NAMIC Wiki - User contributions [en]

2017 Winter Project Week/QuantitativeReporting

2017-01-13T15:22:07Z

Ch399:

==Key Investigators==

* Christian Herz, BWH
* Andrey Fedorov, BWH
* Andras Lasso, Queen's
* Csaba Pinter, Queen's

==Project Description==
An extension of 3D Slicer to support segmentation-based measurements with DICOM-based import and export of the results.
{| 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;"
|

* utilizes dcmqi library for reading/writing of DICOM SEG/SR
* demonstrate Quantitative Reporting extension
* improve documentation
* discuss next steps and specific open issues
|

* get rid of hacks that hide SegmentEditor components individually by iterating over GUI components
* add functionality for continuing a saved report
* communication of measurements tables and integrated support into Slicer Table node (CSV/JSON/other approaches - see https://github.com/QIICR/QuantitativeReporting/issues/105)
* integration of measurement quantities/units into Slicer for volume nodes
|

* discussions with Csaba Pinter about SegmentEditor and making UI components easier accessible to developers by providing methods
* implementation for continuing a partially completed measurement report
** works with Slicer created measurement report
** problems:
*** recalculation of measurements might not be possible (no information about algorithms that have been used for that)
*** Quantitative Reporting for now only uses SegmentStatistics module for computing measurements
** TODO: reference to original measurement report for being able to trace modifications
|}

[[image:QuantitativeReporting-screenshot.jpg|1024px]]

==Background and References==

* dcmqi home page: http://github.com/qiicr/dcmqi
* Fedorov A, Clunie D, Ulrich E, Bauer C, Wahle A, Brown B, Onken M, Riesmeier J, Pieper S, Kikinis R, Buatti J, Beichel RR. (2016) DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research. PeerJ 4:e2057 https://doi.org/10.7717/peerj.2057

2017 Winter Project Week/QuantitativeReporting

2017-01-13T15:21:07Z

Ch399: /* Project Description */

==Key Investigators==

* Christian Herz, BWH
* Andrey Fedorov, BWH
* Andras Lasso, Queen's
* Csaba Pinter, Queen's

==Project Description==
An extension of 3D Slicer to support segmentation-based measurements with DICOM-based import and export of the results.
{| 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;"
|

* utilizes dcmqi library for reading/writing of DICOM SEG/SR
* demonstrate Quantitative Reporting extension
* improve documentation
* discuss next steps and specific open issues
|

* get rid of hacks that hide SegmentEditor components individually by iterating over GUI components
* add functionality for continuing a saved report
* communication of measurements tables and integrated support into Slicer Table node (CSV/JSON/other approaches - see https://github.com/QIICR/QuantitativeReporting/issues/105)
* integration of measurement quantities/units into Slicer for volume nodes
|

* discussions with Csaba Pinter about SegmentEditor and making UI components easier accessible to developers by providing methods
* implementation for continuing a partially completed measurement report
** problems:
*** recalculation of measurements might not be possible (no information about algorithms that have been used for that)
*** Quantitative Reporting for now only uses SegmentStatistics module for computing measurements
** TODO: reference to original measurement report for being able to trace modifications
|}

[[image:QuantitativeReporting-screenshot.jpg|1024px]]

==Background and References==

* dcmqi home page: http://github.com/qiicr/dcmqi
* Fedorov A, Clunie D, Ulrich E, Bauer C, Wahle A, Brown B, Onken M, Riesmeier J, Pieper S, Kikinis R, Buatti J, Beichel RR. (2016) DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research. PeerJ 4:e2057 https://doi.org/10.7717/peerj.2057

2017 Winter Project Week/QuantitativeReporting

2017-01-12T15:19:25Z

Ch399: Added progress

==Key Investigators==

* Christian Herz, BWH
* Andrey Fedorov, BWH
* Andras Lasso, Queen's
* Csaba Pinter, Queen's

==Project Description==
An extension of 3D Slicer to support segmentation-based measurements with DICOM-based import and export of the results.
{| 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;"
|

* utilizes dcmqi library for reading/writing of DICOM SEG/SR
* demonstrate Quantitative Reporting extension
* improve documentation
* discuss next steps and specific open issues
|

* get rid of hacks that hide SegmentEditor components individually by iterating over GUI components
* add functionality for continuing a saved report
* communication of measurements tables and integrated support into Slicer Table node (CSV/JSON/other approaches - see https://github.com/QIICR/QuantitativeReporting/issues/105)
* integration of measurement quantities/units into Slicer for volume nodes
|

* Discussions with Csaba Pinter about SegmentEditor and making UI components easier accessible to developers by providing methods like:
** <code>getEffectButton({effectname})</code>
* Loading a measurement report from DICOM and continuing a non-completed one
** creating a copy of the original one where the user can go ahead and continue working on it:
** TODO: reference to original measurement report for being able to "log" modifications
|}

[[image:QuantitativeReporting-screenshot.jpg|1024px]]

==Background and References==

* dcmqi home page: http://github.com/qiicr/dcmqi
* Fedorov A, Clunie D, Ulrich E, Bauer C, Wahle A, Brown B, Onken M, Riesmeier J, Pieper S, Kikinis R, Buatti J, Beichel RR. (2016) DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research. PeerJ 4:e2057 https://doi.org/10.7717/peerj.2057

2017 Winter Project Week/QuantitativeReporting

2017-01-09T22:38:01Z

Ch399: /* Project Description */

==Key Investigators==

* Christian Herz, BWH
* Andrey Fedorov, BWH
* Andras Lasso, Queen's
* Csaba Pinter, Queen's

==Project Description==
An extension of 3D Slicer to support segmentation-based measurements with DICOM-based import and export of the results.
{| 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;"
|

* utilizes dcmqi library for reading/writing of DICOM SEG/SR
* demonstrate Quantitative Reporting extension
* improve documentation
* discuss next steps and specific open issues
|

* get rid of hacks that hide SegmentEditor components individually by iterating over GUI components
* add functionality for continuing a saved report
* communication of measurements tables and integrated support into Slicer Table node (CSV/JSON/other approaches - see https://github.com/QIICR/QuantitativeReporting/issues/105)
* integration of measurement quantities/units into Slicer for volume nodes
|

|}

[[image:QuantitativeReporting-screenshot.jpg|1024px]]

==Background and References==

dcmqi home page: http://github.com/qiicr/dcmqi

Fedorov A, Clunie D, Ulrich E, Bauer C, Wahle A, Brown B, Onken M, Riesmeier J, Pieper S, Kikinis R, Buatti J, Beichel RR. (2016) DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research. PeerJ 4:e2057 https://doi.org/10.7717/peerj.2057

2017 Winter Project Week/QuantitativeReporting

2017-01-09T22:35:11Z

Ch399:

==Key Investigators==

* Christian Herz, BWH
* Andrey Fedorov, BWH
* Andras Lasso, Queen's
* Csaba Pinter, Queen's

==Project Description==
An extension of 3D Slicer to support segmentation-based measurements with DICOM-based import and export of the results.
{| 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;"
|

* demonstrate Quantitative Reporting extension
* improve documentation
* discuss next steps and specific open issues
|

