** Try to use PLUS as backend for the Ultrasonix scanner.
*** Write a lightweight OpenIGTLink server for proprietary scanners.
*** Framegrabber/OpenCV-based streaming based on PLUS (?).

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink

2016-06-02T06:09:37Z

Christian.askeland: /* Key Investigators */

2016 Summer Project Week

2016-06-02T06:09:10Z

Christian.askeland: /* IGT */

2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink

2016-06-02T06:08:10Z

Christian.askeland: Christian.askeland moved page 2016 Summer Project Week/PLUS integration in CustusX via OpenIGTLink to 2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink: Generalized project content.

2016 Summer Project Week/PLUS integration in CustusX via OpenIGTLink

2016-06-02T06:08:10Z

#REDIRECT [[2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink]]

2016 Summer Project Week

2016-06-01T11:36:12Z

Christian.askeland: /* Registrants */

2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink

2016-05-31T11:21:27Z

Christian.askeland: /* Project Description */

2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink

2016-05-31T11:20:16Z

Christian.askeland: /* Project Description */

2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink

2016-05-31T11:18:58Z

Christian.askeland: Created page with "__NOTOC__ <gallery> Image:PW-Summer2016.png|Projects List </gallery> ==Key Investigators== * Christian Askeland * Janne Beate Bakeng * O..."

2016 Summer Project Week

2016-05-31T11:06:04Z

Christian.askeland: /* IGT */

2016 Summer Project Week

2016-05-31T11:00:40Z

Christian.askeland: /* Registrants */

2016 Summer Project Week

2016-05-11T06:42:34Z

Christian.askeland: /* Registrants */

__NOTOC__

[[image:PW-Summer2016.png|300px]]
<br><br>
=Welcome to the web page for the 23rd Project Week!=
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) 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.
**'''Monday''' at German Cancer Research Center - DKFZ
**'''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.

==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:10%" |Time
!style="width:15%" |Monday, June 20 <br> DKFZ
!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"|'''9:00am-12:00pm'''
|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"|
|-
|bgcolor="#ffffdd"|'''3:00pm-5:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|-
|}

== '''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. 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].

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.

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)

=Projects=
* [[2016_Summer_Project_Week_Template | Template for project pages]]

#[[2016_VRPN_Integration | VRPN Integration]]
#Needle Segmentation from MRI (Tina Kapur, Andre Mastmeyer, Guillaume Pernelle)
#Guided Ultrasound Calibration (Elvis Chen, Robarts Research) http://link.springer.com/article/10.1007/s11548-016-1390-7

= '''Registrants''' =

'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html and then add your name to this list. DKFZ members who will only be attending Monday should only add their name to this list.

#Tina Kapur, BWH/HMS, Boston, USA
# Dženan Zukić, Kitware, USA
# Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal.
# Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School
# Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany
# Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy
# Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy
# Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy
# Steve Pieper, Isomics, Inc., USA
# Nicole Aucoin, Brigham and Women's Hospital
# Simon Drouin, Montreal Neurological Institute
# Thomas Kirchner, German Cancer Research Center
# Elvis Chen, Robarts Research Institute, Canada
# Christian Askeland, SINTEF, Norway

2016 Winter Project Week/Projects/IntegrationCustusX

2016-01-08T14:21:24Z

Christian.askeland: added results for project week

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

</gallery>

==Key Investigators==


* Christian Askeland (implementation)
* Andras Lasso (discussion)

==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;"
|
* Improve PLUS support in CustusX.
* Add RT streaming from BK scanner.
* Add streaming of tracking data from BrainLab.
|

* Connect to PLUS simulator, add necessary support in CustusX.
* Discuss missing features with PLUS team, add features to PLUS and/or add workarounds in CustusX.
* Synchronize with US-OpenIGTLink standardization effort.
|

* A protocol for transmitting tracked US images along with metadata has been agreed on.
* The protocol will be used as a basis for integration CustusX<->PLUS.
* The goal is to replace IGSTK with PLUS as the tracking backend in CustusX, and to add scanners as well.

|}

==Background and References==

2016 Winter Project Week/Projects/TrackedUltrasoundStandardization

2016-01-07T19:44:13Z

Christian.askeland: link

<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

=== Command ===
* COMMAND
** Command ID (uint32) 4
** Command name (uint8[32]) 32
** Content encoding (uint16) 2
** Content (uint8*) - rest of the body

* RTS_COMMAND: (return to sender command)
** Command ID (uint32) 4
** Command status (uint8[32]) 32
** Content encoding (uint16) 2
** Content (uint8*) - rest of the body

===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.

