NAMIC Wiki - User contributions [en]

2016 Winter Project Week/Projects/MITK Plus Integration

2016-01-08T14:21:42Z

Jgroehl: /* Project Description */

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

==Key Investigators==
*Thomas Kirchner
*Janek Groehl

==Project Description==
<div style="margin: 20px;">
The MITK supports streaming IGT Data via OpenIGTLink for several months now. When trying to send and receive data to/from the plus toolkit several issues were noticed. During the project week a concrete plan for a solid integration of different platforms via OpenIGTLink should be investigated.<br/>

{| 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;"
|

* Obtaining a better understanding of the PLUS configuration possibilities and capabilities.
* Solidify the current way of MITK-Plus integration on the side of the MITK platform.
* Ensure that the integration is done utilizing the PLUS toolkit optimally.

* Two simple scenarios must be realizable:
** Use PLUS Toolkit to connect to imaging device and stream image data to MITK
** Acquire image data with MITK and use PLUS Toolkit to post-process, then send back the processing result to the MITK.
|

* Talk to people knowing the PLUS Toolkit.
* Determine current status of integration.
* Find out key weaknesses of current implementation.
* Develop integration strategy.
|

* With a lot of help from Adam we found out that our desired use cases are supported by the PLUS Toolkit.
* The key weaknesses from within the MITK OIGTL-Client implementation are that receiving multiple different messagetypes at once is not supported at the moment. Also, MITK does not distinguish in receiving images from different devices and displaying them seperately.
* For integration the MITK OIGTL Module must be optimized.
** The following features should be added:
*** Sending and Receiving message on multiple ports from multiple modalities.
*** Handling messages of the same message type from multiple different devices.
*** Being able to receive different message types on the same port.
*** Being able to handle large images.
* Having a common OIGTL Client as described in the [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] Project would be a great thing to achieve a more solid MITK OIGTL integration.

|}

2016 Winter Project Week/Projects/MITK Plus Integration

2016-01-08T14:20:46Z

Jgroehl: /* Project Description */

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

==Key Investigators==
*Thomas Kirchner
*Janek Groehl

==Project Description==
<div style="margin: 20px;">
The MITK supports streaming IGT Data via OpenIGTLink for several months now. When trying to send and receive data to/from the plus toolkit several issues were noticed. During the project week a concrete plan for a solid integration of different platforms via OpenIGTLink should be investigated.<br/>

{| 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;"
|

* Obtaining a better understanding of the PLUS configuration possibilities and capabilities.
* Solidify the current way of MITK-Plus integration on the side of the MITK platform.
* Ensure that the integration is done utilizing the PLUS toolkit optimally.

* Two simple scenarios must be realizable:
** Use PLUS Toolkit to connect to imaging device and stream image data to MITK
** Acquire image data with MITK and use PLUS Toolkit to post-process, then send back the processing result to the MITK.
|

* Determine current status of integration.
* Find out key weaknesses of current implementation.
* Develop integration strategy.
|

* With a lot of help from Adam we found out that our desired use cases are supported by the PLUS Toolkit.
* The key weaknesses from within the MITK OIGTL-Client implementation are that receiving multiple different messagetypes at once is not supported at the moment. Also, MITK does not distinguish in receiving images from different devices and displaying them seperately.
* For integration the MITK OIGTL Module must be optimized.
** The following features should be added:
*** Sending and Receiving message on multiple ports from multiple modalities.
*** Handling messages of the same message type from multiple different devices.
*** Being able to receive different message types on the same port.
*** Being able to handle large images.
* Having a common OIGTL Client as described in the [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] Project would be a great thing to achieve a more solid MITK OIGTL integration.

|}

2016 Winter Project Week

2016-01-08T14:17:38Z

Jgroehl: /* IGT */

__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"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|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 | Slicer Extensions Birds of a Feather]]
|
'''10:00-11:30am:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/SlicerForMedicalRoboticsResearch| Slicer for Medical Robotics Research]]
<br>
|'''8:30-9:30am''' MR, US, Mass Spect guided Breast Surgery (Melissa Mallory, Nathalie Agar, Gabrielle Gauvin, Andras Lasso) <br>
'''9:30-10:30am''' Clinical perspective on Image Guided Neurosurgery (Alexandra Golby) <br>
'''10:30-11:30am''' Clinical perspective on Multiparametric MRI (Fiona Fennessy)<br>
'''11:30am-12pm''' Drug Delivery to Brain (Jason White) <br>
|'''10:00am-12:00pm:''' [[#Projects|Project Progress Updates]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''12pm:''' [[Winter2016TutorialContest|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]] <br>
'''3:30-5:00pm:''' Breakout Session: [[Events:TutorialContestJanuary2016 |2016 Tutorial Contest Review (Kiva)]]
| [[AMIGO Tours#Project Week 22|AMIGO Tour]]
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#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) [[2016_Winter_Project_Week/Dinner|Dinner on Thursday Night]]
|
|}

==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20160103%2F20160110
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20160103/20160110
}}