* get rid of hacks that hide SegmentEditor components individually by iterating over GUI components
* add functionality for continuing a saved report
* communication of measurements tables and integrated support into Slicer Table node (CSV/JSON/other approaches - see https://github.com/QIICR/QuantitativeReporting/issues/105)
* integration of measurement quantities/units into Slicer for volume nodes
|

|}

[[image:QuantitativeReporting-screenshot.jpg|1024px]]

==Background and References==

dcmqi home page: http://github.com/qiicr/dcmqi

Fedorov A, Clunie D, Ulrich E, Bauer C, Wahle A, Brown B, Onken M, Riesmeier J, Pieper S, Kikinis R, Buatti J, Beichel RR. (2016) DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research. PeerJ 4:e2057 https://doi.org/10.7717/peerj.2057

2017 Winter Project Week/QuantitativeReporting

2017-01-09T18:27:02Z

Ch399:

==Key Investigators==

* Christian Herz, BWH
* Andrey Fedorov, BWH
* Andras Lasso, Queen's
* Csaba Pinter, Queen's

==Project Description==
An extension of 3D Slicer to support segmentation-based measurements with DICOM-based import and export of the results.
{| 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;"
|

* demonstrate Quantitative Reporting extension
* improve documentation
* discuss next steps and specific open issues
|

* get rid of hacks that hide SegmentEditor components individually by iterating over GUI components
* add functionality for continuing a saved report
* communication of measurements tables and integrated support into Slicer Table node (CSV/JSON/other approaches - see https://github.com/QIICR/QuantitativeReporting/issues/105)
* integration of measurement quantities/units into Slicer for volume nodes
|

|}

[[image:QuantitativeReporting-screenshot.jpg|1024px]]

==References==

Fedorov A, Clunie D, Ulrich E, Bauer C, Wahle A, Brown B, Onken M, Riesmeier J, Pieper S, Kikinis R, Buatti J, Beichel RR. (2016) DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research. PeerJ 4:e2057 https://doi.org/10.7717/peerj.2057

2017 Winter Project Week/QuantitativeReporting

2017-01-09T15:45:19Z

Ch399: /* Project Description */

==Key Investigators==

* Christian Herz, BWH
* Andrey Fedorov, BWH
* Andras Lasso, Queen's
* Csaba Pinter, Queen's

==Project Description==
An extension of 3D Slicer to support segmentation-based measurements with DICOM-based import and export of the results.
{| 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;"
|

* demonstrate Quantitative Reporting extension
* improve documentation
* discuss next steps and specific open issues
|

* optimize integration with Terminology Editor (UI specific)
* get rid of hacks that hide SegmentEditor components individually by iterating over GUI components
* add functionality for continuing a saved report
* communication of measurements tables and integrated support into Slicer Table node (CSV/JSON/other approaches - see https://github.com/QIICR/QuantitativeReporting/issues/105)
* integration of measurement quantities/units into Slicer for volume nodes
|

|}

[[image:QuantitativeReporting-screenshot.jpg|1024px]]

==References==

Fedorov A, Clunie D, Ulrich E, Bauer C, Wahle A, Brown B, Onken M, Riesmeier J, Pieper S, Kikinis R, Buatti J, Beichel RR. (2016) DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research. PeerJ 4:e2057 https://doi.org/10.7717/peerj.2057

2017 Winter Project Week/QuantitativeReporting

2017-01-09T13:55:00Z

Ch399:

File:QuantitativeReporting-screenshot.jpg

2017-01-09T13:51:40Z

Ch399: Screenshot of the extension

Screenshot of the extension

2017 Winter Project Week/QuantitativeReporting

2017-01-09T06:59:10Z

Ch399:

2017 Winter Project Week/dcmqi

2017-01-09T06:44:35Z

Ch399: removed Quantitative Reporting

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


</gallery>

==Key Investigators==

* Andrey Fedorov, BWH
* Christian Herz, BWH
* Steve Pieper, Isomics
* Jean-Christophe Fillion-Robin, Kitware
* Andras Lasso, Queen's
* Csaba Pinter, Queen's
* Curt Lisle, KnowledgeVis, LLC

==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;"
|

* Introduce dcmqi to the community
* improve documentation
* discuss next steps and specific open issues
|

* Present, meet collaborators...
* discuss pros and cons of integration as an external project into Slicer, and agree on the plan
* discuss the process of integration of new segmentation contexts by the user
* passing DICOM instances to the converters
* support of units/quantities in Slicer (also see [https://www.slicer.org/wiki/Documentation/Labs/Units labs page])
|

*
|}

==Background and References==
* dcmqi home page: http://github.com/qiicr/dcmqi
* dcmqi Slicer extension: https://www.slicer.org/wiki/Documentation/Nightly/Extensions/DCMQI
* DICOM4QI at RSNA2016: https://fedorov.gitbooks.io/rsna2016-qirr-dicom4qi/content/

2017 Winter Project Week/QuantitativeReporting

2017-01-09T06:41:31Z

Ch399:

2017 Winter Project Week/QuantitativeReporting

2017-01-09T06:39:50Z

Ch399:

==Key Investigators==

* Christian Herz, BWH
* Andrey Fedorov, BWH
* Andras Lasso, Queen's
* Csaba Pinter, Queen's

==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;"
|

* demonstrate Quantitative Reporting extension
* improve documentation
* discuss next steps and specific open issues
|

* Terminology Editor
* communication of measurements tables and integrated support into Slicer Table node (CSV/JSON/other approaches - see https://github.com/QIICR/QuantitativeReporting/issues/105)
|

*
|}

2017 Winter Project Week/QuantitativeReporting

2017-01-09T06:37:59Z

Ch399:

==Key Investigators==

* Christian Herz, BWH
* Andrey Fedorov, BWH

==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;"
|

* demonstrate Quantitative Reporting extension
* improve documentation
* discuss next steps and specific open issues
|

* Terminology Editor
* communication of measurements tables and integrated support into Slicer Table node (CSV/JSON/other approaches - see https://github.com/QIICR/QuantitativeReporting/issues/105)
|

*
|}

2017 Winter Project Week/QuantitativeReporting

2017-01-09T06:36:13Z

Ch399: Key Investigators

==Key Investigators==

* Christian Herz, BWH
* Andrey Fedorov, BWH

2017 Winter Project Week

2017-01-09T06:34:51Z

Ch399: /* Projects */

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

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

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

==Logistics==

*'''Dates:''' January 9-13, 2017.
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)
*'''Transportation:''' Public transportation is highly encouraged, as no parking permits will be issued by MIT. For a list of local garages, please see [http://web.mit.edu/facilities/transportation/parking/visitors/public_parking.html here]
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]

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

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 researchers. As of August 2014, it is a [http://www.miccai.org/organization MICCAI] endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO].

A summary of all previous Project Events is available [[Project_Events#Past_Project_Weeks|here]].

