NAMIC Wiki - User contributions [en]

User:Inorton

2018-07-13T20:17:22Z

Inorton: Blanked the page

User:Inorton/Slicer4:Issues

2018-07-13T20:17:08Z

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User:Inorton/Slicer4:DTMRI Thoughts

2018-07-13T20:16:59Z

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User:Inorton/Slicer4:Python

2018-07-13T20:16:14Z

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User:Inorton

2018-07-13T20:15:54Z

Inorton:

Isaiah Norton, Golby Lab, Department of Neurosurgery, Brigham & Women's Hospital

contact: [mailto:inorton@bwhd-tharvardd0tedu inorton @bwh d-t harvard d0t edu]

==Slicer Notes==

Things that aren't fleshed-out enough to go into Mantis, or if I can't fully reproduce yet, can't share the data right now, etc..

===Bugs===

*Can't load high-res MEMPRAGE MRI from MGH for AG case in Slicer3. workaround: loaded fine in slicer2, then saved as nrrd. DicomToNRRD also works.
*CropVolume changes image intensity

===Feature Wishes===

*Better transform handling in the reg meta-code: should sort out any hierarchies for cross-registration (ie, want to register to something that is already inside another transform)
*Put models inside appropriate transform after generation
*Editing volume inside of transform - don't want to have to move source volumes out of transform for every Editor use in a complex scene with transform hierarchies.
*Slice intersections in 3D viewer, ie lines/gray/highlight/etc. at the intersection point (helps with depth perception). In Slicer3 this is only supported in 2d widgets.
*intelligent fiducial picking: for example, jump to nearest local min/max in some search region (like spm)
*option to load nrrd immediately after DicomToNrrd (cli need tweak to add post-handling options?)
*dynamic (python) module reload
*debug: to work around MRML scene-load crashes need either 1) cl debug option to output each tag as it is being processed, so that I know which node causes the crash or 2) load prompt for each node in the scene (like the Windows XP selective dll load)
*snap window focus range to the full extent of the enclosed controls when a large collapsible widget is opened

===DTI===

*Tract (hyperstreamline) intersection with MR planes (highlighted with color change, ring, etc.)
*FiberBundle editing!!!
**context menu on (eg) Ctrl-R click in 3D view to save tracts (could also be used for annotation functionality)
*fiber bundle reduction filter: Large FiberBundle datasets can cause degraded performance of the 3d view. This could be potentially be mitigated by sparsifying or volumizing the FiberBundle in regions with high tract overlap (common) so that the rendering load is reduced.

==Slicer4==
*[[User:inorton/Slicer4:Issues]]
*[[User:inorton/Slicer4:DTMRI_Thoughts]]
*[[User:inorton/Slicer4:Python]]

User:Inorton/Slicer3SuperBuildWindows7

2018-07-13T20:15:17Z

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ImageConversionUtilities

2018-07-13T20:14:41Z

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LoadfMRIIntoInstaTrak

2018-07-13T20:14:01Z

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LoadAnalyzeIntoBrainLab

2018-07-13T20:13:31Z

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CTPhantomSegmentation

2018-07-13T20:12:43Z

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LinuxScreenCaptureMovieNotes

2018-07-13T20:11:43Z

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ExternalConnectionsToSPL

2018-07-13T20:11:22Z

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Tidbits

2018-07-13T20:10:56Z

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UseIntelMKLwithMatlabForFasterSPM

2018-07-13T20:10:16Z

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Project Week 27

2017-11-28T15:05:12Z

Inorton: /* Conference Calls for Preparation */

{{Clear}}{{TOC right}}
Back to [[Events]]

A summary of all past [[Project_Events#Past_Project_Weeks|Project Events]].

[[image:PW27.png|300px]]
 

=Welcome to the web page for the 27th Project Week!=
The 27th NA-MIC Project Week will be held during the week of January 8-12, 2018 at MIT.

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

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

==Logistics==

*'''Dates:''' January 8-12, 2018.
*'''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: R&D)
*'''Transportation:''' Please plan to use public transportation. No parking permits are available by MIT. For a list of local garages, please see [http://web.mit.edu/facilities/transportation/parking/visitors/public_parking.html here]

*'''REGISTRATION:''' Register [http://regonline.com/projectweek2018 here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.

== Introduction ==
The National Alliance for Medical Image Computing (NAMIC), chartered with building a computational infrastructure to support biomedical research, was seeded in 2005 and funded through 2015 by the [http://www.ncbcs.org/ NIH 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].

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==

[https://meet.google.com/wzh-syuy-otj Google Hangouts Link] (see calendar below for dates and details)

=== Notes ===

Conference call notes are available [[PW27_Hangouts_Notes|here]].

=== Planning Call Calendar ===

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=Conference Calls for Preparation
|view=WEEK
}}

=== Project Week Joining Info ===
To join the preparation hangout, click on the event above, then "more details" and finally click on the video link under "Joining Info".

[[File:2018-winter-projectweek-calendar-joining.png]]

==Calendar==



{{#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=20180108/20180112
}}

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

='''Projects'''=

== How to add a new project ? ==

# Join the weekly [[#Conference_Calls_for_Preparation|preparation call]] to discuss your idea
# Add a new entry in the category below by copying the [[2018_Project_Week_Template | Project Template]]

== Visualization and Interaction ==
#[[Project_Week_27/SlicerVR | SlicerVR Updates]] (JC Fillon-Robin, Beatriz Paniagua, and others)

== Deep Learning. Radiomics and GPUs ==
#[[Project_Week_27/Pkmodeling | Refactoring of Pkmodeling and related tools for easier expandability]] (Michael Schwier, Andrey Fedorov)

== Web Technologies ==

== IGT: Navigation, Robotics, Surgical Planning ==

==dMRI==

==Quantitative Imaging Informatics==
#[[Project_Week_27/Pyradiomics Repeatability| Repeatability of Pyradiomics Features]] (Michael Schwier, Andrey Fedorov)

== Shape Analysis, Segmentation ==
#[[Project_Week_27/SlicerSALT | SlicerSALT Shape Analysis Toolbox Updates]] (Laura Pascal, JC Fillon-Robin, Beatriz Paniagua, Juan Prieto, Loic Michaud)
#[[Project_Week_27/SegmentationInverseChallenge | Segmentation Inverse Challenge Playoff]] (Tina Kapur, Csaba Pinter, Steve Pieper, Andras Lasso)
#[[Project_Week_27/ShapeVariationAnalyzer | Shape Variation analyzer]] (Juan Prieto, Nina Tubau)
#[[Project_Week_27/SelfLearningApplications | Shape self-learning applications]] (Juan Prieto, Loic Michaud)

== Infrastructure ==
#[[Project_Week_27/Slicer Custom Application | Slicer Custom Application]] (Jc Fillon-Robin, Andras Lasso)
#[[Project_Week_27/Slicer Documentation | Slicer Documentation @ ReadTheDocs]] (Jc Fillon-Robin, Andras Lasso)

==Training and Dissemination==

= '''Registrants''' =

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

2017 Winter Project Week/DiPy in Slicer

2017-01-13T16:10:37Z

Inorton: /* Project Description */

2017 Winter Project Week/DiPy in Slicer

2017-01-13T15:24:41Z

Inorton:

2017 Winter Project Week/DiPy in Slicer

2017-01-13T15:21:38Z

Inorton: /* Project Description */

File:20170112-dipy-rtop-ssn.png

2017-01-13T15:20:43Z

Inorton: RTOP map calculated in DiPy and loaded in Slicer

RTOP map calculated in DiPy and loaded in Slicer

2017 Winter Project Week/DiPy in Slicer

2017-01-09T19:04:55Z

Inorton: /* Key Investigators */

2017 Winter Project Week/DiPy in Slicer

2017-01-09T18:56:59Z

Inorton:

2017 Winter Project Week/DiPy in Slicer

2017-01-09T18:27:01Z

Inorton: /* Project Description */

2017 Winter Project Week

2017-01-09T18:26:05Z

Inorton: /* dMRI */

__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==

'''''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.''''' 