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

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

== IGT ==
* [[2016_Winter_Project_Week/Projects/SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard, Jayender Jagadeesan)
* [[2016_Winter_Project_Week/Projects/External_beam_planning | External Beam Radiotherapy Planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week/Projects/CryoPlanningSlicerModule | CryoPlanning Module in Slicer]] (Jayender Jagadeesan, Steve Pieper, Sandy Wells)
* [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin, Thomas Kirchner, Janek Groehl)
*[[2016_Winter_Project_Week/Projects/IntegrationCustusX|Integration of CustusX with PLUS on BK System]] (Christian A, Andras Lasso, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
*[[2016_Winter_Project_Week/Projects/IntegrationImFusion| Integration of ImFusion MR-US Registration with BWH AMIGO Neurosurgery Setup]] (Sarah Frisken, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso, Christian Askelan)
* [[2016_Winter_Project_Week/Projects/PLUS | Improvement of PLUS communication with Slicer (skip, see US standardization)]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/SliceTracker | Prostate motion tracking and navigation in Slicer ]] (Christian Herz, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/EVD |Measuring Anatomic Factors for Extraventricular Drain Placement]] (Kirby Vosburgh, P. Jason White)
* [[2016_Winter_Project_Week/Projects/GABA_Delivery |Localized GABA delivery via BBB disruption]] (Nick Todd)
* [[2016_Winter_Project_Week/Projects/3DNrrdSequences | Sequences extension support for 3D+t NRRD]] (Adam Rankin)

== 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)

==Image Analysis==
* [[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/SphericalWaveletShapeAnalysis|Spherical Wavelet Shape Analysis]] (Yi Gao, Erich Bremer, Allen Tannenbaum, Ron Kikinis)
* [[2016_Winter_Project_Week/Projects/DigitalPathologyNuclearSegmentation|Digital Pathology Nuclear Segmentation]] (Erich Bremer, Yi Gao, Nicole Aucoin, Andrey Fedorov)
* [[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/ChestImagingPlatform|Chest Imaging Platform: COPD and Other Pulmonary Diseases]] (Raúl San José, Jorge Onieva, James Ross)
* [[2016_Winter_Project_Week/Projects/ChestImagingPlatformWorkflows|Nipype Workflows for the Chest Imaging Platform]] (James Ross, Raúl San José)
* [[2016 Winter Project Week/Projects/Cluster-Driven Lung Segmentation | Cluster-Driven Segmentation of Lung Nodules]] (Vivek Narayan, Raúl San José, Daniel Blezek, Steve Pieper, Chintan Parmar)
* [[2016_Winter_Project_Week/Projects/BatchImageAnalysis | Batch Clinical Image Analysis]] (Sandy Wells, Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Randy Gollub)
* [[2016_Winter_Project_Week/Projects/SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/Interactive4DSegmentation | Interactive 4D Segmentation Module]] (Ethan Ulrich, Andrey Fedorov, Andras Lasso)
* [[2016_Winter_Project_Week/Projects/CongenitalHeart | Interactive patch-based segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)
* [[2016_Winter_Project_Week/Projects/DSCAnalysis | Dynamic Susceptibility Contrast (DSC) MRI Analysis]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)

* [[2016_Winter_Project_Week/Projects/ShapeAnalysis | Low-dimensional Principal Geodesic Analysis On the Manifold of Diffeomorphisms]] (Miaomiao Zhang, Polina Golland)

==Infrastructure==
*[[2016_Winter_Project_Week/Projects/UpgradeNAMICSlicerWiki|Upgrade the NAMIC + Slicer Web Infrastructure]] (Mike Halle, JC)
* [[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]] (Nicole Aucoin, Csaba Pinter, 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, ??)
* [[2016_Winter_Project_Week/Projects/SlicerEnhancedMR | Developing support for Enhanced MR in Slicer]] (Michael Onken, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/CLIImprovement| Improve CLI robustness and testing]] (Johan Andruejol)

= '''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
#Beatriz 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
#Kelli Xu, MIT
#Christian Askeland, SINTEF
#Katharine Carter, BWH
#Nick Todd, BWH
#Ye Cheng, BWH
#Andriy Fedorov, BWH/HMS
#Sudhanshu Semwal, UCCS Professor
#Michael Halle, BWH
#Kallirroi Retzepi, MGH
#Jayender Jagadeesan, BWH
#Nathalie Agar, BWH
#Curtis Lisle, KnowledgeVis, LLC
#Andras Lasso, PerkLab, Queen's University
#Sarah Frisken, BWH
#Yi Gao, Stony Brook University
#Christian Herz, BWH
#Prashin Unadkat, SPL/BWH
#Jorge Onieva, BWH
#James Ross, BWH
#Raul SanJose, BWH
#Jayashree Kalpathy-Cramer, MGH/HMS
#Daniel Glazer, BWH
#Valentin Demeusy, SPL Intern
#Ameet Jain, Phillips Research
#Utsav Soni, BWH
#Matthew Toews, Ecole de Technologie Superieure
#Isaiah Norton, BWH
#Sean Doyle, MGH
#Stuart Pomerantz, MGH
#Randy Gollub, MGH
#Melissa Mallory, BWH
#Axel Krieger, Children's National Medical Center
#Nobuhiko Hata, BWH
#Carl-Fredrik Westin, BWH/HMS
#Terry Yoo, NLM-NIH/Harvard IACS

AMIGO Tours

2016-01-08T14:16:04Z

Jgroehl: /* Project Week 22 */

==Project Week 22==

If you are interested in visiting [http://ncigt.org/amigo the AMIGO suite at Brigham and Women's Hospital] on Friday afternoon, please list your name here.