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

==Conference Calls for Preparation==

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

==Calendar==

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

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

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

='''Projects'''=

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

== Learning and GPUs ==
#[[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Tina Kapur, Ziyang Wang, Guillaume Pernelle, Paolo Zaffino)
#[[2017 Winter Project Week/DeepInfer| DeepInfer: Open-source Deep Learning Deployment Toolkit]] (Alireza Mehrtash, Mehran Pesteie, Yang (Silvia) Yixin, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)
#[[2017 Winter Project Week/Diffusely abnormal white matter segmentation with 3d U-net| Diffusely abnormal white matter segmentation with 3d U-net]] (Mohsen Ghafoorrian, Bram Platel, Sandy Wells, Tina Kapur)
# [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)
#[[2017 Winter Project Week/An open-source tool to classify TMJ OA condyles | An open-source tool to classify TMJ OA condyles]] (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)
#[[2017 Winter Project Week/Evaluate Deep Learning for binary cancer legion classification | Evaluate Deep Learning for binary cancer lesion classification]] (Curt Lisle)

== Web Technologies ==
#[[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)
#[[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
#[[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
#[[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)
#[[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)
#[[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper, Teodora Szasz)
#[[2017 Winter Project Week/Electron App to add, navigate and visualize DICOM images | Electron App to add, navigate and visualize DICOM images]] (Smruti Padhy, Satrajit Ghosh, Mathias Goncalves)
#[[2017 Winter Project Week/AMI: A 3D Medical Imaging Javascript Library | AMI: A 3D Medical Imaging Javascript Library]] (Rudolph Pienaar, Teodora Szasz)
#[[2017_Winter_Project_Week/MedicalVisualizerUsingParaViewWeb | Medical Visualizer using ParaViewWeb]] (Teodora Szasz)

== IGT: Navigation, Robotics, Surgical Planning ==
#[[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
#[[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)
#[[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]] (Peter Traneus Anderson)
#[[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
#[[2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction| 3D surgical planning solution for autologous breast reconstruction]] (Michael Chae, Andras Lasso, Julian Smith, Warren Rozen, David Hunter-Smith)

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

==Quantitative Imaging Informatics==
#[[2017 Winter Project Week/dcmqi | dcmqi library]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)
#[[2017 Winter Project Week/QuantitativeReporting | DICOM QuantitativeReporting]] (Christian Herz, Andrey Fedorov)
#[[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)
#[[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)
#[[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)

== Shape Analysis, Segmentation, and Visualization ==
#[[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
#[[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)
#[[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)
#[[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
#[[2017 Winter Project Week/GeodesicSegmentationandLungtumorAnalysis| Geodesic Segmentation and Lung tumor Analysis]] (Patmaa S, Sarthak Pati, Ratheesh k, Mark B, Yong F, Despina K, Ragini V, Christos D)
#[[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov)
#[[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)
#[[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)
#[[2017 Winter Project Week/CoronarySegmentationTool| Automatic and Manual Segmentation Tool of Coronary Artery from CTA imaging]] (Haoyin Zhou, Jayender Jagadeesan)

== Infrastructure ==
#[[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)
#[[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
#[[2017 Winter Project Week/UpdatingCommunityForums | Updating Community Forums (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)
#[[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
#[[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Pieper)
#[[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault, Andras Lasso)

==Training and Dissemination==
#[[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)

= '''Registrants''' =

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [https://www.regonline.com/2017projectweek registration site].

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

2017 Winter Project Week

2017-01-09T06:34:04Z

Ch399: /* Projects */

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

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

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

==Logistics==

*'''Dates:''' January 9-13, 2017.
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)
*'''Transportation:''' Public transportation is highly encouraged, as no parking permits will be issued by MIT. For a list of local garages, please see [http://web.mit.edu/facilities/transportation/parking/visitors/public_parking.html here]
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]

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

[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 researchers. As of August 2014, it is a [http://www.miccai.org/organization MICCAI] endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO].

A summary of all previous Project Events is available [[Project_Events#Past_Project_Weeks|here]].

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

==Conference Calls for Preparation==

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

==Calendar==

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

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

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

='''Projects'''=

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

== Learning and GPUs ==
#[[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Tina Kapur, Ziyang Wang, Guillaume Pernelle, Paolo Zaffino)
#[[2017 Winter Project Week/DeepInfer| DeepInfer: Open-source Deep Learning Deployment Toolkit]] (Alireza Mehrtash, Mehran Pesteie, Yang (Silvia) Yixin, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)
#[[2017 Winter Project Week/Diffusely abnormal white matter segmentation with 3d U-net| Diffusely abnormal white matter segmentation with 3d U-net]] (Mohsen Ghafoorrian, Bram Platel, Sandy Wells, Tina Kapur)
# [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)
#[[2017 Winter Project Week/An open-source tool to classify TMJ OA condyles | An open-source tool to classify TMJ OA condyles]] (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)
#[[2017 Winter Project Week/Evaluate Deep Learning for binary cancer legion classification | Evaluate Deep Learning for binary cancer lesion classification]] (Curt Lisle)

== Web Technologies ==
#[[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)
#[[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
#[[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
#[[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)
#[[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)
#[[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper, Teodora Szasz)
#[[2017 Winter Project Week/Electron App to add, navigate and visualize DICOM images | Electron App to add, navigate and visualize DICOM images]] (Smruti Padhy, Satrajit Ghosh, Mathias Goncalves)
#[[2017 Winter Project Week/AMI: A 3D Medical Imaging Javascript Library | AMI: A 3D Medical Imaging Javascript Library]] (Rudolph Pienaar, Teodora Szasz)
#[[2017_Winter_Project_Week/MedicalVisualizerUsingParaViewWeb | Medical Visualizer using ParaViewWeb]] (Teodora Szasz)

== IGT: Navigation, Robotics, Surgical Planning ==
#[[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
#[[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)
#[[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]] (Peter Traneus Anderson)
#[[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
#[[2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction| 3D surgical planning solution for autologous breast reconstruction]] (Michael Chae, Andras Lasso, Julian Smith, Warren Rozen, David Hunter-Smith)

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

==Quantitative Imaging Informatics==
#[[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)
#[[2017 Winter Project Week/QuantitativeReporting | QuantitativeReporting]] (Christian Herz, Andrey Fedorov)
#[[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)
#[[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)
#[[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)

== Shape Analysis, Segmentation, and Visualization ==
#[[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
#[[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)
#[[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)
#[[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
#[[2017 Winter Project Week/GeodesicSegmentationandLungtumorAnalysis| Geodesic Segmentation and Lung tumor Analysis]] (Patmaa S, Sarthak Pati, Ratheesh k, Mark B, Yong F, Despina K, Ragini V, Christos D)
#[[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov)
#[[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)
#[[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)
#[[2017 Winter Project Week/CoronarySegmentationTool| Automatic and Manual Segmentation Tool of Coronary Artery from CTA imaging]] (Haoyin Zhou, Jayender Jagadeesan)

== Infrastructure ==
#[[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)
#[[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
#[[2017 Winter Project Week/UpdatingCommunityForums | Updating Community Forums (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)
#[[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
#[[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Pieper)
#[[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault, Andras Lasso)

==Training and Dissemination==
#[[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)

= '''Registrants''' =

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [https://www.regonline.com/2017projectweek registration site].

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

2017 Winter Project Week

2016-12-23T20:36:22Z

Ch399: /* Registrants */

2016 Summer Project Week/SliceTracker

2016-06-25T08:22:13Z

Ch399: /* Background and References */

==Key Investigators==
* Christian Herz (BWH)
* Peter Behringer (Basler AG)
* Andriy Fedorov (BWH)

==Project Description==

Slicetracker is a Slicer extension which focuses on tracking the prostate during MR-guided prostate biopsies.
It combines registration of the prostate in pre-procedural and intra-procedural images which improves the chance to find the exact same target position in intra-procedural images.