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

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

='''Projects'''=

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

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

== Web Technologies ==
#[[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)
#[[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
#[[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
#[[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)
#[[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)
#[[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper, 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, Jorge Luis Bernal Rusiel, Nicolas Rannou)
#[[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)
#[[2017 Winter Project Week/Intraoperative_Functional_Visualization | Visualization Concept for Intraoperative Use of Functional Mapping Data ]] (Rebekka Lauer, Anna Roethe, Prashin Unadkat, Sarah Frisken)

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

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

== Shape Analysis, Segmentation ==
#[[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
#[[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)
#[[2017 Winter Project Week/Slicer_HoloLens | Slicer & 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, Alireza Mehrtash, Christian Hansen)
#[[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)
#[[2017 Winter Project Week/Integrative_Intraoperative_Interface | Integrative Interface for Intraoperative Software Applications ]] (Rebekka Lauer, Anna Roethe, Prashin Unadkat, Sarah Frisken)

==Training and Dissemination==
#[[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)
#[[2017 Winter Project Week/2017 NVIDIA Demo Contest|NVIDIA Demo Contest]] (Abdul Halabi, Abel Brown)

==Next project week==
#[[2017 Winter Project Week/Next project week| Next project week]] (Paolo Zaffino, Maria Francesca Spadea, Tina Kapur)

= '''Registrants''' =

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

# Aman Shboul, Zaina :: Old Dominion University
# Aerts, Hugo :: DFCI-Harvard
# Alam, Mahbubul :: Old Dominion University
# Anderson, Peter :: Retired
# Andruejol, Johan :: Kitware, Inc.
# Bakeng, Janne Beate :: SINTEF
# Beers, Andrew :: Massachusetts General Hospital
# Bernal Rusiel, Jorge Luis :: Boston Children's Hospital
# Bremer, Erich :: Stony Brook University
# Burke, Brice :: American University of Antigua College of Medicine
# Cetin Karayumak, Suheyla :: Brigham and Women's Hospital
# Chae, Michael :: Monash University
# Chauvin, Laurent :: ETS
# Dalca, Adrian :: Massachusetts Institute of Technology
# DiPrima, Tammy :: Stony Brook University
# Drouin, Simon :: Montreal Neurological Institute
# Fan, Zhipeng :: Brigham and Women's Hospital
# Fedorov, Andriy :: Brigham and Women's Hospital
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.
# Fishbaugh, James :: New York University
# Frank, Tobias :: Leibniz Universität Hannover
# Frisken, Sarah :: Brigham and Women's Hospital
# García Mato, David :: Queen´s University / Universidad Carlos III de Madrid
# Ghafoorian, Mohsen :: Brigham and Women's Hospital
# Ghosh, Satrajit :: Massachusetts Institute of Technology
# Girault, Alexis :: Kitware, Inc.
# Golland, Polina :: Massachusetts Institute of Technology
# Gollub, Randy :: Massachusetts General Hospital
# Goncalves, Mathias :: Massachusetts Institute of Technology
# Gong, Shun :: Brigham and Women's Hospital
# Guerrier de Dumast, Priscille :: University of Michigan
# Halle, Michael :: Brigham and Women's Hospital
# Harris, Gordon :: Massachusetts General Hospital
# Helba, Brian :: Kitware, Inc.
# Herz, Christian :: Brigham and Women's Hospital
# Hong, Sungmin :: New York University
# Hosny, Ahmed :: Dana-Farber
# Jagadeesan, Jayender :: Brigham and Women's Hospital
# Jarecka, Dorota :: Massachusetts Institute of Technology
# Jensen, Henrik G. :: University of Copenhagen
# Kaczmarzyk, Jakub :: Massachusetts Institute of Technology
# Kapur, Tina :: Brigham and Women's Hospital
# Kennedy, David :: UMass Medical School
# Kikinis, Ron :: Brigham and Women's Hospital
# Lasso, Andras :: PerkLab, Queen's University
# Lauer, Rebekka :: Humboldt University Berlin
# Lisle, Curtis :: KnowledgeVis, LLC
# Mastrogiacomo, Katie :: Brigham and Women's Hospital
# Mateus, D. :: TUM
# Mehrtash, Alireza :: Brigham and Women's Hospital
# Meine, Hans :: University of Bremen
# Meyer, Anneke :: University of Magdeburg
# Miller, James :: GE Research
# Mirabel, Clement :: University of Michigan
# 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
# Prieto, Juan :: NIRAL
# Pujol, Sonia :: Brigham and Women's Hospital/Harvard Medical School
# Rankin, Adam :: Robarts Research Institute
# Rheault, Francois :: Université de Sherbrooke
# Roethe, Anna :: Humboldt University / Charité University Hospital Berlin
# Szczepankiewicz, Filip :: Lund University
# 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/UpdatingCommunityForums

2017-01-09T17:04:58Z

Inorton: /* Project Description */

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

</gallery>

==Key Investigators==
* Andrey Fedorov
* Andras Lasso
* Mike Halle
* Steve Pieper
* Isaiah Norton
* The COMMUNITY

==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;"
|

* Discuss the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Consider mailing list proposal to move Slicer and possibly several related discussion forums to the Discourse platform.
* Discuss new community-interaction possibilities such as Gitter.
* Consider the long-discussed proposals to move to github hosting for the web site
|

* Document the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Discourse
** Assess Discourse with broader community.
** Identify funding mechanism.
** Logistics to move if chosen:
*** Hosting: fully-managed service? vs DigitalOcean or other provider?
*** Domain name: 'discourse.slicer.org'?
*** SSL certificate for domain: can use Letsencrypt after host and DNS record are configured
*** SMTP service: included in hosted option. For self-hosting: strongly recommended, and mandatory for email-only signup and mailing list mode; not mandatory if using only oauth provider (GitHub/Google/etc.)
* GitHub
** Identify remaining action items to complete the long-awaited move of Slicer source hosting to GitHub.
* Web-site
** Organize web-site content on github
** Consider moving hosting to github
|

*
|}

==Background and References==
* Discourse discussion / proposal on the Slicer mailing list
** http://slicer-users.65878.n3.nabble.com/Starting-Q-A-Community-on-StackExchange-tp4031469p4031496.html
* Discussions of GitHub hosting:
** http://slicer-devel.65872.n3.nabble.com/Slicer-binary-download-is-extremely-slow-consider-github-for-hosting-packaged-binaries-td4036985.html
* [https://meta.discourse.org/t/discourse-and-slack-or-other-group-chat-apps-like-irc-hipchat-gitter-etc/39630 Discourse and Slack (or other group chat apps like IRC, HipChat, Gitter, etc)]
* https://www.slicer.org/wiki/Documentation/Labs/DocumentationImprovments
* NodeBB - like Discourse https://nodebb.org/pricing
* https://experts.feverbee.com/t/discourse-vs-nodebb/1384/6

2017 Winter Project Week/UpdatingCommunityForums

2017-01-09T17:04:22Z

Inorton: /* Project Description */

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

</gallery>

==Key Investigators==
* Andrey Fedorov
* Andras Lasso
* Mike Halle
* Steve Pieper
* Isaiah Norton
* The COMMUNITY

==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;"
|

* Discuss the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Consider mailing list proposal to move Slicer and possibly several related discussion forums to the Discourse platform.
* Discuss new community-interaction possibilities such as Gitter.
* Consider the long-discussed proposals to move to github hosting for the web site
|