#Christian Askeland
#Miaomiao Zhang
#Thomas Kirchner

2016 Winter Project Week/Projects/MITK Plus Integration

2016-01-08T14:11:57Z

Jgroehl: /* Project Description */

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

==Key Investigators==
*Thomas Kirchner
*Janek Groehl

==Project Description==
<div style="margin: 20px;">
The MITK supports streaming IGT Data via OpenIGTLink for several months now. When trying to send and receive data to/from the plus toolkit several issues were noticed. During the project week a concrete plan for a solid integration of different platforms via OpenIGTLink should be investigated.<br/>

{| 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;"
|

* The objective is to solidify the current way of MITK-Plus integration on the side of the MITK platform.
* In detail, it should be ensured that the integration is done optimally utilizing the PLUS toolkit to its fullest potential.
* Two simple scenarios must be realizable:
** Use PLUS Toolkit to connect to imaging device and stream image data to MITK
** Acquire image data with MITK and use PLUS Toolkit to post-process, then send back the processing result to the MITK.
|

* Determine current status of integration.
* Find out key weaknesses of current implementation.
* Develop integration strategy.
|

* With a lot of help from Adam we found out that our desired use cases are supported by the PLUS Toolkit.
* The key weaknesses from within the MITK OIGTL-Client implementation are that receiving multiple different messagetypes at once is not supported at the moment. Also, MITK does not distinguish in receiving images from different devices and displaying them seperately.
* For integration the MITK OIGTL Module must be optimized.
** The following features should be added:
*** Sending and Receiving message on multiple ports from multiple modalities.
*** Handling messages of the same message type from multiple different devices.
*** Being able to receive different message types on the same port.
*** Being able to handle large images.
* Having a common OIGTL Client as described in the [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] Project would be a great thing to achieve a more solid MITK OIGTL integration.

|}

2016 Winter Project Week/Projects/MITK Plus Integration

2016-01-08T14:10:58Z

Jgroehl: /* Project Description */

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

==Key Investigators==
*Thomas Kirchner
*Janek Groehl

==Project Description==
<div style="margin: 20px;">
The MITK supports streaming IGT Data via OpenIGTLink for several months now. When trying to send and receive data to/from the plus toolkit several issues were noticed. During the project week a concrete plan for a solid integration of different platforms via OpenIGTLink should be investigated.<br/>

{| 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;"
|

* The objective is to solidify the current way of MITK-Plus integration on the side of the MITK platform.
* In detail, it should be ensured that the integration is done optimally utilizing the PLUS toolkit to its fullest potential.
* Two simple scenarios must be realizable:
** Use PLUS Toolkit to connect to imaging device and stream image data to MITK
** Acquire image data with MITK and use PLUS Toolkit to post-process
|

* Determine current status of integration.
* Find out key weaknesses of current implementation.
* Develop integration strategy.
|

* With a lot of help from Adam we found out that our desired use cases are supported by the PLUS Toolkit.
* The key weaknesses from within the MITK OIGTL-Client implementation are that receiving multiple different messagetypes at once is not supported at the moment. Also, MITK does not distinguish in receiving images from different devices and displaying them seperately.
* For integration the MITK OIGTL Module must be optimized.
** The following features should be added:
*** Sending and Receiving message on multiple ports from multiple modalities.
*** Handling messages of the same message type from multiple different devices.
*** Being able to receive different message types on the same port.
*** Being able to handle large images.
* Having a common OIGTL Client as described in the [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] Project would be a great thing to achieve a more solid MITK OIGTL integration.

|}

AMIGO Tours

2016-01-08T13:58:29Z

Jgroehl: /* Project Week 22 */

2016 Winter Project Week/Projects/TrackedUltrasoundStandardization

2016-01-07T19:28:49Z

Jgroehl: /* Implementation plan */

<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

==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

2016-01-07T19:28:14Z

Jgroehl: /* Implementation plan */

<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 ==

=== 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

==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

2016-01-07T19:26:39Z

Jgroehl: /* Implementation plan */

<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 ==

=== Tasks ===
* Clean up the vtkMRMLIGTLConnectorNode to be logic, MRML and Slicer free
* Creating a new converter base class which does not depend on MRML

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

==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

2016-01-07T19:17:42Z

Jgroehl: /* Implementation plan */

<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 ==

=== Tasks ===
* Clean up the vtkMRMLIGTLConnectorNode to be Logic, MRML and Slicer free
*

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

==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]]

AMIGO Tours

2016-01-07T17:12:21Z

Jgroehl:

2016 Winter Project Week/Dinner

2016-01-06T14:26:19Z

Jgroehl: /* RSVPs */

==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
# Lucia Cevidanes
# Fan Zhang
# Pegah Kahali
# Simon Drouin
# Thomas Kirchner
# Janek Groehl

File:MITKTrackedProbes.pdf

2016-01-04T20:12:28Z

Jgroehl:

2016 Winter Project Week/Projects/TrackedUltrasoundStandardization

2016-01-04T20:12:03Z

Jgroehl:

__NOTOC__
<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]]
|}

==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/MITK Plus Integration

2016-01-04T00:41:16Z

Jgroehl: /* Project Description */

2016 Winter Project Week/Breakout Sessions/Ultrasound

2016-01-02T19:54:53Z

Jgroehl: /* Breakout Session: Ultrasound */

=Breakout Session: Ultrasound=

Moderator: Tina Kapur

This breakout session is for all those who are using ultrasound for image-guided surgery and will serve as a kickoff discussion for the [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | ultrasound standardization project]]. The goal is to share demos, information, code, and challenges that each of us are facing. When it makes sense, we will also discuss standardization. Analyzing ultrasound images -- segmentation, registration -- can be set up as a followup breakout session if there is need.

