https://www.na-mic.org/w/api.php?action=feedcontributions&user=Prisgdd&feedformat=atomNAMIC Wiki - User contributions [en]2024-03-28T10:50:58ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/An_open-source_tool_to_classify_TMJ_OA_condyles&diff=950902017 Winter Project Week/An open-source tool to classify TMJ OA condyles2017-01-13T15:41:33Z<p>Prisgdd: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
File:tensorboard.png<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
<!-- Add a bulleted list of investigators and their institutions here --><br />
* Priscille de Dumast (University of Michigan)<br />
* Juan Carlos Prieto (University of North Carolina)<br />
* Beatriz Paniagua (Kitware, Inc.)<br />
<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Develop a Neural Network to classify 3D osteoarthritic morphological variations using 3D models <br />
* Develop a Slicer extension to disseminate that methodology<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Data preprocess : Point distribution models (PDM) with 1002 correspondent points constructed using SPHARM-PDM software, features extraction from the shapes<br />
* Implementation of a deep learning network using Tensorflow and create classification using the features extracted before<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
* Display the actual network in tensorboard<br />
* Combined with the web-based system from another project, the network is usable from a Slicer extension with remote computations<br />
* Design ideas for an standalone Slicer extension<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --><br />
[https://github.com/pdedumast/CondylesFeaturesExtractor Features extraction source code]<br><br />
[https://github.com/pdedumast/CondylesClassification Classification source code]</div>Prisgddhttps://www.na-mic.org/w/index.php?title=File:Tensorboard.png&diff=95089File:Tensorboard.png2017-01-13T15:40:40Z<p>Prisgdd: </p>
<hr />
<div></div>Prisgddhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/SlicerShape&diff=950602017 Winter Project Week/SlicerShape2017-01-13T15:22:01Z<p>Prisgdd: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
File:SALT_SoftwareWorkflow_Paniagua2017.jpg<br />
File:SALT_DataImporter_Paniagua2017.jpg<br />
File:SlicerSALT_Dashboards.png<br />
File:Shape_regression_slicer.png<br />
File:GroupsExtensionGUI.png<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
<!-- Add a bulleted list of investigators and their institutions here --><br />
* Beatriz Paniagua (Kitware, Inc.)<br />
* Johan Andruejol (Kitware, Inc.)<br />
* JC Fillon-Robin (Kitware, Inc.)<br />
* James Fishbaugh (NYU)<br />
* Priscille de Dumast (UofM)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* SALT Shape AnaLysis Toolbox, will be a comprehensive software that will allow biomedical scientists to precisely locate shape changes in their imaging studies. SALT will enhance the intuitiveness and ease of use for such studies, as well as allow researchers to find shape changes with higher statistical power. Altogether this constitutes a crucial resource for the imaging field that will enable many and important new findings in biomedical imaging studies.<br />
* SALT will be a packaged as a customized version of Slicer, but all different functional units of SALT will be disseminated as extensions as well and will contribute back to the platform. <br />
* The main objective of this project will be touching base with the Slicer community and making sure our efforts are synergetic for other Slicer researchers. <br />
|<br />
<!-- Approach and Plan bullet points --><br />
* We will have a breakout session 9am on Wednesday to talk about the different shape functionalities of Slicer, and how Slicer can help SALT and how SALT can help the platform. Come join us!!<br />
* I would like to continue some discussions on how the customized versions of Slicer and Slicer co-exist. During Project Week 2016, there were discussions on how the new website was going to be and how the different Slicer eco-systems were going to be acknowledged, I wonder what happened with that. I would like to identify some key players and make a decision.<br />
* I will get started developing the dissemination infrastructure and dashboards during the week<br />
* I will get started developing a customized version of Slicer for SALT.<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
* Got started with setting up the testing infrastructure<br />
** Dashboard created.<br />
** [https://github.com/Kitware/slicerSALT Repository created]<br />
* Important design decisions were made thanks to the breakout session<br />
** Batch processing approaches<br />
** Slicer interaction<br />
* Some modules have started to make progress and have working prototypes<br />