* Document the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Discourse
** Assess Discourse with broader community.
** Identify funding mechanism.
** Logistics to move if chosen:
*** Hosting: DigitalOcean? Others?
*** Domain name: 'discourse.slicer.org'?
*** SSL certificate for domain: can use Letsencrypt after host and DNS record are configured
*** SMTP service: included in hosted option. For self-hosting: strongly recommended, and mandatory for email-only signup and mailing list mode; not mandatory if using only oauth provider (GitHub/Google/etc.)
* GitHub
** Identify remaining action items to complete the long-awaited move of Slicer source hosting to GitHub.
* Web-site
** Organize web-site content on github
** Consider moving hosting to github
|

*
|}

==Background and References==
* Discourse discussion / proposal on the Slicer mailing list
** http://slicer-users.65878.n3.nabble.com/Starting-Q-A-Community-on-StackExchange-tp4031469p4031496.html
* Discussions of GitHub hosting:
** http://slicer-devel.65872.n3.nabble.com/Slicer-binary-download-is-extremely-slow-consider-github-for-hosting-packaged-binaries-td4036985.html
* [https://meta.discourse.org/t/discourse-and-slack-or-other-group-chat-apps-like-irc-hipchat-gitter-etc/39630 Discourse and Slack (or other group chat apps like IRC, HipChat, Gitter, etc)]
* https://www.slicer.org/wiki/Documentation/Labs/DocumentationImprovments
* NodeBB - like Discourse https://nodebb.org/pricing
* https://experts.feverbee.com/t/discourse-vs-nodebb/1384/6

2017 Winter Project Week/UpdatingCommunityForums

2017-01-09T16:45:51Z

Inorton: /* Project Description */

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

</gallery>

==Key Investigators==
* Andrey Fedorov
* Andras Lasso
* Mike Halle
* Steve Pieper
* Isaiah Norton
* The COMMUNITY

==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;"
|

* Discuss the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Consider mailing list proposal to move Slicer and possibly several related discussion forums to the Discourse platform.
* Discuss new community-interaction possibilities such as Gitter.
* Consider the long-discussed proposals to move to github hosting for the web site
|

* Document the procedure for reaching consensus and making decision for the infrastructure issues that will have effect on large number of users
* Discourse
** Assess Discourse with broader community.
** Identify funding mechanism.
** Logistics to move if chosen:
*** Hosting: DigitalOcean? Others?
*** Domain name: 'discourse.slicer.org'?
*** SSL certificate for domain: can use Letsencrypt after host and DNS record are configured
*** SMTP service: strongly recommended, and mandatory for email-only signup and mailing list mode; not mandatory if using only oauth provider (GitHub/Google/etc.)
* GitHub
** Identify remaining action items to complete the long-awaited move of Slicer source hosting to GitHub.
* Web-site
** Organize web-site content on github
** Consider moving hosting to github
|

*
|}

==Background and References==
* Discourse discussion / proposal on the Slicer mailing list
** http://slicer-users.65878.n3.nabble.com/Starting-Q-A-Community-on-StackExchange-tp4031469p4031496.html
* Discussions of GitHub hosting:
** http://slicer-devel.65872.n3.nabble.com/Slicer-binary-download-is-extremely-slow-consider-github-for-hosting-packaged-binaries-td4036985.html
* [https://meta.discourse.org/t/discourse-and-slack-or-other-group-chat-apps-like-irc-hipchat-gitter-etc/39630 Discourse and Slack (or other group chat apps like IRC, HipChat, Gitter, etc)]
* https://www.slicer.org/wiki/Documentation/Labs/DocumentationImprovments
* NodeBB - like Discourse https://nodebb.org/pricing
* https://experts.feverbee.com/t/discourse-vs-nodebb/1384/6

2017 Winter Project Week/UpdatingCommunityForums

2017-01-05T18:53:30Z

Inorton: Created page with "__NOTOC__ <gallery> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|Projects List <!-- Use the "Upload file" link on the l..."

2017 Winter Project Week

2017-01-05T18:36:19Z

Inorton: /* Infrastructure */

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

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

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

==Logistics==

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

'''''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.''''' 

{{#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]] (Ziyang Wang, Guillaume Pernelle, Paolo Zaffino, 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/DeepInfer| DeepInfer: Open-source Deep Learning Deployment Toolkit]] (Alireza Mehrtash, Mehran Pesteie, Yang (Silvia) Yixin, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)

== 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/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, 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/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
* [[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/Electron App to add, navigate and visualize DICOM images | Electron App to add, navigate and visualize DICOM images
]] (Smruti Padhy, Satrajit Ghosh, Mathias Goncalves)

== 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/OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab | OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab ]] (Scheherazade Kraß (Shery), Junichi Tokuda, Longquan Chen, )
* [[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
* [[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)

==dMRI==
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (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-Frederik 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/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)

== Visualization ==
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)
== Infrastructure ==
* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy refactoring]] (Csaba Pinter)
* [[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
* [[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)
* [[2017 Winter Project Week/UpdatingCommunityForums | Updating Community Forums (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)

==To be Categorized==

* [[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Piper)
* [[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault, Andras Lasso)
* [[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
* [[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/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
* [[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].

# A, Zeina :: SHBOUL
# 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
# Fedorov, Andriy :: Brigham and Women's Hospital
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.
# Fishbaugh, James :: New York University
# Frank, Tobias :: Leibniz Universität Hannover
# García Mato, David :: Queen´s University / Universidad Carlos III de Madrid
# Girault, Alexis :: Kitware, Inc.
# Golland, Polina :: Massachusetts Institute of Technology
# Gollub, Randy :: Massachusetts General Hospital
# Gong, Shun :: Brigham and Women's Hospital
# Guerrier de Dumast, Priscille :: University of Michigan
# Harris, Gordon :: Massachusetts General Hospital
# Herz, Christian :: Brigham and Women's Hospital
# Hong, Sungmin :: New York University
# Hosny, Ahmed :: Dana-Farber
# Jagadeesan, Jayender :: Brigham and Women's Hospital
# Jensen, Henrik G. :: University of Copenhagen
# Kapur, Tina :: Brigham and Women's Hospital
# 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
# 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
# Vidyaratne, Lasitha :: Old Dominion University
# Wang, Yaofei :: Brigham and Women's Hospital
# Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School
# 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
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital

2017 Winter Project Week/SlicerDMRIDocumentationAndTesting

2016-12-27T17:34:27Z

Inorton: /* Background and References */

2017 Winter Project Week/DiPy in Slicer

2016-12-27T16:50:28Z

Inorton: Created page with "__NOTOC__ <gallery> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|Projects List <!-- Use the "Upload file" link on the l..."

2017 Winter Project Week

2016-12-27T16:47:15Z

Inorton: /* Infrastructure */

2016 Winter Project Week/Projects/SlicerDMRI documentation

2016-01-08T15:16:16Z

Inorton:

2016 Winter Project Week/Projects/SlicerDMRI documentation

2016-01-08T15:15:59Z

Inorton:

2016 Winter Project Week/Projects/Tractography format interoperability

2016-01-08T14:58:34Z

Inorton:

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

</gallery>

==Key Investigators==
* Michael Onken, OFFIS
* Isaiah Norton, BWH
* Lauren O'Donnell, 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;"
|
* Aim 1: Develop DCMTK and Slicer support for DICOM tractography objects (supplement 181).
* Aim 2: Develop Slicer support for DiPy tractography i/o.
|
* Aim 1:
** planning emails and data exchange before project week.
** prototype DCMTK support for supplement 181.
** (implement Slicer interface to load objects and metadata from DCMTK into tractography nodes?)
* Aim 2:
** implement support for DPY and TrackVis tractography file formats.
|
* Aim 1:
** productive discussions explaining data processing and structure.
** designed high-level DCMTK API for accessing tractography objects.
* Aim 2:
** Prototyped stand-alone TrackVis reader (custom binary format)
* Bonus:
** Finished and submitted PR to move diffusion modules to remote module build: https://github.com/Slicer/Slicer/pull/442
|}