* PerkLab (PerkLab, Queen's University) - Andras Lasso
** Includes ultrasound-guided EM-navigated breast lumpectomy demo on a phantom
* SINTEF - Christian Askeland
** Demo of [http://custusx.org/ CustusX], with connection to dummy US data.
** How CustusX uses OpenIGTLink.
** Article can be found [http://dx.doi.org/10.1007/s11548-015-1292-0 here].
* McGill/MNI - Simon Drouin
* Western - Adam Rankin
* MITK - Thomas/Janek
** EchoTrack [https://www.dkfz.de/en/mbi/research/CAI/workflow-optimized_navigation.html link].
** Photoacoustics
* Philips Research - Ameet Jain

2016 Winter Project Week/Projects/MITK Plus Integration

2016-01-02T17:20:16Z

Jgroehl: /* Project Description */

2016 Winter Project Week/Projects/TrackedUltrasoundStandardization

2015-12-10T15:33:12Z

Jgroehl:

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

==Key Investigators==
* 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==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* 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/ServicesSoftwareVisualization/IBIS IBIS]
** [http://www.imaging.robarts.ca/petergrp/Technology Echelon]
** [http://mitk.org/wiki/IGT MITK-IGT]
</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>

<h3>Preparation meetings</h3>

<h4>Christian's list of potential topics of collaboration</h4>

''Enhance connection of CustusX client to PLUS server''

Background: CustusX has used PLUS to connect to an Ultrasonix scanner with an attached tracking device from Ascension (Sonix GPS), as part of the EU RASimAs project. CustusX also has tracking support from the IGSTK toolkit, and own direct support for a number of video/US devices. We would like to add PLUS to this family, poosibly replacing some of our older components.

Topics:
* Tracking of BrainLab devices.
* Connection to BK medical scanners.
* Enhance transfer of US probe metadata. Might include extending the OpenIGTLink standard.
* Use of PLUS US reconstruction algorithms in CustusX as an alternative to CX internal algorithms, and enable comparison of algorithms.

''Standardization of IGT software''

Background:
* Emails, major players converge towards IGTLink. Several groups are using PLUS and/or Slicer, but also open-sourcing their own software and want to be compatible with each other.
* Data should be usable by several systems in order to ease comparison in e.g. studies.
* Our group need to communicate models and volumes with Slicer, and would like to use PLUS.

There are several areas where standardization would be beneficial:
* messaging between applications.
* file formats.
* algorithms/shared libraries.
It is important to build as much as possible on existing material and de facto standards.

Topics:
* Messaging: OpenIGTLink is the de facto standard for messaging. Is the standard complete? What do we need? US-probe data, polydata colors, volume transfer functions /LUTs.
* File Formats: Models, Volumes, Video streams, US metadata, scenegraph. Some of these objects are already somewhat standardized, but not all.
* Algorithms: A library of IGT algorithms would be welcome. It might be included into an existing library (VTK, CTK, …) or emerge as a new one.

<h4>Meeting 2015-11-23</h4>

Participants: Andras Lasso, Tamas Ungi, Steve Pieper, Junichi Tokuda, Adam Rankin, Simon Drouin, Ole Vegard Solberg, Ingerid Reinertsen, Christian Askeland

Notes:
* Introduction of all present. Everyone seems to have a strong interest in IGT and systems integration.
* Junichi: Funded OpenIGTLink grant scope is well aligned with this standardization effort.
* Christian: project manager for CustusX, Plus is used for data acquisition, 3D Slicer used for pre/post operative processing
* Ingrid: research scientist, IGT and CustusX user, uses Slicer for pre-processing, segmentation, registration, post-processing; clinicians use Slicer for tumor segmentation, becoming a routine
* Simon: IBIS has been developed for 10 years, next step is integration with Plus, plan is to move features to 3D Slicer/SlicerIGT/Plus and use that as a platform (grant application submitted for getting funding)
* Walkthrough of (some of) Christian’s topics
** CustusX - BrainLab connection through PLUS: BrainLab already supports OpenIGTLink, connection either through Plus or directly to the application should be straightforward.
** CustusX - BK connection through PLUS: Partially implemented in PLUS. NOTE: Must buy additional license from BK to access continuous image streaming (GRAB ON/OFF command). Without that the maximum acquisition rate is limited to a few FPS. GRAB ON/OFF interface implementation is partially complete in Plus. If a BK machine is available that supports this command then implementation in Plus requires a couple of days.
** 4D (3D+t) US acquisition support: Robarts has access to a private Philips API, SINTEF has access to a private GE API. Both have converter to OpenIGTLink (Philips converter is implemented in Plus, GE is external).
** Ultrasound scanner two-way communication support in OpenIGTLink (data query, device control - depth, imaging mode): several of those present (Adam, Christian, ..) and others need this, and several slightly different implementations exist (Plus, CustusX, MUSiiC). Junichi agrees that this should be standardized into OpenIGTLink. We need a backward and forward compatible solution, possibly XML in STRING OpenIGTLink message. '''Needs further discussion'''
** Shared file formats: All IGT data (pose tracking, 2D+t, 3D, 3D+t images) should be stored in a common format. '''Needs further discussion'''
*** Steve suggests DICOM. Some work already in progress on using DICOM as interchange format between BrainLab and Slicer (BrainLab already uses DICOM as its internal data representation). Most of the required structures are present, possibly excluding tracking positions. This can be (with time and work) added to the standard. General agreement on DICOM, but more discussion needed. Real-time streaming to DICOM file may be problematic (DICOM header has to be prepended to image data; if image data is several GB then it may take long time, not convenient for intra-operative use).
*** Can also discuss with Michael Onken/DCMTK when in Boston.
* General agreement that standardization and cooperation is needed, and that more discussions are needed before Boston.