== Implementation plan ==
=== Github Fork ===
OpenIGTLinkIF fork: https://github.com/drouin-simon/OpenIGTLinkIF
=== 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

[https://github.com/SINTEFMedtek/CustusX/blob/master/source/resource/OpenIGTLinkUtilities/cxIGTLinkConversionImage.h link to example custusx class]

==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

2016-01-07T19:43:40Z

Christian.askeland: link

<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

=== Command ===
* COMMAND
** Command ID (uint32) 4
** Command name (uint8[32]) 32
** Content encoding (uint16) 2
** Content (uint8*) - rest of the body

* RTS_COMMAND: (return to sender command)
** Command ID (uint32) 4
** Command status (uint8[32]) 32
** Content encoding (uint16) 2
** Content (uint8*) - rest of the body

===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.

== Implementation plan ==
=== Github Fork ===
OpenIGTLinkIF fork: https://github.com/drouin-simon/OpenIGTLinkIF
=== 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

[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/Dinner

2016-01-05T19:52:37Z

Christian.askeland: added to dinner list

==Dinner Specs==

*Date and Time: Thursday, January 7th, 6pm
*Location: Desi Dhaba, 401 Massachusetts Ave, Cambridge (about 10 minute walk from Project Week)
*Food: Indian. (Veg and non-veg options, naan, rice)
*Cost: $25 to be paid in cash when you get to the restaurant (for BWH attendees, this is reimbursable)
*Drinks: tap water is included in this price. Beyond that each person pays individually for their drinks - alcohol or otherwise

<b>Disclaimer</b>: We went yesterday (Monday) and they were not serving alcohol. - Adam Rankin

==RSVPs==
#Tina Kapur
#Ron Kikinis
#Steve Pieper
# Andrey Fedorov
# Sonia Pujol
#Hans Meine
#Michael Onken
# Junichi Tokuda
# Dan Blezek
# Beatriz Paniagua
# Johan Andruejol
# Christian Askeland

2016 Winter Project Week

2015-12-22T13:54:20Z

Christian.askeland: Added Andras to CustusX project

__NOTOC__
[[image:PW-MIT2016.png|300px]]

'''Dates:''' January 4-8, 2016

'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)

'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here].
<br>

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

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a [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]

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 4
!style="width:18%" |Tuesday, January 5
!style="width:18%" |Wednesday, January 6
!style="width:18%" |Thursday, January 7
!style="width:18%" |Friday, January 8
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-12:00pm'''
|'''10:30am-12pm:''' [Tutorial] Diffeomorphic registration and geodesic shooting methods (I). (Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10:00-11:30am:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/NewSlicerExtensions | New Slicer Extensions]]
|
'''10:00-11:30am:''' Breakout Session: [[2016_Winter_Project_Week/SlicerROSIntegration| Slicer for Medical Robotics Research]]
<br>
|'''8:30-9:30am''' TBD <br>
'''9:30-10:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Image-guided Neurosurgery| Clinical perspective on Image Guided Neurosurgery]] (Alexandra Golby) <br>
'''10:30-11:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Multiparametric MRI| Clinical perspective on Multiparametric MRI]] (Fiona Fennessy)<br>
'''11:30am-12:30pm''' TBD <br>
|'''10:00am-12:00pm:''' [[#Projects|Project Progress Updates]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''12pm:''' [[Events:TutorialContestJanuary2016|Tutorial Contest Winner Announcement]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|-
|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-1:05pm: <font color="#503020">Welcome</font>'''<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''2:45-4:00pm:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Ultrasound]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>

'''4:00-5:30pm:''' [Tutorial] Diffeomorphic registration geodesic shooting methods (II). (Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|
|'''1:00-2:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/DiffusionMRI| Diffusion MRI]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br>
'''3:00-4:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/QIICRTools| QIICR Tools]]
|'''1:00-3:00pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Session/What's_Planned_for_Slicer_Core|What's Planned for Slicer Core]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|
|-
|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
|
|}
==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|title=NAMIC Winter Project Week
|view=WEEK
}}