==Background and References==

[ftp://medical.nema.org/medical/dicom/final/sup181_ft_TractographyResultsStorage.pdf DICOM Supplement 181]

2016 Winter Project Week/Projects/Tractography format interoperability

2016-01-08T14:30:51Z

Inorton:

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

</gallery>

==Key Investigators==
* Michael Onken, OFFIS
* Isaiah Norton, BWH
* Lauren O'Donnell, 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;"
|
* Aim 1: Develop DCMTK and Slicer support for DICOM tractography objects (supplement 181).
* Aim 2: Develop Slicer support for DiPy tractography i/o.
|
* Aim 1:
** planning emails and data exchange before project week.
** prototype DCMTK support for supplement 181.
** (implement Slicer interface to load objects and metadata from DCMTK into tractography nodes?)
* Aim 2:
** implement support for DPY and TrackVis tractography file formats.
|
* Aim 1:
** productive discussions explaining data processing and structure.
** designed high-level DCMTK API for accessing tractography objects.
* Aim 2:
** Prototyped stand-alone TrackVis reader (custom binary format)

|}

==Background and References==

[ftp://medical.nema.org/medical/dicom/final/sup181_ft_TractographyResultsStorage.pdf DICOM Supplement 181]

2016 Winter Project Week/Breakout Session/What's Planned for Slicer Core

2016-01-07T18:43:23Z

Inorton: /* Maintenance needed for core libraries */

=Introduction=
*Ron Kikinis: [http://wiki.na-mic.org/Wiki/images/e/ec/2015-11-11-Slicer-Status.pptx State of the Slicer world and strategic plans for Slicer]

=Maintenance needed for core libraries=
* VTK7 (rapid changes coming to VTK due to maintenance grant)
* Python: [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Labs/SlicerCondaIntegration conda] (and?)or cmake/wheels?
** note: for Python 3.5, the Python.org, Anaconda, and Gohlke package builds have converged to MSVC 2015 ([https://groups.google.com/a/continuum.io/d/msg/anaconda/cTz7cVPQkKM/4ydIH0szAgAJ discussion])
* Qt5: improvements, plus 4.8 may eventually stop supporting new systems
* support for latest WebKit

=Organization=
* Establish a mechanism to install multiple extension packages by default. Ron: I frequently download Slicer nightly build. Having to manually install the 10 packages that I need routinely is a pain. This will be a disincentive for me to download the nightly.
** would it be possible instead to recognize previous settings on the first launch of the new nightly, and ask user if s/he wants to re-install all or selection of the extensions installed before the update?
* Move modules to extension - See also [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DeprecatedModules Documentation/Labs/DeprecatedModules]
** Moving diffusion to extension (in progress: [https://github.com/SlicerDMRI/SlicerDMRI/tree/remaster5 SlicerDMRI] as [https://github.com/ihnorton/Slicer/tree/remove_dmri Slicer remote module])
** Moving EMSegmenter to extension: very large, with lots of data; it would significantly reduce the Slicer installation package size
** Move BRAINS, SimpleITK, OpenIGTLinkIF to extension: frequently used modules but they are quite large, also by having them in extensions they could be updated without the need to create a new Slicer release
** Moving Endoscopy, PET SUV, various filters to extensions: small modules, they are just too specific to be included in the core
** ...other things to extensions?
* revise DICOM plugins organization - if the data is not recognized by installed plugins, there is no way for the user to know what extension to install to handle the dataset

Other suggestions:
* Keep official version of tier I extensions in GitHub in the Slicer organization so that any Slicer core developer can fix and update them easily.
* Move orphan extensions (that developers cannot maintain anymore) to GitHub under Slicer organization's ownership so that they can be kept in a working condition. See [http://na-mic.org/Mantis/view.php?id=2779 #2779]

=Key requests from the community=
* faster startup time (particularly mac). See http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/StartupTimeImprovement
* Less confusing UI
** Every module should be display an initial subset of the functionality (as minimal as possible) and a closed "Advanced" tab that contains everything else.
** cursor modes? http://www.na-mic.org/Bug/view.php?id=2419
** Slicer logo steals a lot of precious space - can we move it to the tools buttons toolbar? http://www.na-mic.org/Bug/view.php?id=3797
* Add orientation information to vtkImageData (request for VTK, not just Slicer but all VTK-based medical image computing groups suffer a lot because of this).
** See [https://github.com/SlicerRt/SlicerRT/blob/master/SegmentationCore/vtkOrientedImageData.h vtkOrientedImageData class] and [https://github.com/SlicerRt/SlicerRT/blob/master/SegmentationCore/vtkOrientedImageDataResample.h related utility]
** http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/VTK-Orientation
* Make it easy to add custom slice and 3D widgets (for various custom quantification, segmentation, planning, targeting, etc. tasks - currently we can observe markup points and create custom models for visualization, but the method is very fragile and many things are missing, for example, no way to detect if the user clicks on a markup, no way to limit number of markups or restrict them to be placed on a certain surface, etc.)
* Modern, integrated revision control, issue tracking, dashboard, code review, documentation, etc. toolset
* Simplify data import/export/saving/loading (single-click save to database, direct data loading by drag-and-drop - by inspection of file contents instead of just checking file extension and asking the user how the data should be interpreted, automatic loading of just imported DICOM data, etc.)
* (add your favorites here...)

Some short-term but high-priority issues:
* GPU-based volume rendering (due to problem in VTK)
* Faster nightly builds (extensions appear in the extension manager too late for nightly builds)

Documentation and support
* improved integration of Slicer YouTube channel?
** What to do about China? http://slicer-devel.65872.n3.nabble.com/youtube-in-China-td4035615.html
* documentation page usage statistics to rank relevance of modules?
* discuss alternatives to mailing list?
** example from ITCR community (discussed at the ITCR Training and Outrech call, provided here from the meeting minutes by Andrey Fedorov)
*** https://support.bioconductor.org/
*** Bioconductor migrated their mailing list content to Biostars-based support forum site (modeled on stack overflow). Biostars is free and open source. Community core members were somewhat reluctant. Email list remains for technical/dev forum and support site is used for users. Email list is more like a back and forth dialogue. In contrast the support site has less back and forth. It’s made it easier for people to ask less knowledgeable questions.
*** Bioconductor recognizes individuals for their contributions to the support site.
*** Another factor in favor of the support site is that there is incentive nd motivation to contribute (upvotes, counts of # of responses, etc)
** (another datapoint: NiPy moved user discussion to https://neurostars.org/)

* improve outreach and visibility by being more "google friendly" ? http://www.na-mic.org/Bug/view.php?id=3938 Ron: how about China?