TODO:
* Contact others if they were interested to join these efforts (MUSiiC, MITK-IGT, Nifty-IGT) - Andras
* Ask Tina about possibility for Amigo visit (BK ultrasound, BrainLab integration) - Andras
* Talk to BrainLab engineers about tracked ultrasound (and general IGT) information storage in DICOM format - Steve

'''Next meeting''': December 7., 0900 EST (1500 Trondheim time)

<h4>Meeting 2015-12-07</h4>

Date: December 7., 0900 EST (1500 Trondheim/Heidelberg time)

Participants: Andras Lasso, Tamas Ungi, Steve Pieper, Junichi Tokuda, Adam Rankin, Simon Drouin, Ole Vegard Solberg, Christian Askeland, Alfred Franz, Thomas Kirchner, Janek Groehl

'''Topics of interests'''
* Tracking and imaging data stream (image includes distance maps, various color images, etc):
** Storage file format
*** MetaImage (mha/mhd), NRRD [http://perk-software.cs.queensu.ca/plus/doc/nightly/user/FileSequenceMetafile.html with custom fields]
**** Very simple, flexible, human-readable file format
**** Lossless compression, special image types (4D, color, etc.) are supported
**** Basic support is available in all research software, C++ and Matlab libraries are available for reading/writing
**** Reading/writing is fully supported by [http://wwww.plustoolkit.org Plus], [http://www.slicer.org 3DSlicer]/[http://www.slicerigt.org SlicerIGT]/[https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/Sequences Sequences]
**** Limitations: only one image stream per file, no per-frame fields (simulated by adding per-file custom fields; standard libraries cannot associate them with frames); numbers stored as text, some precision is lost
*** DICOM: Ultrasound image IOD, Ultrasound multi-frame image IOD, Ehanced ultrasound volume IOD
**** [http://dicom.nema.org/Dicom/2013/output/chtml/part17/sect_PP.2.html#sect_PP.2.2 use cases], [http://dicom.nema.org/medical/dicom/2014c/output/chtml/part17/sect_PP.3.html overview]
**** Standard exists for tracked 2D, 3D ultrasound sequences (frame of reference relative to probe, patient, other)
**** Physiological waveforms (cardiac, respiratory)
**** Physical units, real world values (speed, etc), color calibration
**** Custom per-frame fields can be specified (could be added to standard)
**** Multiple image regions (biplane, etc)
**** Limitation: no standard for storing navigation data (only probe and image position) - to be confirmed with David Clunie
** Storage in memory for visualization and processing
*** Plus: rotating buffer for image frames (vtkImageData + custom fields), tool tracking data (pose, status); TrackedFrameList (list of image data with string field list)
*** 3D Slicer: sequences of data nodes (vtkMRMLScalarVolume, vtkTransform)
** Real-time transfer: colors, volume transfer functions / LUTs?
* Ultrasound metadata: imaging parameters (depth, dynamic range, etc.), image geometry (clipping rectangle, clipping fan, image spacing, axis directions, transducer center position), freeze state, probe
* Surgical microscope metada: focus, zoom
* Calibration info: from/to coordinate system name, linear transform
** File storage: In Plus: XML, CoordinateDefinitions element
** In memory: vtkMatrix4x4, TransformRepository
** Real-time transfer: application receives as TRANSFORM message, set by OpenIGTLink command
* Meshes, point cloud
** File storage: vtkPolyData, VTK file formats are OK but there is no coordinate system information; DICOM?
** Memory: VTK class
** Real-time transfer: is anything missing in OpenIGTLink?
* Dependency, data provenance
** Data represenation for segmentation, keeping relationship to source structures in DICOM
** Make sure there is a way to store DICOM UIDs, use definitions that are already specified in DICOM
button press
** File storage: currently in XML in Plus
** In memory storage: XML data elements
** Real-time transfer: MUSiiC custom OpenIGTLink messages have some info
* Scene:
** File storage: Slicer uses MRML - alternatives?
** Memory: MRML library
** Real-time transfer?
* Common algorithms:
** Pivot calibration (with robust point matching, error rejection, error metrics, etc.)
** Landmark registration (with automatic landmark detection, etc.)
** Volume reconstruction
** Scan conversion, brightness conversion
** Bone surface detection
** Ultrasound simulation
** US/MRI registration
** Custom reader/writer classes for tracked image data (supporting compressed streaming, compressed seeking, all necessary metadata, etc.)