Furthermore a so called z-Frame registration is included for correlating the patient and 3D Slicers coordinate system. For guidance of the needle a template grid with 15x14 holes is placed in front of the z-Frame. The optimal hole is computed for inserting the needle and obtaining the tissue sample.

{| 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;"
|

* Use SliceTracker currently used in shadow mode + collecting feedback from Kemal about usability
** At least 5 cases in a row which has to run without having any issues, then production use
* Integration of Z-Frame registration
* Calculation of template hole and depth to apply for reaching targets
|

* Discussions and feedback about usability and improvements
|

* Discussions about implementing SliceTracker as a Slicelet (for prevent users from making mistakes/pushing wrong buttons etc.)
* Next Steps:
** Will soon run in production mode replacing the "old" Slicer 3 cart
** As soon as it is in its final state: create extension
|}

==Background and References==


[[File:Slicetracker.gif]]

SliceTracker code: https://github.com/SlicerProstate/SliceTracker

Previous project week resources:
* Winter 2015: http://www.na-mic.org/Wiki/index.php/ProstateNavigation_workflow
* Summer 2015: http://www.na-mic.org/Wiki/index.php/2015_Refinement_Registration_Module
* Winter 2016: http://www.na-mic.org/Wiki/index.php/2016_Winter_Project_Week/Projects/SliceTracker

2016 Summer Project Week/SliceTracker

2016-06-25T08:15:20Z

Ch399: /* Project Description */

2016 Summer Project Week/SliceTracker

2016-06-25T08:07:55Z

Ch399: /* Project Description */

==Key Investigators==
* Christian Herz (BWH)
* Peter Behringer (Basler AG)
* Andriy Fedorov (BWH)

==Project Description==

Slicetracker is a Slicer extension which focuses on tracking the prostate during MR-guided prostate biopsies.
It combines registration of the prostate in pre-procedural and intra-procedural images which improves the chance to find the exact same target position in intra-procedural images.

Furthermore a so called z-Frame registration is included for correlating the patient and 3D Slicers coordinate system. For guidance of the needle a template grid with 15x14 holes is placed in front of the z-Frame. The optimal hole is computed for inserting the needle and obtaining the tissue sample.

{| 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;"
|

* Use SliceTracker currently used in shadow mode + collecting feedback from Kemal about usability
** At least 5 cases in a row which has to run without having any issues, then production use
* Integration of Z-Frame registration
* Calculation of template hole and depth to apply for reaching targets
|

* Discussions and feedback about usability and improvements
|

* Discussions about implementing SliceTracker as a Slicelet (for prevent users from making mistakes/pushing wrong buttons etc.)
* Next Steps:
** Will soon run in production mode replacing the "old" Slicer 3 cart
|}

==Background and References==


[[File:Slicetracker.gif]]

SliceTracker code: https://github.com/SlicerProstate/SliceTracker

2016 Summer Project Week/dcmqi

2016-06-25T08:00:23Z

Ch399: /* Project Description */

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

==Key Investigators==
* Andrey Fedorov
* Christian Herz
* Marco Nolden
* Hans Meine
* Csaba Pinter
* Steve Pieper
* Caspar Goch (Mon)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* [https://github.com/qiicr/dcmqi dcmqi] (DICOM for Quantitative Imaging) is a library to help with the DICOM data handling and conversion tasks in quantitative image analysis.
* This week we will work to improve functionality of the library, discuss API with the prospective users, and collect feedback.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Work on the web application for populating SEG metadata
* Add testing and integrate refactoring of the DICOM SEG converter
** Discuss options for hosting test data: Midas, git-lfs [https://github.com/QIICR/dcmqi/pull/11], ...
* Work on DICOM SR TID1500 converter
* Explore integration with MITK, MevisLab and Slicer Segmentation Editor
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress and Next Steps</h3>
* Implemented web application for populating SEG metadata: http://qiicr.org/dcmqi
* Parametric maps:
** Created metadata file which describes required information in order to create DICOM parametric maps
** Started extending dcmqi API for converting itk to DICOM parametric map and vice versa
* Experimental addition of Brainlab segmentation objects [https://github.com/QIICR/dcmqi/pull/22]
* Next Steps:
** Finish implementation of dcmqi API, testing and (extending) web application for populating parametric maps metadata
** Creation of demo for RSNA 2016 that will include SEG and SR support
</div>
</div>
<br style="clear:left;">

==References==
* Fedorov A, Clunie D, Ulrich E, Bauer C, Wahle A, Brown B, Onken M, Riesmeier J, Pieper S, Kikinis R, Buatti J, Beichel RR. (2016) DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research. PeerJ 4:e2057 https://doi.org/10.7717/peerj.2057

2016 Summer Project Week/dcmqi

2016-06-24T21:47:21Z

Ch399: /* Project Description */

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

==Key Investigators==
* Andrey Fedorov
* Christian Herz
* Marco Nolden
* Hans Meine
* Csaba Pinter
* Steve Pieper
* Caspar Goch (Mon)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* [https://github.com/qiicr/dcmqi dcmqi] (DICOM for Quantitative Imaging) is a library to help with the DICOM data handling and conversion tasks in quantitative image analysis.
* This week we will work to improve functionality of the library, discuss API with the prospective users, and collect feedback.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Work on the web application for populating SEG metadata
* Add testing and integrate refactoring of the DICOM SEG converter
** Discuss options for hosting test data: Midas, git-lfs, ...
* Work on DICOM SR TID1500 converter
* Explore integration with MITK, MevisLab and Slicer Segmentation Editor
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress and Next Steps</h3>
* Implemented web application for populating SEG metadata: http://qiicr.org/dcmqi
* Regarding parametric maps:
** Created metadata file which describes required information in order to create DICOM parametric maps
** Extended QIIRC API for converting itk to DICOM parametric map and vv (not complete)
* Experimental addition of Brainlab segmentation objects [https://github.com/QIICR/dcmqi/pull/22]
* Next Steps:
** Finish implementation of dcmqi API, testing and (extending) web application for populating parametric maps metadata
** Creation of demo for RSNA 2016
</div>
</div>
<br style="clear:left;">

==References==
* Fedorov A, Clunie D, Ulrich E, Bauer C, Wahle A, Brown B, Onken M, Riesmeier J, Pieper S, Kikinis R, Buatti J, Beichel RR. (2016) DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research. PeerJ 4:e2057 https://doi.org/10.7717/peerj.2057

2016 Summer Project Week/dcmqi

2016-06-24T21:39:19Z

Ch399: /* Project Description */

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

==Key Investigators==
* Andrey Fedorov
* Christian Herz
* Marco Nolden
* Hans Meine
* Csaba Pinter
* Steve Pieper
* Caspar Goch (Mon)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* [https://github.com/qiicr/dcmqi dcmqi] (DICOM for Quantitative Imaging) is a library to help with the DICOM data handling and conversion tasks in quantitative image analysis.
* This week we will work to improve functionality of the library, discuss API with the prospective users, and collect feedback.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Add testing and integrate refactoring of the DICOM SEG converter
** discuss options for hosting test data: Midas, git-lfs, ...
* Work on DICOM SR TID1500 converter
* Explore integration with MITK, MevisLab and Slicer Segmentation Editor
* Work on the web application for populating SEG metadata
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* created/extended web app for populating SEG metadata: http://qiicr.org/dcmqi
* Regarding parametric maps:
** Created metadata file which describes required information in order to create DICOM parametric maps
** Extended QIIRC API for converting itk to DICOM parametric map and vv (not complete)
* experimental addition of Brainlab segmentation objects [https://github.com/QIICR/dcmqi/pull/22]
</div>
</div>
<br style="clear:left;">

==References==
* Fedorov A, Clunie D, Ulrich E, Bauer C, Wahle A, Brown B, Onken M, Riesmeier J, Pieper S, Kikinis R, Buatti J, Beichel RR. (2016) DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research. PeerJ 4:e2057 https://doi.org/10.7717/peerj.2057

2016 Summer Project Week/DICOM Parametric Maps

2016-06-24T21:37:04Z

Ch399: /* Project Description */

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

==Key Investigators==
* Michael Onken
* Jan Schlamelcher
* Andrey Fedorov
* Christian Herz

==Project Description==

This software project is part of the [http://qiicr.org/ QIICR project].