=Roadmaps=
*Steve Pieper: Chronicle, ctkjs, CommonGL
*JC Fillion-Robin: [http://girder.readthedocs.org/en/latest/ Girder], Anaconda, Factory machines
*Andras Lasso: [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/Sequences Sequences]
*Csaba Pinter: [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Segmentations Segmentations]
*Mike Halle: Slicer webinfrastructure and github
*Andrey Fedorov: DICOM objects for interoperability
** focus areas: segmentations, enhanced multiframe (single-file MR series, parametric maps), volumetric measurement structured reports
** approach
*** developer API in DCMTK
*** reusable command-line converters for extension developers
*** user-level domain-specific applications
** open question for discussion: should this functionality be in the core or extension

2016 Winter Project Week/Breakout Session/What's Planned for Slicer Core

2016-01-07T18:42:51Z

Inorton: /* Maintenance needed for core libraries */

=Introduction=
*Ron Kikinis: [http://wiki.na-mic.org/Wiki/images/e/ec/2015-11-11-Slicer-Status.pptx State of the Slicer world and strategic plans for Slicer]

=Maintenance needed for core libraries=
* VTK7 (rapid changes coming to VTK due to maintenance grant)
* Python: [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Labs/SlicerCondaIntegration conda] (and?)or cmake/wheels?
** note: Python.org, Anaconda, and Gohlke package builds have converged to MSVC 2015 ([https://groups.google.com/a/continuum.io/d/msg/anaconda/cTz7cVPQkKM/4ydIH0szAgAJ discussion])
* Qt5: improvements, plus 4.8 may eventually stop supporting new systems
* support for latest WebKit

=Organization=
* Establish a mechanism to install multiple extension packages by default. Ron: I frequently download Slicer nightly build. Having to manually install the 10 packages that I need routinely is a pain. This will be a disincentive for me to download the nightly.
** would it be possible instead to recognize previous settings on the first launch of the new nightly, and ask user if s/he wants to re-install all or selection of the extensions installed before the update?
* Move modules to extension - See also [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DeprecatedModules Documentation/Labs/DeprecatedModules]
** Moving diffusion to extension (in progress: [https://github.com/SlicerDMRI/SlicerDMRI/tree/remaster5 SlicerDMRI] as [https://github.com/ihnorton/Slicer/tree/remove_dmri Slicer remote module])
** Moving EMSegmenter to extension: very large, with lots of data; it would significantly reduce the Slicer installation package size
** Move BRAINS, SimpleITK, OpenIGTLinkIF to extension: frequently used modules but they are quite large, also by having them in extensions they could be updated without the need to create a new Slicer release
** Moving Endoscopy, PET SUV, various filters to extensions: small modules, they are just too specific to be included in the core
** ...other things to extensions?
* revise DICOM plugins organization - if the data is not recognized by installed plugins, there is no way for the user to know what extension to install to handle the dataset

Other suggestions:
* Keep official version of tier I extensions in GitHub in the Slicer organization so that any Slicer core developer can fix and update them easily.
* Move orphan extensions (that developers cannot maintain anymore) to GitHub under Slicer organization's ownership so that they can be kept in a working condition. See [http://na-mic.org/Mantis/view.php?id=2779 #2779]

=Key requests from the community=
* faster startup time (particularly mac). See http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/StartupTimeImprovement
* Less confusing UI
** Every module should be display an initial subset of the functionality (as minimal as possible) and a closed "Advanced" tab that contains everything else.
** cursor modes? http://www.na-mic.org/Bug/view.php?id=2419
** Slicer logo steals a lot of precious space - can we move it to the tools buttons toolbar? http://www.na-mic.org/Bug/view.php?id=3797
* Add orientation information to vtkImageData (request for VTK, not just Slicer but all VTK-based medical image computing groups suffer a lot because of this).
** See [https://github.com/SlicerRt/SlicerRT/blob/master/SegmentationCore/vtkOrientedImageData.h vtkOrientedImageData class] and [https://github.com/SlicerRt/SlicerRT/blob/master/SegmentationCore/vtkOrientedImageDataResample.h related utility]
** http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/VTK-Orientation
* Make it easy to add custom slice and 3D widgets (for various custom quantification, segmentation, planning, targeting, etc. tasks - currently we can observe markup points and create custom models for visualization, but the method is very fragile and many things are missing, for example, no way to detect if the user clicks on a markup, no way to limit number of markups or restrict them to be placed on a certain surface, etc.)
* Modern, integrated revision control, issue tracking, dashboard, code review, documentation, etc. toolset
* Simplify data import/export/saving/loading (single-click save to database, direct data loading by drag-and-drop - by inspection of file contents instead of just checking file extension and asking the user how the data should be interpreted, automatic loading of just imported DICOM data, etc.)
* (add your favorites here...)

Some short-term but high-priority issues:
* GPU-based volume rendering (due to problem in VTK)
* Faster nightly builds (extensions appear in the extension manager too late for nightly builds)

Documentation and support
* improved integration of Slicer YouTube channel?
** What to do about China? http://slicer-devel.65872.n3.nabble.com/youtube-in-China-td4035615.html
* documentation page usage statistics to rank relevance of modules?
* discuss alternatives to mailing list?
** example from ITCR community (discussed at the ITCR Training and Outrech call, provided here from the meeting minutes by Andrey Fedorov)
*** https://support.bioconductor.org/
*** Bioconductor migrated their mailing list content to Biostars-based support forum site (modeled on stack overflow). Biostars is free and open source. Community core members were somewhat reluctant. Email list remains for technical/dev forum and support site is used for users. Email list is more like a back and forth dialogue. In contrast the support site has less back and forth. It’s made it easier for people to ask less knowledgeable questions.
*** Bioconductor recognizes individuals for their contributions to the support site.
*** Another factor in favor of the support site is that there is incentive nd motivation to contribute (upvotes, counts of # of responses, etc)
** (another datapoint: NiPy moved user discussion to https://neurostars.org/)

* improve outreach and visibility by being more "google friendly" ? http://www.na-mic.org/Bug/view.php?id=3938 Ron: how about China?

=Roadmaps=
*Steve Pieper: Chronicle, ctkjs, CommonGL
*JC Fillion-Robin: [http://girder.readthedocs.org/en/latest/ Girder], Anaconda, Factory machines
*Andras Lasso: [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/Sequences Sequences]
*Csaba Pinter: [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Segmentations Segmentations]
*Mike Halle: Slicer webinfrastructure and github
*Andrey Fedorov: DICOM objects for interoperability
** focus areas: segmentations, enhanced multiframe (single-file MR series, parametric maps), volumetric measurement structured reports
** approach
*** developer API in DCMTK
*** reusable command-line converters for extension developers
*** user-level domain-specific applications
** open question for discussion: should this functionality be in the core or extension

2016 Winter Project Week/Breakout Session/What's Planned for Slicer Core

2016-01-07T18:22:45Z

Inorton: /* Organization */

=Introduction=
*Ron Kikinis: [http://wiki.na-mic.org/Wiki/images/e/ec/2015-11-11-Slicer-Status.pptx State of the Slicer world and strategic plans for Slicer]

=Maintenance needed for core libraries=
* VTK7 (rapid changes coming to VTK due to maintenance grant)
* Python: [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Labs/SlicerCondaIntegration conda] (and?)or cmake/wheels?
* Qt5: improvements, plus 4.8 may eventually stop supporting new systems
* support for latest WebKit

=Organization=
* Establish a mechanism to install multiple extension packages by default. Ron: I frequently download Slicer nightly build. Having to manually install the 10 packages that I need routinely is a pain. This will be a disincentive for me to download the nightly.
** would it be possible instead to recognize previous settings on the first launch of the new nightly, and ask user if s/he wants to re-install all or selection of the extensions installed before the update?
* Move modules to extension - See also [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DeprecatedModules Documentation/Labs/DeprecatedModules]
** Moving diffusion to extension (in progress: [https://github.com/SlicerDMRI/SlicerDMRI/tree/remaster5 SlicerDMRI] as [https://github.com/ihnorton/Slicer/tree/remove_dmri Slicer remote module])
** Moving EMSegmenter to extension: very large, with lots of data; it would significantly reduce the Slicer installation package size
** Move BRAINS, SimpleITK, OpenIGTLinkIF to extension: frequently used modules but they are quite large, also by having them in extensions they could be updated without the need to create a new Slicer release
** Moving Endoscopy, PET SUV, various filters to extensions: small modules, they are just too specific to be included in the core
** ...other things to extensions?
* revise DICOM plugins organization - if the data is not recognized by installed plugins, there is no way for the user to know what extension to install to handle the dataset