'''Current implementations'''
* Tracked ultrasound storage in file:
** Plus: sequence metafile
** CustusX:
*** Saving during recording: a new folder is created, each image frame is written to a separate file (optionally compressed), separate file stores tracking data and metadata
*** Sequence metafile (MetaImage format with Plus custom fields) is also used
*** Application state is saved to an XML file (similar to MRML scene) that links to other files (sequence metafile, VTK polydata, etc)
*** The entire procedure is also recorded to a separate, simple, compressed file
** IBIS:
*** Sequence of MINC files: each frame is a separate MINC file, contains both tracking transform and calibration transform that was current when the frame was acquired. All provenance information is kept in the header of each file (up to the original data source, DICOM, etc.)
** MITK-IGT:
*** There is not really a standard, images can be saved as a 3D NRRD image using ITK, tracking data can be saved as xml or csv
*** Sometimes sequence metafile is used
* Tracked ultrasound storage in memory:
** Plus: TrackedFrameList class, list of PlusVideoFrame, PlusVideoFrame is a VTK class with vtkImageData (with zero origin and unit spacing), timestamp, and custom string fields (with convenience function to store/retrieve transforms, numerical values, etc.)
** CustusX:
*** Uses VTK as main backend (with ITK converters for algorithms)
*** Custom image class that contains vtkImageData (with zero position, unit spacing), additional with orientation, in vtk image data position is 0
*** all transforms in eigen
*** sequences of video and ultrasound in a class
** IBIS:
*** vtkImageData data and separate transform vtkMatrix4x4 for individual frame and separate for registration
*** Everything is kept in memory, no streaming writing to disk
** MITK-IGT:
*** OpenCV mat image for image acquisition and pre-processing
*** MITK image sequence could be used as well
*** Calibration is a property of the MITK image
*** Tracking data: tracking data set is a separate structure
* Tracked ultrasound streaming:
** Plus:
*** Transforms: receive TRANSFORM or TDATA, send TRANSFORM (TDATA implementation is in progress)
*** Images: IMAGE, USMESSAGE (MUSiiC ultrasound message), TRACKEDFRAME (Plus tracked frame: image data + string fields)
** CustusX:
*** OpenIGTLink: has been used for 4 years, Plus for about half year
*** Image: both 3D and 4D US, using own image message type, non-standard message
*** Tracking: TRANSFORM
** IBIS: everything is in the same process, no IPC
** MITK: TDATA or TRANSFORM messages, depending on the application

'''Plans'''
* We focus on real-time data transfer standardization first, then file storage, in-memory representation, reader/writer and processing software library

'''Next meeting''': December 14., 0900 EST (1500 Trondheim/Heidelberg time)

'''Homework before next meeting''': Add to this wiki page the description of all data to be transferred in real-time using OpenIGTLink

'''Data necessary to be transferred in real time'''

* MITK-IGT group:
** For image data:
*** Option to add meta data for different modalities (e.g: ultrasound- and photoacoustic imaging):
*** Additional metadata for PAI:
**** Wavelength (for multispectral image shots)
**** Laser pulse energy (for normalisation of signals)
**** Adding specific message types based on IMGMETA could be of use [optional/custom fields?]
** For tracking data:
*** Consistent format
*** TDATA message suits our needs

2016 Winter Project Week

2015-12-10T14:43:18Z

Jgroehl: /* Projects */

__NOTOC__

[[image:PW-MIT2016.png|300px|left]]
<br><br><br><br><br><br><br><br><br><br><br><br>
'''Dates:''' January 4-8, 2016

'''Location:''' MIT, 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 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==

Tentative 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"|'''9am-12pm'''
|'''10:30am-12pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 1 by Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10-11:30am:''' <font color="#503020">Breakout Session: New Slicer Extensions'''</font><br>
|
'''10-11:30am:''' <font color="#503020">Breakout Session: [[2015_Winter_Project_Week:SlicerROSIntegration| Slicer for Medical Robotics Research]] </font>
<br>
|'''9:00-10:30am''' TBD <br>
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD <br>
|'''10am-12pm:''' [[#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"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">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>
'''2:45-4pm:''' [[Breakout Session: Ultrasound]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>

'''4:00pm-5:30pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 2 by Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''1-3pm:''' <font color="#503020"> [[Breakout Session: What's Planned for Slicer Core]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[Breakout Session: Diffusion MRI]]
[[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
|
|}

<googlecalendar>kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com</googlecalendar>

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

* [[2015_Winter_Project_Week:SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard)
* [[2016_Winter_Project_Week:TrackedUltrasoundStandardization | Tracked ultrasound standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*Integration of CustusX with PLUS on BK System (Christian A, Adam Rankin)
*Integration of ImFusion MR-US registration with BWH AMIGO neurosurgery setup (Christian A, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso)
*Digital Pathology Nuclear Segmentation (Erich Bremer, Nicole Aucoin)
*Chest Imaging Platform: COPD and other pulmonary diseases (Raúl San José, Jorge Onieva)
*Upgrade the namic (and Slicer?) wiki (JC, Mike Halle)
* [[2016_Winter_Project_Week:BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week:ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week:PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week:MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)