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Add API to DCMTK (library called dcmpmap) which allows easy creation and reading of DICOM Parametric Map objects
* Parametric Map objects have been introduced in DICOM with [ftp://medical.nema.org/medical/dicom/final/sup172_ft2.pdf Supplement 172] in 2014.
* From the Supplement: DICOM Parametric Maps include quantitative derived images computed from acquired images, where each pixel value has a "meaning" in the real world, and the name "parametric" alludes to the meaning being the parameter of something, such as a pharmacokinetic model. In general, the term "parametric map" is loosely used to refer to any derived image whose pixel values have a quantitative meaning, as opposed to acquired images, whose pixel values may or may not have meaning
* This week we will work to discuss and finalize the API of the the library and prepare it for checkin to DCMTK
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discuss existing API and refine it
* Finalize it (documentation, cleanup) for checkin into DCMTK
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress and Next Steps</h3>
* There is already a first version of a code generator that creates code for DICOM modules, functional groups and partly IODs
</div>
</div>
<br style="clear:left;">

== References ==
* RWVM sample dataset: [[File:QIN-HEADNECK-rwvm.dcm.zip]]
* RWVM generation code: https://github.com/QIICR/Slicer-PETDICOMExtension/blob/master/SUVFactorCalculatorCLI/SUVFactorCalculator.cxx#L856-L965

2016 Summer Project Week/DICOM Parametric Maps

2016-06-24T15:34:21Z

Ch399: /* Project Description */

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

==Key Investigators==
* Michael Onken
* Jan Schlamelcher
* Andrey Fedorov
* Christian Herz

==Project Description==

This software project is part of the [http://qiicr.org/ QIICR project].

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Add API to DCMTK (library called dcmpmap) which allows easy creation and reading of DICOM Parametric Map objects
* Parametric Map objects have been introduced in DICOM with [ftp://medical.nema.org/medical/dicom/final/sup172_ft2.pdf Supplement 172] in 2014.
* From the Supplement: DICOM Parametric Maps include quantitative derived images computed from acquired images, where each pixel value has a "meaning" in the real world, and the name "parametric" alludes to the meaning being the parameter of something, such as a pharmacokinetic model. In general, the term "parametric map" is loosely used to refer to any derived image whose pixel values have a quantitative meaning, as opposed to acquired images, whose pixel values may or may not have meaning
* This week we will work to discuss and finalize the API of the the library and prepare it for checkin to DCMTK
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discuss existing API and refine it
* Finalize it (documentation, cleanup) for checkin into DCMTK
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress and Next Steps</h3>
* There is already a first version of a code generator that creates code for DICOM modules, functional groups and partly IODs
* Extended QIIRC API for converting itk to DICOM parametric map and vv (not complete)
</div>
</div>
<br style="clear:left;">

== References ==
* RWVM sample dataset: [[File:QIN-HEADNECK-rwvm.dcm.zip]]
* RWVM generation code: https://github.com/QIICR/Slicer-PETDICOMExtension/blob/master/SUVFactorCalculatorCLI/SUVFactorCalculator.cxx#L856-L965

2016 Summer Project Week/DICOM Parametric Maps

2016-06-24T15:32:08Z

Ch399: /* Project Description */

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

==Key Investigators==
* Michael Onken
* Jan Schlamelcher
* Andrey Fedorov
* Christian Herz

==Project Description==

This software project is part of the [http://qiicr.org/ QIICR project].

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Add API to DCMTK (library called dcmpmap) which allows easy creation and reading of DICOM Parametric Map objects
* Parametric Map objects have been introduced in DICOM with [ftp://medical.nema.org/medical/dicom/final/sup172_ft2.pdf Supplement 172] in 2014.
* From the Supplement: DICOM Parametric Maps include quantitative derived images computed from acquired images, where each pixel value has a "meaning" in the real world, and the name "parametric" alludes to the meaning being the parameter of something, such as a pharmacokinetic model. In general, the term "parametric map" is loosely used to refer to any derived image whose pixel values have a quantitative meaning, as opposed to acquired images, whose pixel values may or may not have meaning
* This week we will work to discuss and finalize the API of the the library and prepare it for checkin to DCMTK
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discuss existing API and refine it
* Finalize it (documentation, cleanup) for checkin into DCMTK
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress and Next Steps</h3>
* There is already a first version of a code generator that creates code for DICOM modules, functional groups and partly IODs
* Extended qiicr api for converting itk to DICOM parametric map and vv (not complete)
</div>
</div>
<br style="clear:left;">

== References ==
* RWVM sample dataset: [[File:QIN-HEADNECK-rwvm.dcm.zip]]
* RWVM generation code: https://github.com/QIICR/Slicer-PETDICOMExtension/blob/master/SUVFactorCalculatorCLI/SUVFactorCalculator.cxx#L856-L965

2016 Summer Project Week/dcmqi

2016-06-24T13:06:24Z

Ch399:

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

==Key Investigators==
* Andrey Fedorov
* Christian Herz
* Marco Nolden
* Hans Meine
* Csaba Pinter
* Steve Pieper
* Caspar Goch (Mon)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* [https://github.com/qiicr/dcmqi dcmqi] (DICOM for Quantitative Imaging) is a library to help with the DICOM data handling and conversion tasks in quantitative image analysis.
* This week we will work to improve functionality of the library, discuss API with the prospective users, and collect feedback.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Add testing and integrate refactoring of the DICOM SEG converter
** discuss options for hosting test data: Midas, git-lfs, ...
* Work on DICOM SR TID1500 converter
* Explore integration with MITK, MevisLab and Slicer Segmentation Editor
* Work on the web application for populating SEG metadata
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* created/extended web app for populating SEG metadata: http://qiicr.org/dcmqi
* experimental addition of Brainlab segmentation objects [https://github.com/QIICR/dcmqi/pull/22]
</div>
</div>
<br style="clear:left;">

==References==
* Fedorov A, Clunie D, Ulrich E, Bauer C, Wahle A, Brown B, Onken M, Riesmeier J, Pieper S, Kikinis R, Buatti J, Beichel RR. (2016) DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research. PeerJ 4:e2057 https://doi.org/10.7717/peerj.2057

2016 Summer Project Week/SliceTracker

2016-06-24T12:57:35Z

Ch399: /* Project Description */

==Key Investigators==
* Christian Herz (BWH)
* Peter Behringer (Basler AG)
* Andriy Fedorov (BWH)

==Project Description==

Slicetracker is a Slicer extension which focuses on tracking the prostate during MR-guided prostate biopsies.
It combines registration of the prostate in pre-procedural and intra-procedural images which improves the chance to find the exact same target position in intra-procedural images.