Other suggestions:
* Keep official version of tier I extensions in GitHub in the Slicer organization so that any Slicer core developer can fix and update them easily.
* Move orphan extensions (that developers cannot maintain anymore) to GitHub under Slicer organization's ownership so that they can be kept in a working condition. See [http://na-mic.org/Mantis/view.php?id=2779 #2779]

=Key requests from the community=
* faster startup time (particularly mac). See http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/StartupTimeImprovement
* Less confusing UI
** Every module should be display an initial subset of the functionality (as minimal as possible) and a closed "Advanced" tab that contains everything else.
** cursor modes? http://www.na-mic.org/Bug/view.php?id=2419
** Slicer logo steals a lot of precious space - can we move it to the tools buttons toolbar? http://www.na-mic.org/Bug/view.php?id=3797
* Add orientation information to vtkImageData (request for VTK, not just Slicer but all VTK-based medical image computing groups suffer a lot because of this). See [https://github.com/SlicerRt/SlicerRT/blob/master/SegmentationCore/vtkOrientedImageData.h vtkOrientedImageData class] and [https://github.com/SlicerRt/SlicerRT/blob/master/SegmentationCore/vtkOrientedImageDataResample.h related utility]
* Make it easy to add custom slice and 3D widgets (for various custom quantification, segmentation, planning, targeting, etc. tasks - currently we can observe markup points and create custom models for visualization, but the method is very fragile and many things are missing, for example, no way to detect if the user clicks on a markup, no way to limit number of markups or restrict them to be placed on a certain surface, etc.)
* Modern, integrated revision control, issue tracking, dashboard, code review, documentation, etc. toolset
* Simplify data import/export/saving/loading (single-click save to database, direct data loading by drag-and-drop - by inspection of file contents instead of just checking file extension and asking the user how the data should be interpreted, automatic loading of just imported DICOM data, etc.)
* (add your favorites here...)

Some short-term but high-priority issues:
* GPU-based volume rendering (due to problem in VTK)
* Faster nightly builds (extensions appear in the extension manager too late for nightly builds)

Documentation and support
* improved integration of Slicer YouTube channel?
** What to do about China? http://slicer-devel.65872.n3.nabble.com/youtube-in-China-td4035615.html
* documentation page usage statistics to rank relevance of modules?
* discuss alternatives to mailing list?
** example from ITCR community (discussed at the ITCR Training and Outrech call, provided here from the meeting minutes by Andrey Fedorov)
*** https://support.bioconductor.org/
*** Bioconductor migrated their mailing list content to Biostars-based support forum site (modeled on stack overflow). Biostars is free and open source. Community core members were somewhat reluctant. Email list remains for technical/dev forum and support site is used for users. Email list is more like a back and forth dialogue. In contrast the support site has less back and forth. It’s made it easier for people to ask less knowledgeable questions.
*** Bioconductor recognizes individuals for their contributions to the support site.
*** Another factor in favor of the support site is that there is incentive nd motivation to contribute (upvotes, counts of # of responses, etc)
** (another datapoint: NiPy moved user discussion to https://neurostars.org/)

* improve outreach and visibility by being more "google friendly" ? http://www.na-mic.org/Bug/view.php?id=3938 Ron: how about China?

=Roadmaps=
*Steve Pieper: Chronicle, ctkjs, CommonGL
*JC Fillion-Robin: [http://girder.readthedocs.org/en/latest/ Girder], Anaconda, Factory machines
*Andras Lasso: [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/Sequences Sequences]
*Csaba Pinter: [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Segmentations Segmentations]
*Mike Halle: Slicer webinfrastructure and github
*Andrey Fedorov: DICOM objects for interoperability
** focus areas: segmentations, enhanced multiframe (single-file MR series, parametric maps), volumetric measurement structured reports
** approach
*** developer API in DCMTK
*** reusable command-line converters for extension developers
*** user-level domain-specific applications
** open question for discussion: should this functionality be in the core or extension

2016 Winter Project Week/Breakout Session/What's Planned for Slicer Core

2016-01-07T18:17:32Z

Inorton: /* Key requests from the community */

=Introduction=
*Ron Kikinis: [http://wiki.na-mic.org/Wiki/images/e/ec/2015-11-11-Slicer-Status.pptx State of the Slicer world and strategic plans for Slicer]

=Maintenance needed for core libraries=
* VTK7 (rapid changes coming to VTK due to maintenance grant)
* Python: [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Labs/SlicerCondaIntegration conda] (and?)or cmake/wheels?
* Qt5: improvements, plus 4.8 may eventually stop supporting new systems
* support for latest WebKit

=Organization=
* Establish a mechanism to install multiple extension packages by default. Ron: I frequently download Slicer nightly build. Having to manually install the 10 packages that I need routinely is a pain. This will be a disincentive for me to download the nightly.
** would it be possible instead to recognize previous settings on the first launch of the new nightly, and ask user if s/he wants to re-install all or selection of the extensions installed before the update?
* Move modules to extension - See also [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DeprecatedModules Documentation/Labs/DeprecatedModules]
** Moving diffusion to extension
** Moving EMSegmenter to extension: very large, with lots of data; it would significantly reduce the Slicer installation package size
** Move BRAINS, SimpleITK, OpenIGTLinkIF to extension: frequently used modules but they are quite large, also by having them in extensions they could be updated without the need to create a new Slicer release
** Moving Endoscopy, PET SUV, various filters to extensions: small modules, they are just too specific to be included in the core
** ...other things to extensions?
* revise DICOM plugins organization - if the data is not recognized by installed plugins, there is no way for the user to know what extension to install to handle the dataset

Other suggestions:
* Keep official version of tier I extensions in GitHub in the Slicer organization so that any Slicer core developer can fix and update them easily.
* Move orphan extensions (that developers cannot maintain anymore) to GitHub under Slicer organization's ownership so that they can be kept in a working condition. See [http://na-mic.org/Mantis/view.php?id=2779 #2779]

=Key requests from the community=
* faster startup time (particularly mac). See http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/StartupTimeImprovement
* Less confusing UI
** Every module should be display an initial subset of the functionality (as minimal as possible) and a closed "Advanced" tab that contains everything else.
** cursor modes? http://www.na-mic.org/Bug/view.php?id=2419
** Slicer logo steals a lot of precious space - can we move it to the tools buttons toolbar? http://www.na-mic.org/Bug/view.php?id=3797
* Add orientation information to vtkImageData (request for VTK, not just Slicer but all VTK-based medical image computing groups suffer a lot because of this). See [https://github.com/SlicerRt/SlicerRT/blob/master/SegmentationCore/vtkOrientedImageData.h vtkOrientedImageData class] and [https://github.com/SlicerRt/SlicerRT/blob/master/SegmentationCore/vtkOrientedImageDataResample.h related utility]
* Make it easy to add custom slice and 3D widgets (for various custom quantification, segmentation, planning, targeting, etc. tasks - currently we can observe markup points and create custom models for visualization, but the method is very fragile and many things are missing, for example, no way to detect if the user clicks on a markup, no way to limit number of markups or restrict them to be placed on a certain surface, etc.)
* Modern, integrated revision control, issue tracking, dashboard, code review, documentation, etc. toolset
* Simplify data import/export/saving/loading (single-click save to database, direct data loading by drag-and-drop - by inspection of file contents instead of just checking file extension and asking the user how the data should be interpreted, automatic loading of just imported DICOM data, etc.)
* (add your favorites here...)