==Infrastructure==
* [[2016_Winter_Project_Week:SlicerProjectName | Project Name]] (List of people working on this project)
* [[2016_Winter_Project_Week:CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week:WebTechnologies | Web Technologies and Slicer]] (Steve Pieper, Hans Meine)
* [[2016_Winter_Project_Week:CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week:CLI_Dashboard | Kibana dashboard for browsing all available CLI modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week:SegmentationEditorWidget | Editor widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:DICOMSegObjIntegration | Integration of DICOM SegObj with Segmentations]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week:Data Persisting | Mechanism to persist clinical user data from different modules based on SQLite and/or other database engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week:Workflows | Workflow module that enables the navigation and data sharing between different modules in a clinical workflow ]] (Raúl San José, Jorge Onieva)

= '''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 [https://www.regonline.com/namic16 this registration url].

2016 Winter Project Week/Projects/MITK Plus Integration

2015-12-10T14:42:25Z

Jgroehl: /* Project Description */

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

==Key Investigators==
- Thomas Kirchner, Janek Groehl

==Project Description==
<div style="margin: 20px;">
The MITK supports streaming IGT Data via OpenIGTLink for several months now. When trying to send and receive data to/from the plus toolkit several issues where noticed. During the project week a concrete plan for a solid integration of different platforms via OpenIGTLink should be investigated.<br/>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
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<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2016 Winter Project Week/Projects/MITK Plus Integration

2015-12-10T14:30:16Z

Jgroehl:

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

==Key Investigators==
- Thomas Kirchner, Janek Groehl

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

2016 Winter Project Week/Projects/MITK Plus Integration

2015-12-10T14:29:43Z

Jgroehl:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|[[2016_Winter_Project_Week#Projects|Projects List]]
Image:WMH_T1.png|Clinical Stroke Image
</gallery>

==Key Investigators==
- Thomas Kirchner, Janek Groehl

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

2016 Winter Project Week/Projects/MITK Plus Integration

2015-12-10T14:28:18Z

Jgroehl: Created page with "==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;..."

==Project Description==
<div style="margin: 20px;">
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<h3>Objective</h3>
*
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*
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<h3>Progress</h3>
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2016 Winter Project Week

2015-12-10T14:27:36Z

Jgroehl: /* Projects */

__NOTOC__

[[image:PW-MIT2016.png|300px|left]]
<br><br><br><br><br><br><br><br><br><br><br><br>
'''Dates:''' January 4-8, 2016

'''Location:''' MIT, 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 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==

Tentative 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"|'''9am-12pm'''
|'''10:30am-12pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 1 by Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10-11:30am:''' <font color="#503020">Breakout Session: New Slicer Extensions'''</font><br>
|
'''10-11:30am:''' <font color="#503020">Breakout Session: [[2015_Winter_Project_Week:SlicerROSIntegration| Slicer for Medical Robotics Research]] </font>
<br>
|'''9:00-10:30am''' TBD <br>
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD <br>
|'''10am-12pm:''' [[#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"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">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>
'''2:45-4pm:''' [[Breakout Session: Ultrasound]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>

'''4:00pm-5:30pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 2 by Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''1-3pm:''' <font color="#503020"> [[Breakout Session: What's Planned for Slicer Core]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[Breakout Session: Diffusion MRI]]
[[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
|
|}

<googlecalendar>kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com</googlecalendar>

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

* [[2015_Winter_Project_Week:SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard)
* [[2016_Winter_Project_Week:TrackedUltrasoundStandardization | Tracked ultrasound standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*Integration of CustusX with PLUS on BK System (Christian A, Adam Rankin)
*Integration of ImFusion MR-US registration with BWH AMIGO neurosurgery setup (Christian A, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso)
*Digital Pathology Nuclear Segmentation (Erich Bremer, Nicole Aucoin)
*Chest Imaging Platform: COPD and other pulmonary diseases (Raúl San José, Jorge Onieva)
*Upgrade the namic (and Slicer?) wiki (JC, Mike Halle)
* [[2016_Winter_Project_Week:BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week:ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week:PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week:MITK_Plus_Integration | Integration of Plus and MITK via OpenIGTLink]] (Thomas Kirchner, Janek Groehl)

==Infrastructure==
* [[2016_Winter_Project_Week:SlicerProjectName | Project Name]] (List of people working on this project)
* [[2016_Winter_Project_Week:CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week:WebTechnologies | Web Technologies and Slicer]] (Steve Pieper, Hans Meine)
* [[2016_Winter_Project_Week:CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week:CLI_Dashboard | Kibana dashboard for browsing all available CLI modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week:SegmentationEditorWidget | Editor widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:DICOMSegObjIntegration | Integration of DICOM SegObj with Segmentations]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week:Data Persisting | Mechanism to persist clinical user data from different modules based on SQLite and/or other database engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week:Workflows | Workflow module that enables the navigation and data sharing between different modules in a clinical workflow ]] (Raúl San José, Jorge Onieva)

= '''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 [https://www.regonline.com/namic16 this registration url].