Furthermore a so called z-Frame registration is included for correlating the patient and 3D Slicers coordinate system. For guidance of the needle a template grid with 15x14 holes is placed in front of the z-Frame. The optimal hole is computed for inserting the needle and obtaining the tissue sample.

{| 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;"
|

* Use SliceTracker currently used in shadow mode + collecting feedback from Kemal about usability
** At least 5 cases in a row which has to run without having any issues, then production use
* Integration of Z-Frame registration
* Calculation of template hole and depth to apply for reaching targets
|

* Discussions and feedback about usability and improvements
|

* Discussions about implementing SliceTracker as a Slicelet (for prevent users from making mistakes/pushing wrong buttons etc.)
* Will soon run in production mode replacing the "old" Slicer 3 cart
|}

==Background and References==


[[File:Slicetracker.gif]]

SliceTracker code: https://github.com/SlicerProstate/SliceTracker

2016 Summer Project Week

2016-06-22T10:36:39Z

Ch399: Typo in Guildelts

__NOTOC__

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

= '''Registrants''' =

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

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

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

2016 Summer Project Week/SliceTracker

2016-06-19T21:58:15Z

Ch399: Added animated gif for workflow

==Key Investigators==
* Christian Herz (BWH)
* Peter Behringer (Basler AG)
* Andriy Fedorov (BWH)

==Project Description==

Slicetracker is a Slicer extension which focuses on tracking the prostate during MR-guided prostate biopsies.
It combines registration of the prostate in pre-procedural and intra-procedural images which improves the chance to find the exact same target position in intra-procedural images.

Furthermore a so called z-Frame registration is included for correlating the patient and 3D Slicers coordinate system. For guidance of the needle a template grid with 15x14 holes is placed in front of the z-Frame. The optimal hole is computed for inserting the needle and obtaining the tissue sample.

{| 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;"
|

* Use SliceTracker currently used in shadow mode + collecting feedback from Kemal about usability
** At least 5 cases in a row which has to run without having any issues, then production use
* Integration of Z-Frame registration
* Calculation of template hole and depth to apply for reaching targets
|

* Discussions and feedback about usability and improvements
|


|}

==Background and References==


[[File:Slicetracker.gif]]

SliceTracker code: https://github.com/SlicerProstate/SliceTracker

File:Slicetracker.gif

2016-06-19T21:54:44Z

Ch399: SliceTracker Workflow Animation

SliceTracker Workflow Animation

2016 Summer Project Week/SliceTracker

2016-06-19T17:49:42Z

Ch399: Added some more content to project description

==Key Investigators==
* Christian Herz (BWH)
* Peter Behringer (Basler AG)
* Andriy Fedorov (BWH)

==Project Description==

Slicetracker is a Slicer extension which focuses on tracking the prostate during MR-guided prostate biopsies.
It combines registration of the prostate in pre-procedural and intra-procedural images which improves the chance to find the exact same target position in intra-procedural images.

Furthermore a so called z-Frame registration is included for correlating the patient and 3D Slicers coordinate system. For guidance of the needle a template grid with 15x14 holes is placed in front of the z-Frame. The optimal hole is computed for inserting the needle and obtaining the tissue sample.

{| 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;"
|

* Use SliceTracker currently used in shadow mode + collecting feedback from Kemal about usability
** At least 5 cases in a row which has to run without having any issues, then production use
* Integration of Z-Frame registration
* Calculation of template hole and depth to apply for reaching targets
|

* Discussions and feedback about usability and improvements
|


|}

==Background and References==

SliceTracker code: https://github.com/SlicerProstate/SliceTracker

2016 Summer Project Week/SliceTracker

2016-06-15T17:25:25Z

Ch399: Added source link

==Key Investigators==
* Christian Herz (BWH)
* Peter Behringer (Basler AG)
* Andriy Fedorov (BWH)

==Project Description==

Slicetracker is a Slicer extension which focuses on tracking the prostate during prostate biopsies. In order to set the needle at the right position, SliceTracker includes a so called Z-Frame registration and calculates the optimal hole of a grid with 15x14 holes to be used for guiding the needle.

{| 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;"
|

* Use SliceTracker currently used in shadow mode + collecting feedback from Kemal about usability
** At least 5 cases in a row which has to run without having any issues, then production use
* Integration of Z-Frame registration
* Calculation of template hole and depth to apply for reaching targets
|

* Discussions and feedback about usability and improvements
|


|}

==Background and References==

SliceTracker code: https://github.com/SlicerProstate/SliceTracker

2016 Summer Project Week/SliceTracker

2016-06-14T15:26:07Z

Ch399:

==Key Investigators==
* Christian Herz (BWH)
* Peter Behringer (Basler AG)
* Andriy Fedorov (BWH)

==Project Description==

Slicetracker is a Slicer extension which focuses on tracking the prostate during prostate biopsies. In order to set the needle at the right position, SliceTracker includes a so called Z-Frame registration and calculates the optimal hole of a grid with 15x14 holes to be used for guiding the needle.

{| 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;"
|

* Use SliceTracker currently used in shadow mode + collecting feedback from Kemal about usability
** At least 5 cases in a row which has to run without having any issues, then production use
* Integration of Z-Frame registration
* Calculation of template hole and depth to apply for reaching targets
|

* Discussions and feedback about usability and improvements
|


|}

2016 Summer Project Week/SliceTracker

2016-06-07T14:18:59Z

Ch399: typo

==Key Investigators==
* Christian Herz (BWH)
* Peter Behringer (Basler AG)
* Andriy Fedorov (BWH)

==Project Description==

Slicetracker is a Slicer extension which focuses on tracking the prostate during prostate biopsies including Z-Frame registration and calculation of the hole to be used for insertion of the needle to be able to reach the target. Including a lot of discussions we were able to make it even more usable than it was in the first stage.

{| 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;"
|

* Use SliceTracker currently mostly in shadow mode including collecting feedback from Kemal about usability
* Integration of Z-Frame registration
* Calculation of template hole and depth to apply for reaching targets
|


|


|}

2016 Summer Project Week/SliceTracker

2016-06-07T13:00:41Z

Ch399: added content

==Key Investigators==
* Christian Herz (BWH)
* Peter Behringer (Basler AG)
* Andriy Fedorov (BWH)

==Project Description==

Slicetrakcer is a Slicer extension which focuses on tracking the prostate during prostate biopsies including Z-Frame registration and calculation of the hole to be used for insertion of the needle to be able to reach the target. Including a lot of discussions we were able to make it even more usable than it was in the first stage.