Some short-term but high-priority issues:
* GPU-based volume rendering (due to problem in VTK)
* Faster nightly builds (extensions appear in the extension manager too late for nightly builds)

Documentation and support
* improved integration of Slicer YouTube channel?
** What to do about China? http://slicer-devel.65872.n3.nabble.com/youtube-in-China-td4035615.html
* documentation page usage statistics to rank relevance of modules?
* discuss alternatives to mailing list?
** example from ITCR community (discussed at the ITCR Training and Outrech call, provided here from the meeting minutes by Andrey Fedorov)
*** https://support.bioconductor.org/
*** Bioconductor migrated their mailing list content to Biostars-based support forum site (modeled on stack overflow). Biostars is free and open source. Community core members were somewhat reluctant. Email list remains for technical/dev forum and support site is used for users. Email list is more like a back and forth dialogue. In contrast the support site has less back and forth. It’s made it easier for people to ask less knowledgeable questions.
*** Bioconductor recognizes individuals for their contributions to the support site.
*** Another factor in favor of the support site is that there is incentive nd motivation to contribute (upvotes, counts of # of responses, etc)
** (another datapoint: NiPy moved user discussion to https://neurostars.org/)

* improve outreach and visibility by being more "google friendly" ? http://www.na-mic.org/Bug/view.php?id=3938 Ron: how about China?

=Roadmaps=
*Steve Pieper: Chronicle, ctkjs, CommonGL
*JC Fillion-Robin: [http://girder.readthedocs.org/en/latest/ Girder], Anaconda, Factory machines
*Andras Lasso: [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/Sequences Sequences]
*Csaba Pinter: [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Segmentations Segmentations]
*Mike Halle: Slicer webinfrastructure and github
*Andrey Fedorov: DICOM objects for interoperability
** focus areas: segmentations, enhanced multiframe (single-file MR series, parametric maps), volumetric measurement structured reports
** approach
*** developer API in DCMTK
*** reusable command-line converters for extension developers
*** user-level domain-specific applications
** open question for discussion: should this functionality be in the core or extension

2016 Winter Project Week/Dinner

2016-01-07T15:26:16Z

Inorton:

==Dinner Specs==

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

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

==RSVPs==
#Tina Kapur
#Ron Kikinis
#Steve Pieper
# Andrey Fedorov
# Sonia Pujol
#Hans Meine
#Michael Onken
# Junichi Tokuda
# Dan Blezek
# Johan Andruejol
# Christian Askeland
# Lucia Cevidanes
# Fan Zhang
# Pegah Kahali
# Simon Drouin
# Thomas Kirchner
# Janek Groehl
# Andras Lasso
# Adam Rankin
# Kyle Sunderland
# Csaba Pinter
# Beatriz Paniagua
# Beatriz Panigua Friend
# Jean-Christophe Fillion-Robin
# Matthew Toews
# Prashin Unadkat
# Utsav Soni

2016 Winter Project Week/Dinner

2016-01-06T16:36:15Z

Inorton:

==Dinner Specs==

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

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

==RSVPs==
#Tina Kapur
#Ron Kikinis
#Steve Pieper
# Andrey Fedorov
# Sonia Pujol
#Hans Meine
#Michael Onken
# Junichi Tokuda
# Dan Blezek
# Beatriz Paniagua
# Johan Andruejol
# Christian Askeland
# Lucia Cevidanes
# Fan Zhang
# Pegah Kahali
# Simon Drouin
# Thomas Kirchner
# Janek Groehl
# Katie Mastrogiacomo
# Ellie Zucker
# Andras Lasso
# Adam Rankin
# Kyle Sunderland
# Csaba Pinter
# Isaiah Norton

2016 Winter Project Week/Projects/Tractography format interoperability

2016-01-04T18:31:05Z

Inorton:

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

</gallery>

==Key Investigators==
* Michael Onken, OFFIS
* Isaiah Norton, BWH
* Lauren O'Donnell, 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;"
|
* Aim 1: Develop DCMTK and Slicer support for DICOM tractography objects (supplement 181).
* Aim 2: Develop Slicer support for DiPy's HDF5-based "dpy" tract format.
|
* Aim 1:
** planning emails and data exchange before project week.
** prototype DCMTK support for supplement 181.
** implement Slicer interface to load objects and metadata from DCMTK into tractography nodes.
* Aim 2:
** utilize VTK's built-in HDF support to read and write dpy files.
** write adapters to interface data and metadata with tractography MRML nodes.
|
*

|}

==Background and References==

[ftp://medical.nema.org/medical/dicom/final/sup181_ft_TractographyResultsStorage.pdf DICOM Supplement 181]

2016 Winter Project Week/Projects/SlicerDMRI documentation

2015-12-14T16:03:44Z

Inorton: /* Key Investigators */

2016 Winter Project Week/Projects/SlicerDMRI documentation

2015-12-14T16:03:33Z

Inorton: Created page with "__NOTOC__ <gallery> Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|Projects List <!-- Use the "Upload file" link on the left..."

2016 Winter Project Week

2015-12-14T16:02:17Z

Inorton: /* Non-categorized */

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

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

'''Location:''' MIT, Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)

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

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

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

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

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

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

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

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

==Agenda==

Tentative Agenda

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 4
!style="width:18%" |Tuesday, January 5
!style="width:18%" |Wednesday, January 6
!style="width:18%" |Thursday, January 7
!style="width:18%" |Friday, January 8
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|'''10:30am-12pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 1 by Sarang Joshi) Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10-11:30am:''' Breakout Session: New Slicer Extensions''' 
|
'''10-11:30am:''' Breakout Session: [[2015_Winter_Project_Week:SlicerROSIntegration| Slicer for Medical Robotics Research]] 
 
|'''9:00-10:30am''' TBD 
 ---------------------------------------- 
'''10am-12pm: Breakout Session:''' TBD 
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ---------------------------------------- 
'''12pm''' [[Events:TutorialContestJanuary2016|Tutorial Contest Winner Announcement]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: Welcome''' 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ---------------------------------------- 
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads) 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ---------------------------------------- 
'''2:45-4pm:''' [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Breakout Session Ultrasound]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ---------------------------------------- 

'''4:00pm-5:30pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 2 by Sarang Joshi) Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''1-3pm:''' [[2016_Winter_Project_Week/Breakout_Session/What's_Planned_for_Slicer_Core|What's Planned for Slicer Core]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' Breakout Session:''' [[2016_Winter_Project_Week/Breakout_Sessions/Diffusion MRI| Diffusion MRI]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]] -------- 
'''3-4:30pm:''' Breakout Session:''' [[2016_Winter_Project_Week/Breakout_Sessions/QIICR Tools| QIICR Tools]]
|
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}
<googlecalendar>kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com</googlecalendar>

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

== Non-categorized ==
*Digital Pathology Nuclear Segmentation (Erich Bremer, Nicole Aucoin, Andrey Fedorov)
*Chest Imaging Platform: COPD and other pulmonary diseases (Raúl San José, Jorge Onieva)
*Upgrade the namic (and Slicer?) wiki (JC, Mike Halle)
* [[2016_Winter_Project_Week:BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week:ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week:PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week:External_beam_planning | External beam radiotherapy planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week:SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[2016_Winter_Project_Week:CommonDataStructure | Common data structure for CMF modules in Slicer]] (Françoi Budin, Lucia Cevidanes, Beatriz Paniagua, Steeve Pieper, Juan Carlos Prieto, Jean-Baptiste Vimort)
* [[2016_Winter_Project_Week:Tract_io_interop | Tractography format interoperability]] (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week:SlicerDMRI_documentation | Slicer diffusion MR / tractography workflow documentation]] (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)

== IGT ==
* [[2016_Winter_Project_Week:TrackedUltrasoundStandardization | Tracked ultrasound standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*Integration of CustusX with PLUS on BK System (Christian A, Adam Rankin)
* [[2016_Winter_Project_Week:MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
*Integration of ImFusion MR-US registration with BWH AMIGO neurosurgery setup (Christian A, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso)
* [[2015_Winter_Project_Week:SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard)

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

= '''Logistics''' =

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

= '''Registrants''' =

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

2016 Winter Project Week

2015-12-14T16:01:56Z

Inorton: /* Non-categorized */

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

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

'''Location:''' MIT, Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)