2016 Winter Project Week

2015-12-10T14:26:31Z

Jgroehl: /* Infrastructure */

__NOTOC__

[[image:PW-MIT2016.png|300px|left]]
<br><br><br><br><br><br><br><br><br><br><br><br>
'''Dates:''' January 4-8, 2016

'''Location:''' MIT, 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 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==

Tentative 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"|'''9am-12pm'''
|'''10:30am-12pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 1 by Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10-11:30am:''' <font color="#503020">Breakout Session: New Slicer Extensions'''</font><br>
|
'''10-11:30am:''' <font color="#503020">Breakout Session: [[2015_Winter_Project_Week:SlicerROSIntegration| Slicer for Medical Robotics Research]] </font>
<br>
|'''9:00-10:30am''' TBD <br>
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD <br>
|'''10am-12pm:''' [[#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"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">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>
'''2:45-4pm:''' [[Breakout Session: Ultrasound]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>

'''4:00pm-5:30pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 2 by Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''1-3pm:''' <font color="#503020"> [[Breakout Session: What's Planned for Slicer Core]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[Breakout Session: Diffusion MRI]]
[[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
|
|}

<googlecalendar>kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com</googlecalendar>

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

* [[2015_Winter_Project_Week:SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard)
* [[2016_Winter_Project_Week:TrackedUltrasoundStandardization | Tracked ultrasound standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*Integration of CustusX with PLUS on BK System (Christian A, Adam Rankin)
*Integration of ImFusion MR-US registration with BWH AMIGO neurosurgery setup (Christian A, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso)
*Digital Pathology Nuclear Segmentation (Erich Bremer, Nicole Aucoin)
*Chest Imaging Platform: COPD and other pulmonary diseases (Raúl San José, Jorge Onieva)
*Upgrade the namic (and Slicer?) wiki (JC, Mike Halle)
* [[2016_Winter_Project_Week:BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week:ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week:PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)

==Infrastructure==
* [[2016_Winter_Project_Week:SlicerProjectName | Project Name]] (List of people working on this project)
* [[2016_Winter_Project_Week:CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week:WebTechnologies | Web Technologies and Slicer]] (Steve Pieper, Hans Meine)
* [[2016_Winter_Project_Week:CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week:CLI_Dashboard | Kibana dashboard for browsing all available CLI modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week:SegmentationEditorWidget | Editor widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:DICOMSegObjIntegration | Integration of DICOM SegObj with Segmentations]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week:Data Persisting | Mechanism to persist clinical user data from different modules based on SQLite and/or other database engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week:Workflows | Workflow module that enables the navigation and data sharing between different modules in a clinical workflow ]] (Raúl San José, Jorge Onieva)

= '''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 [https://www.regonline.com/namic16 this registration url].

2016 Winter Project Week

2015-12-10T14:25:54Z

Jgroehl: /* Projects */

__NOTOC__

[[image:PW-MIT2016.png|300px|left]]
<br><br><br><br><br><br><br><br><br><br><br><br>
'''Dates:''' January 4-8, 2016

'''Location:''' MIT, 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 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==

Tentative 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"|'''9am-12pm'''
|'''10:30am-12pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 1 by Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10-11:30am:''' <font color="#503020">Breakout Session: New Slicer Extensions'''</font><br>
|
'''10-11:30am:''' <font color="#503020">Breakout Session: [[2015_Winter_Project_Week:SlicerROSIntegration| Slicer for Medical Robotics Research]] </font>
<br>
|'''9:00-10:30am''' TBD <br>
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD <br>
|'''10am-12pm:''' [[#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"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">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>
'''2:45-4pm:''' [[Breakout Session: Ultrasound]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>

'''4:00pm-5:30pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 2 by Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''1-3pm:''' <font color="#503020"> [[Breakout Session: What's Planned for Slicer Core]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[Breakout Session: Diffusion MRI]]
[[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
|
|}

<googlecalendar>kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com</googlecalendar>

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

* [[2015_Winter_Project_Week:SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard)
* [[2016_Winter_Project_Week:TrackedUltrasoundStandardization | Tracked ultrasound standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*Integration of CustusX with PLUS on BK System (Christian A, Adam Rankin)
*Integration of ImFusion MR-US registration with BWH AMIGO neurosurgery setup (Christian A, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso)
*Digital Pathology Nuclear Segmentation (Erich Bremer, Nicole Aucoin)
*Chest Imaging Platform: COPD and other pulmonary diseases (Raúl San José, Jorge Onieva)
*Upgrade the namic (and Slicer?) wiki (JC, Mike Halle)
* [[2016_Winter_Project_Week:BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week:ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week:PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)

==Infrastructure==
* [[2016_Winter_Project_Week:SlicerProjectName | Project Name]] (List of people working on this project)
* [[2016_Winter_Project_Week:CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week:WebTechnologies | Web Technologies and Slicer]] (Steve Pieper, Hans Meine)
* [[2016_Winter_Project_Week:CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week:CLI_Dashboard | Kibana dashboard for browsing all available CLI modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week:SegmentationEditorWidget | Editor widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:DICOMSegObjIntegration | Integration of DICOM SegObj with Segmentations]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week:Data Persisting | Mechanism to persist clinical user data from different modules based on SQLite and/or other database engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week: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:MITK_Plus_Integration | Integration of Plus and MITK via OpenIGTLink]] (Thomas Kirchner, Janek Groehl)

= '''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 [https://www.regonline.com/namic16 this registration url].