{| 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;"
|

* Use SliceTracker currently mostly in shadow mode including collecting feedback from Kemal about usability
* Integration of Z-Frame registration
* Calculation of template hole and depth to apply for reaching targets
|


|


|}

File:2016WinterEBP SliceTracker 1.jpg

2016-01-08T15:19:32Z

Ch399:

2016 Winter Project Week/Projects/SliceTracker

2016-01-08T15:10:17Z

Ch399:

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

Image:2016WinterEBP_SliceTracker.jpg|SliceTracker Main Window Screenshot
Image:2016WinterEBP_SliceTracker_1.jpg|SliceTracker Evaluation Window Screenshot</gallery>

==Key Investigators==
* Christian Herz (BWH)
* Andriy Fedorov (BWH)
* Andras Lasso (Queens)

==Project Description==
Prostate biopsies can become a big challenge, especially when the prostate changed from pre-procedural to intra-procedural image acquisition. Motion and deformation of the prostate raises difficulties for positioning the biopsy needle at the right position. The registration module’s goal is to optimize the workflow and provide a solution, that is easy to use.
{| 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;"
|

* Slicer module implemented that allows the registration of the prostate
* Use SliceTracker during prostate biopsies as a replacement to current approach
|

* Present the module to interested members of the community
* Get feedback about the workflow and usability
* Work on the remaining issues
* Discuss about migrating this module into a slicelet
|

* Positive feedback for workflow and usability of the module
* LumpNav is a slicelet example to follow
* TODO:
** Create an extension from that module and provide an appropriate example dataset
** Integrate the z-frame and navigation component into the module
|}

==Progress notes==
* What about simply hiding components (toolbars) that are not needed?
* Trick to hide all toolbars!
<pre>
>>> w = slicer.util.mainWindow()
>>> for c in w.children():
... if str(type(c)).find('ToolBar')>0:
... c.hide()
</pre>

Drawback: after restarting Slicer, the toolbars are still hidden.

==Background and References==

SliceTracker code: https://github.com/SlicerProstate/SliceTracker

File:2016WinterEBP SliceTracker.jpg

2016-01-08T15:08:59Z

Ch399:

2016 Winter Project Week/Projects/SliceTracker

2016-01-08T15:07:56Z

Ch399:

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

Image:2016WinterEBP_SliceTracker.jpg|SliceTracker Main Window Screenshot</gallery>

==Key Investigators==
* Christian Herz (BWH)
* Andriy Fedorov (BWH)
* Andras Lasso (Queens)

==Project Description==
Prostate biopsies can become a big challenge, especially when the prostate changed from pre-procedural to intra-procedural image acquisition. Motion and deformation of the prostate raises difficulties for positioning the biopsy needle at the right position. The registration module’s goal is to optimize the workflow and provide a solution, that is easy to use.
{| 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;"
|

* Slicer module implemented that allows the registration of the prostate
* Use SliceTracker during prostate biopsies as a replacement to current approach
|

* Present the module to interested members of the community
* Get feedback about the workflow and usability
* Work on the remaining issues
* Discuss about migrating this module into a slicelet
|

* Positive feedback for workflow and usability of the module
* LumpNav is a slicelet example to follow
* TODO:
** Create an extension from that module and provide an appropriate example dataset
** Integrate the z-frame and navigation component into the module
|}

==Progress notes==
* What about simply hiding components (toolbars) that are not needed?
* Trick to hide all toolbars!
<pre>
>>> w = slicer.util.mainWindow()
>>> for c in w.children():
... if str(type(c)).find('ToolBar')>0:
... c.hide()
</pre>

Drawback: after restarting Slicer, the toolbars are still hidden.

==Background and References==

SliceTracker code: https://github.com/SlicerProstate/SliceTracker

2016 Winter Project Week/Projects/SliceTracker

2016-01-07T21:26:53Z

Ch399:

==Key Investigators==
* Christian Herz (BWH)
* Andriy Fedorov (BWH)
* Andras Lasso (Queens)

==Project Description==
Prostate biopsies can become a big challenge, especially when the prostate changed from pre-procedural to intra-procedural image acquisition. Motion and deformation of the prostate raises difficulties for positioning the biopsy needle at the right position. The registration module’s goal is to optimize the workflow and provide a solution, that is easy to use.
{| 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;"
|

* Slicer module implemented that allows the registration of the prostate
* Use SliceTracker during prostate biopsies as a replacement to current approach
|

* Present the module to interested members of the community
* Get feedback about the workflow and usability
* Work on the remaining issues
* Discuss about migrating this module into a slicelet
|

* Positive feedback for workflow and usability of the module
* LumpNav is a slicelet example to follow
* TODO:
** Create an extension from that module and provide an appropriate example dataset
** Integrate the z-frame and navigation component into the module
|}

==Progress notes==
* What about simply hiding components (toolbars) that are not needed?
* Trick to hide all toolbars!
<pre>
>>> w = slicer.util.mainWindow()
>>> for c in w.children():
... if str(type(c)).find('ToolBar')>0:
... c.hide()
</pre>

Drawback: after restarting Slicer, the toolbars are still hidden.

==Background and References==

SliceTracker code: https://github.com/SlicerProstate/SliceTracker

2016 Winter Project Week/Projects/SliceTracker

2016-01-07T21:23:56Z

Ch399:

==Key Investigators==
* Christian Herz (BWH)
* Andriy Fedorov (BWH)
* Andras Lasso (Queens)

==Project Description==
Prostate biopsies can become a big challenge, especially when the prostate changed from pre-procedural to intra-procedural image acquisition. Motion and deformation of the prostate raises difficulties for positioning the biopsy needle at the right position. The registration module’s goal is to optimize the workflow and provide a solution, that is easy to use.
{| 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;"
|

* Slicer module implemented that allows the registration of the prostate
* Integrate the z-frame and navigation component into the module
* Use SliceTracker during prostate biopsies as a replacement to current approach
|

* Present the module to interested members of the community
* Get feedback about the workflow and usability
* Work on the remaining issues
* Discuss about migrating this module into a slicelet
|

* Positive feedback for workflow and usability of the module
* LumpNav is a slicelet example to follow
* Planning to create an extension from that module and provide an appropriate example dataset
|}

==Progress notes==
* What about simply hiding components (toolbars) that are not needed?
* Trick to hide all toolbars!
<pre>
>>> w = slicer.util.mainWindow()
>>> for c in w.children():
... if str(type(c)).find('ToolBar')>0:
... c.hide()
</pre>

Drawback: after restarting Slicer, the toolbars are still hidden.

==Background and References==

SliceTracker code: https://github.com/SlicerProstate/SliceTracker

2016 Winter Project Week/Projects/SliceTracker

2016-01-07T21:21:49Z

Ch399:

==Key Investigators==
* Christian Herz (BWH)
* Andriy Fedorov (BWH)
* Andras Lasso (Queens)

==Project Description==
Prostate biopsies can become a big challenge, especially when the prostate changed from pre-procedural to intra-procedural image acquisition. Motion and deformation of the prostate raises difficulties for positioning the biopsy needle at the right position. The registration module’s goal is to optimize the workflow and provide a solution, that is easy to use.
{| 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;"
|

* Slicer module implemented that allows the registration of the prostate
* Integrate the z-frame and navigation component into the module
* Use SliceTracker during prostate biopsies as a replacement to current approach
|

* Present the module to interested members of the community
* Get feedback about the workflow and usability
* Work on the remaining issues
* Discuss about migrating this module into a slicelet
|

* LumpNav is a slicelet example to follow
* Planning to create an extension from that module and provide an appropriate example dataset
|}

==Progress notes==
* What about simply hiding components (toolbars) that are not needed?
* Trick to hide all toolbars!
<pre>
>>> w = slicer.util.mainWindow()
>>> for c in w.children():
... if str(type(c)).find('ToolBar')>0:
... c.hide()
</pre>

Drawback: after restarting Slicer, the toolbars are still hidden.