='''Projects'''=
*Use this [[2016_Project_Week_Template | Updated Template for project pages]]

== Tractography==
* [[2016_Winter_Project_Week/Projects/Tractography_format_interoperability | Tractography format interoperability]] (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/SlicerDMRI_documentation | Slicer diffusion MR / tractography workflow documentation]] (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/TractographyModuleDevelop&Test | Tractography Analysis Module Development and Testing]] (Fan Zhang, Pegah Kahaliardabili, Isaiah Norton, Lauren O'Donnell, others)

==Chest and Lung Image Processing==
*[[2016_Winter_Project_Week/Projects/ChestImagingPlatform|Chest Imaging Platform: COPD and other pulmonary diseases]] (Raúl San José, Jorge Onieva)
* [[2016 Winter Project Week/Projects/Cluster-Driven Lung Segmentation | Cluster-Driven Segmentation of Lung Nodules]] (Vivek Narayan, Raúl San José, Daniel Blezek, Steve Pieper, Chintan Parmar)

==Web Presence==
*[[2016_Winter_Project_Week/Projects/UpgradeNAMICSlicerWiki|Upgrade the NAMIC (and Slicer?) Wiki]] (JC, Mike Halle)

==General Image Analysis==
* [[2016_Winter_Project_Week/Projects/BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week/Projects/ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week/Projects/PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
*[[2016_Winter_Project_Week/Projects/DigitalPathologyNuclearSegmentation|Digital Pathology Nuclear Segmentation]] (Erich Bremer, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/Interactive4DSegmentation | Interactive 4D Segmentation Module]] (Ethan Ulrich)
* [[2016_Winter_Project_Week/Projects/SlicerCMFNextSteps | Moving beyond SlicerCMF and future projects]] (Beatriz Paniagua, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)

== IGT ==
* [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked ultrasound standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/IntegrationCustusX|Integration of CustusX with PLUS on BK System]] (Christian A, Andras Lasso, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
*[[2016_Winter_Project_Week/Projects/IntegrationImFusion| Integration of ImFusion MR-US registration with BWH AMIGO neurosurgery setup]] (Sarah Frisken, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso, Christian A, )
* [[2016_Winter_Project_Week/Projects/SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard)
* [[2016_Winter_Project_Week/Projects/CryoPlanningSlicerModule | CryoPlanning Module in Slicer]] (Jayender Jagadeesan, Steve Pieper, Sandy Wells)
* [[2016_Winter_Project_Week/Projects/External_beam_planning | External beam radiotherapy planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week/Projects/EVD |Measuring Anatomic Factors for Extraventricular Drain Placement]] (Kirby Vosburgh, P. Jason White)

==Infrastructure==
* [[2016_Winter_Project_Week/Projects/CommonDataStructure | Common data structure for CMF modules in Slicer]] (Jean-Baptiste Vimort, François Budin, Lucia Cevidanes, Beatriz Paniagua, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/StatisticalShapeModeling | Statistical Shape Modeling in Slicer: OA Index]] (Laura Pascal, Beatriz Paniagua, François Budin, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week/Projects/CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week/Projects/BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week/Projects/CLI_Dashboard | Kibana dashboard for browsing all available CLI modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week/Projects/SegmentationEditorWidget | Editor widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week/Projects/SlicerTerminologyEditor | Terminology Editor]] (Csaba Pinter, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/DICOMSegObjIntegration | Integration of DICOM segmentation image storage with Segmentations module]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week/Projects/CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week/Projects/Data Persisting | Mechanism to persist clinical user data from different modules based on SQLite and/or other database engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/Workflows | Workflow module that enables the navigation and data sharing between different modules in a clinical workflow ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/AIMInteroperability | AIM for interoperability]] (Hans Meine, Andrey Fedorov, ??)

= '''Logistics''' =

*'''Dates:''' January 4-8, 2016
*'''Location:''' MIT, Kiva Conference room; 4th floor of Building 32.
*'''REGISTRATION:''' Register [https://www.regonline.com/namic16 here]. Registration Fee: $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list [[2016_Winter_Project_Week/RoomSharing|here]]

= '''Registrants''' =

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [https://www.regonline.com/namic16 registration site].