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

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

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

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

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

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

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

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

==Agenda==

Tentative Agenda

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 4
!style="width:18%" |Tuesday, January 5
!style="width:18%" |Wednesday, January 6
!style="width:18%" |Thursday, January 7
!style="width:18%" |Friday, January 8
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|'''10:30am-12pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 1 by Sarang Joshi) Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10-11:30am:''' Breakout Session: New Slicer Extensions''' 
|
'''10-11:30am:''' Breakout Session: [[2015_Winter_Project_Week:SlicerROSIntegration| Slicer for Medical Robotics Research]] 
 
|'''9:00-10:30am''' TBD 
 ---------------------------------------- 
'''10am-12pm: Breakout Session:''' TBD 
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ---------------------------------------- 
'''12pm''' [[Events:TutorialContestJanuary2016|Tutorial Contest Winner Announcement]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: Welcome''' 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ---------------------------------------- 
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads) 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ---------------------------------------- 
'''2:45-4pm:''' [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Breakout Session Ultrasound]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ---------------------------------------- 

'''4:00pm-5:30pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 2 by Sarang Joshi) Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''1-3pm:''' [[2016_Winter_Project_Week/Breakout_Session/What's_Planned_for_Slicer_Core|What's Planned for Slicer Core]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' Breakout Session:''' [[2016_Winter_Project_Week/Breakout_Sessions/Diffusion MRI| Diffusion MRI]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]] -------- 
'''3-4:30pm:''' Breakout Session:''' [[2016_Winter_Project_Week/Breakout_Sessions/QIICR Tools| QIICR Tools]]
|
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}
<googlecalendar>kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com</googlecalendar>

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

== Non-categorized ==
*Digital Pathology Nuclear Segmentation (Erich Bremer, Nicole Aucoin, Andrey Fedorov)
*Chest Imaging Platform: COPD and other pulmonary diseases (Raúl San José, Jorge Onieva)
*Upgrade the namic (and Slicer?) wiki (JC, Mike Halle)
* [[2016_Winter_Project_Week:BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week:ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week:PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week:External_beam_planning | External beam radiotherapy planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week:SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[2016_Winter_Project_Week:CommonDataStructure | Common data structure for CMF modules in Slicer]] (Françoi Budin, Lucia Cevidanes, Beatriz Paniagua, Steeve Pieper, Juan Carlos Prieto, Jean-Baptiste Vimort)
* [[2016_Winter_Project_Week:Tract_io_interop | Tractography format interoperability]] (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week:SlicerDMRI_documentation | Slicer diffusion workflow documentation]] (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)

== IGT ==
* [[2016_Winter_Project_Week:TrackedUltrasoundStandardization | Tracked ultrasound standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*Integration of CustusX with PLUS on BK System (Christian A, Adam Rankin)
* [[2016_Winter_Project_Week:MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
*Integration of ImFusion MR-US registration with BWH AMIGO neurosurgery setup (Christian A, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso)
* [[2015_Winter_Project_Week:SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard)

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

= '''Logistics''' =

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

= '''Registrants''' =

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

2016 Winter Project Week

2015-12-14T15:52:16Z

Inorton: /* Non-categorized */

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

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

'''Location:''' MIT, Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)

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

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

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

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

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

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

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

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

==Agenda==

Tentative Agenda

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 4
!style="width:18%" |Tuesday, January 5
!style="width:18%" |Wednesday, January 6
!style="width:18%" |Thursday, January 7
!style="width:18%" |Friday, January 8
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|'''10:30am-12pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 1 by Sarang Joshi) Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10-11:30am:''' Breakout Session: New Slicer Extensions''' 
|
'''10-11:30am:''' Breakout Session: [[2015_Winter_Project_Week:SlicerROSIntegration| Slicer for Medical Robotics Research]] 
 
|'''9:00-10:30am''' TBD 
 ---------------------------------------- 
'''10am-12pm: Breakout Session:''' TBD 
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ---------------------------------------- 
'''12pm''' [[Events:TutorialContestJanuary2016|Tutorial Contest Winner Announcement]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: Welcome''' 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ---------------------------------------- 
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads) 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ---------------------------------------- 
'''2:45-4pm:''' [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Breakout Session Ultrasound]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
 ---------------------------------------- 

'''4:00pm-5:30pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 2 by Sarang Joshi) Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''1-3pm:''' [[2016_Winter_Project_Week/Breakout_Session/What's_Planned_for_Slicer_Core|What's Planned for Slicer Core]] 
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' Breakout Session:''' [[2016_Winter_Project_Week/Breakout_Sessions/Diffusion MRI| Diffusion MRI]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]] -------- 
'''3-4:30pm:''' Breakout Session:''' [[2016_Winter_Project_Week/Breakout_Sessions/QIICR Tools| QIICR Tools]]
|
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}
<googlecalendar>kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com</googlecalendar>

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

== Non-categorized ==
*Digital Pathology Nuclear Segmentation (Erich Bremer, Nicole Aucoin, Andrey Fedorov)
*Chest Imaging Platform: COPD and other pulmonary diseases (Raúl San José, Jorge Onieva)
*Upgrade the namic (and Slicer?) wiki (JC, Mike Halle)
* [[2016_Winter_Project_Week:BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week:ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week:PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week:External_beam_planning | External beam radiotherapy planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week:SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[2016_Winter_Project_Week:CommonDataStructure | Common data structure for CMF modules in Slicer]] (Françoi Budin, Lucia Cevidanes, Beatriz Paniagua, Steeve Pieper, Juan Carlos Prieto, Jean-Baptiste Vimort)
* [[2016_Winter_Project_Week:Tract_io_interop | Tractography format interoperability]] (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)

== IGT ==
* [[2016_Winter_Project_Week:TrackedUltrasoundStandardization | Tracked ultrasound standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*Integration of CustusX with PLUS on BK System (Christian A, Adam Rankin)
* [[2016_Winter_Project_Week:MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
*Integration of ImFusion MR-US registration with BWH AMIGO neurosurgery setup (Christian A, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso)
* [[2015_Winter_Project_Week:SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard)

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

= '''Logistics''' =

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

= '''Registrants''' =

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

2016 Winter Project Week/Projects/Tractography format interoperability

2015-12-14T15:51:07Z

Inorton: Inorton moved page 2016 Winter Project Week:Tract io interop to 2016 Winter Project Week:Tractography format interoperability

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

</gallery>

==Key Investigators==
* Michael Onken, OFFIS
* Isaiah Norton, BWH
* Lauren O'Donnell, BWH

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

* Develop and test Slicer/DCMTK support for DICOM tractography (supplement 181).
* Develop and test Slicer support for DiPy's HDF5-based "dpy" tract format.

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

*

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

*

|}

==Background and References==

[http://dicom.nema.org/Dicom/News/June2015/docs/sups/sup181.pdf DICOM Supplement 181]

2016 Winter Project Week:Tract io interop

2015-12-14T15:51:07Z

Inorton: Inorton moved page 2016 Winter Project Week:Tract io interop to 2016 Winter Project Week:Tractography format interoperability

#REDIRECT [[2016 Winter Project Week:Tractography format interoperability]]

2016 Winter Project Week/Projects/Tractography format interoperability

2015-12-14T15:50:40Z

Inorton: /* Project Description */

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

</gallery>

==Key Investigators==
* Michael Onken, OFFIS
* Isaiah Norton, BWH
* Lauren O'Donnell, BWH

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

* Develop and test Slicer/DCMTK support for DICOM tractography (supplement 181).
* Develop and test Slicer support for DiPy's HDF5-based "dpy" tract format.

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

*

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

*

|}

==Background and References==

[http://dicom.nema.org/Dicom/News/June2015/docs/sups/sup181.pdf DICOM Supplement 181]