==Background and References==

SliceTracker code: https://github.com/SlicerProstate/SliceTracker

2016 Winter Project Week/Projects/SliceTracker

2016-01-07T21:21:31Z

Ch399:

==Key Investigators==
* Christian Herz (BWH)
* Andriy Fedorov (BWH)
* Andras Lasso (Queens)

==Project Description==
Prostate biopsies can become a big challenge, especially when the prostate changed from pre-procedural to intra-procedural image acquisition. Motion and deformation of the prostate raises difficulties for positioning the biopsy needle at the right position. The registration module’s goal is to optimize the workflow and provide a solution, that is easy to use.
{| 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;"
|

* Slicer module implemented that allows the registration of the prostate
* Integrate the z-frame and navigation component into the module
* Use SliceTracker during prostate biopsies as a replacement to current approach
|

* Present the module to interested members of the community
* Get feedback about the workflow and usability
* Work on the remaining issues
* Discuss about migrating this module into a slicelet
|

* LumpNav is a slicelet example to follow
* Planning to create an extension from that module and provide an appropriate example dataset
* What about simply hiding components (toolbars) that are not needed? (see example below)
|}

==Progress notes==
* What about simply hiding components (toolbars) that are not needed?
* Trick to hide all toolbars!
<pre>
>>> w = slicer.util.mainWindow()
>>> for c in w.children():
... if str(type(c)).find('ToolBar')>0:
... c.hide()
</pre>

Drawback: after restarting Slicer, the toolbars are still hidden.

==Background and References==

SliceTracker code: https://github.com/SlicerProstate/SliceTracker

2016 Winter Project Week/Projects/SliceTracker

2016-01-07T16:37:24Z

Ch399: fixed wrong headline Key investigators

==Key Investigators==
* Christian Herz (BWH)
* Andriy Fedorov (BWH)
* Andras Lasso (Queens)

==Project Description==
Prostate biopsies can become a big challenge, especially when the prostate changed from pre-procedural to intra-procedural image acquisition. Motion and deformation of the prostate raises difficulties for positioning the biopsy needle at the right position. The registration module’s goal is to optimize the workflow and provide a solution, that is easy to use.
{| 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;"
|

* Slicer module implemented that allows the registration of the prostate
* Integrate the z-frame and navigation component into the module
* Use SliceTracker during prostate biopsies as a replacement to current approach
|

* Present the module to interested members of the community
* Get feedback about the workflow and usability
* Work on the remaining issues
* Discuss about migrating this module into a slicelet
|

* LumpNav is a slicelet example to follow
* Planning to create an extension from that module and provide an appropriate example dataset
* What about simply hiding components (toolbars) that are not needed? (see example below)
|}

==Progress notes==
* Trick to hide all toolbars!
<pre>
>>> w = slicer.util.mainWindow()
>>> for c in w.children():
... if str(type(c)).find('ToolBar')>0:
... c.hide()
</pre>

Drawback: after restarting Slicer, the toolbars are still hidden.

==Background and References==

SliceTracker code: https://github.com/SlicerProstate/SliceTracker

2016 Winter Project Week/Projects/SliceTracker

2016-01-07T16:35:28Z

Ch399: added progress point

<nowiki>Insert non-formatted text here</nowiki>==Key Investigators==
* Christian Herz (BWH)
* Andriy Fedorov (BWH)
* Andras Lasso (Queens)

==Project Description==
Prostate biopsies can become a big challenge, especially when the prostate changed from pre-procedural to intra-procedural image acquisition. Motion and deformation of the prostate raises difficulties for positioning the biopsy needle at the right position. The registration module’s goal is to optimize the workflow and provide a solution, that is easy to use.
{| 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;"
|

* Slicer module implemented that allows the registration of the prostate
* Integrate the z-frame and navigation component into the module
* Use SliceTracker during prostate biopsies as a replacement to current approach
|

* Present the module to interested members of the community
* Get feedback about the workflow and usability
* Work on the remaining issues
* Discuss about migrating this module into a slicelet
|

* LumpNav is a slicelet example to follow
* Planning to create an extension from that module and provide an appropriate example dataset
* What about simply hiding components (toolbars) that are not needed? (see example below)
|}

==Progress notes==
* Trick to hide all toolbars!
<pre>
>>> w = slicer.util.mainWindow()
>>> for c in w.children():
... if str(type(c)).find('ToolBar')>0:
... c.hide()
</pre>

Drawback: after restarting Slicer, the toolbars are still hidden.

==Background and References==

SliceTracker code: https://github.com/SlicerProstate/SliceTracker

2016 Winter Project Week/Projects/SliceTracker

2016-01-07T16:32:31Z

Ch399:

<nowiki>Insert non-formatted text here</nowiki>==Key Investigators==
* Christian Herz (BWH)
* Andriy Fedorov (BWH)
* Andras Lasso (Queens)

==Project Description==
Prostate biopsies can become a big challenge, especially when the prostate changed from pre-procedural to intra-procedural image acquisition. Motion and deformation of the prostate raises difficulties for positioning the biopsy needle at the right position. The registration module’s goal is to optimize the workflow and provide a solution, that is easy to use.
{| 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;"
|

* Slicer module implemented that allows the registration of the prostate
* Integrate the z-frame and navigation component into the module
* Use SliceTracker during prostate biopsies as a replacement to current approach
|

* Present the module to interested members of the community
* Get feedback about the workflow and usability
* Work on the remaining issues
* Discuss about migrating this module into a slicelet
|

* LumpNav is a slicelet example to follow
* what about simply hiding components (toolbars) that are not needed? (see example below)
|}

==Progress notes==
* Trick to hide all toolbars!
<pre>
>>> w = slicer.util.mainWindow()
>>> for c in w.children():
... if str(type(c)).find('ToolBar')>0:
... c.hide()
</pre>

Drawback: after restarting Slicer, the toolbars are still hidden.

==Background and References==

SliceTracker code: https://github.com/SlicerProstate/SliceTracker

2016 Winter Project Week/Projects/SliceTracker

2016-01-04T17:14:57Z

Ch399: added github link

==Key Investigators==
* Christian Herz (BWH)
* Andriy Fedorov (BWH)

==Project Description==
Prostate biopsies can become a big challenge, especially when the prostate changed from pre-procedural to intra-procedural image acquisition. Motion and deformation of the prostate raises difficulties for positioning the biopsy needle at the right position. The registration module’s goal is to optimize the workflow and provide a solution, that is easy to use.
{| 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;"
|

* Slicer module implemented that allows the registration of the prostate
* Integrate the z-frame and navigation component into the module
* Use SliceTracker during prostate biopsies as a replacement to current approach
|

* Present the module to interested members of the community
* Get feedback about the workflow and usability
* Work on the remaining issues
* Discuss about migrating this module into a slicelet
|

*
|}

==Background and References==

See code [https://github.com/SlicerProstate/SliceTracker here]

2016 Winter Project Week/Projects/SliceTracker

2016-01-04T15:12:07Z

Ch399: description