#Polina Golland, MIT
#Ron Kikinis, BWH
#Nicole Aucoin, BWH/SPL
#Peter Anderson
#Daniel Blezek, Isomics, Inc.
#Lucia Cevidanes, University of Michigan
#Adrian Dalca, MIT
#Simon Drouin, Montreal Neurological Institute
#Janek Groehl, German Cancer Research Center
#Tina Kapur, BWH/HMS
#Thomas Kirchner, German Cancer Research Center
#Hans Meine, University of Bremen/MEVIS
#Vivek Narayan, Dana Farber Cancer Institute
#Danielle Pace, MIT
#Laura Pascal, University of Michigan
#Steve Pieper, Isomics, Inc.
#Csaba Pinter, Queen's University
#Gregory Sharp, MGH
#James Miller, GE Research
#Kyle Sunderland, Queen's University
#Ethan Ulrich, University of Iowa
#Jean-Baptiste Vimort, University of Michigan
#Miaomiao Zhang, MIT
#Beatrize Paniagua, University of North Carolina at Chapel Hill
#Sonia Pujol, BWH
#Junichi Tokuda, BWH
#Katie Mastrogiacomo, BWH
#Niravkumar Patel, Worcester Polytechnic Institute
#Michael Onken, Open Connections (Germany)
#Erich Bremer, Stony Brook University
#Xiao Da, MGH
#Tobias Frank, Leibniz Universität Hannover
#Kirby Vosburgh, BWH
#P. Jason White, BWH
#Lauren O'Donnell, BWH
#Pegah Kahali, BWH
#Fan Zhang, BWH
#Adam Rankin, Robarts Research Institute
#Simon Leoard, Johns Hopkins University
#David Gering, HealthMyne
#Johan Andruejol, Kitware
#Jean-Christophe Fillion-Robin, Kitware
#Kelly Xu, MIT

2016 Winter Project Week/Projects/IntegrationCustusX

2015-12-22T13:52:00Z

Christian.askeland: Added investigators

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

</gallery>

==Key Investigators==


* Christian Askeland (implementation)
* Andras Lasso (discussion)

==Project Description==
{| class="wikitable"
|- style="vertical-align:top;"
! style="text-align: left; width:27%" | Objective

* Improve PLUS support in CustusX.
* Add RT streaming from BK scanner.
* Add streaming of tracking data from BrainLab.

! style="text-align: left; width:27%" | Approach, Plan

* Connect to PLUS simulator, add necessary support in CustusX.
* Discuss missing features with PLUS team, add features to PLUS and/or add workarounds in CustusX.
* Synchronize with US-OpenIGTLink standardization effort.

! style="text-align: left; width:27%" | Progress

*

|}

==Background and References==

2016 Winter Project Week/Projects/IntegrationCustusX

2015-12-22T13:51:15Z

Christian.askeland: Added Description of CustusX project

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

</gallery>

==Key Investigators==


==Project Description==
{| class="wikitable"
|- style="vertical-align:top;"
! style="text-align: left; width:27%" | Objective

* Improve PLUS support in CustusX.
* Add RT streaming from BK scanner.
* Add streaming of tracking data from BrainLab.

! style="text-align: left; width:27%" | Approach, Plan

* Connect to PLUS simulator, add necessary support in CustusX.
* Discuss missing features with PLUS team, add features to PLUS and/or add workarounds in CustusX.
* Synchronize with US-OpenIGTLink standardization effort.

! style="text-align: left; width:27%" | Progress

*

|}

==Background and References==

2016 Winter Project Week/Breakout Sessions/Ultrasound

2015-12-22T13:40:56Z

Christian.askeland: Added description of CustusX presentation

=Breakout Session: Ultrasound=

Each group will present their projects, clinical applications, and plans related to ultrasound-guided interventions.
Available time is 75 minutes in total - about 10 minutes+questions for each group. If you need more time (for demo, etc) then change the allocated time below.

* BWH - Matt [10 min]
* PerkLab (PerkLab, Queen's University) - Andras [10 min + 5 min demo]
** Includes ultrasound-guided EM-navigated breast lumpectomy demo on a phantom
* SINTEF - Christian [10 min]
** Demo of [http://custusx.org/ CustusX], with connection to dummy US data.
** How CustusX uses igtl.
** Article can be found [http://dx.doi.org/10.1007/s11548-015-1292-0 here].
* McGill/MNI - Simon [10 min]
* Western - Adam [10 min]
* MITK - Thomas/Janek [10 min]