** James<br />
** Priscille<br />
* Future steps<br />
** Continue setting software infrastructure<br />
** Start methodology implementation<br />
** <br />
|}<br />
<br />
==Breakout session notes==<br />
[https://docs.google.com/presentation/d/1CbddFklbMS-96CF0XJMZCA9o0MwXh2neo6fc-C6Ia7E/edit?usp=sharing Slides]<br />
<br />
* Slicer.org bridging with all Slicer customizations available<br />
** We will need to change infrastructure of slicer.org to acknowledge all the different customized versions of the program. Bea will give this a go.<br />
** Tutorials, forums, mailing lists should be included there.<br />
<br />
* Architectural design decisions<br />
** Improving support for vtkMRMLModelNode.<br />
*** Visualization - Color maps, Surface pre-processing algorithms<br />
*** Support for 4D support - Sequences<br />
** New vtkMRML*Node classes<br />
** S-reps<br />
<br />
* Improving user experience<br />
** Providing a lot of feedback to the user <br />
*** Quality of inputs and outputs<br />
*** Speed, computation time <br />
**** Obtain some sort of benchmarks of computational performance based on the OS requirements. kwsyslibrary can provide information of the program running. Another idea is to run a small subset of the batch processing and provide some information of how much did it take and how much the rest of the computation is going to take.<br />
**** The user's frustration comes from the unexpected time delay when you run a method (expecting 1 min, waiting 1 h) Slicer has progress bars (Andras Lasso) is saying progress bar have phases and we should use it. They have a preview for parameter tuning and then they run the long method (preview on small data)<br />
**** Running in separate process is good because you can kill the process anytime<br />
<br />
* Thinking about the specific needs of the user base of slicerSALT<br />
** These methods take a lot of time to compute and usually involve a batch process<br />
*** Greg Sharp SlicerRT has a stand-alone tool that submits and logs jobs into Slicer<br />
*** Ron Kikinis' input is that Slicer is not really designed for not interactive things, but you can have non-interactive mode and run things<br />
*** Girder has ways to submit jobs and save outputs into it (Breakout session tomorrow)<br />
<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Prisgddhttps://www.na-mic.org/w/index.php?title=File:GroupsExtensionGUI.png&diff=95057File:GroupsExtensionGUI.png2017-01-13T15:21:01Z<p>Prisgdd: </p>
<hr />
<div></div>Prisgddhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/An_open-source_tool_to_classify_TMJ_OA_condyles&diff=950422017 Winter Project Week/An open-source tool to classify TMJ OA condyles2017-01-13T15:09:16Z<p>Prisgdd: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
<!-- Add a bulleted list of investigators and their institutions here --><br />
* Priscille de Dumast (University of Michigan)<br />
* Juan Carlos Prieto (University of North Carolina)<br />
* Beatriz Paniagua (Kitware, Inc.)<br />
<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Develop a Neural Network to classify 3D osteoarthritic morphological variations using 3D models <br />
* Develop a Slicer extension to disseminate that methodology<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Data preprocess : Point distribution models (PDM) with 1002 correspondent points constructed using SPHARM-PDM software, features extraction from the shapes<br />
* Implementation of a deep learning network using Tensorflow and create classification using the features extracted before<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
* Display the actual network in tensorboard<br />
* Combined with the web-based system from another project, the network is usable from a Slicer extension with remote computations<br />
* Design ideas for an standalone Slicer extension<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --><br />
[https://github.com/pdedumast/CondylesFeaturesExtractor Features extraction source code]<br><br />
[https://github.com/pdedumast/CondylesClassification Classification source code]</div>Prisgddhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/An_open-source_tool_to_classify_TMJ_OA_condyles&diff=943102017 Winter Project Week/An open-source tool to classify TMJ OA condyles2017-01-04T16:25:37Z<p>Prisgdd: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
<!-- Add a bulleted list of investigators and their institutions here --><br />
* Priscille de Dumast (University of Michigan)<br />
* Juan Carlos Prieto (University of North Carolina)<br />
* Beatriz Paniagua (Kitware, Inc.)<br />
<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Develop a Neural Network to classify 3D osteoarthritic morphological variations using 3D models <br />
* Develop a Slicer extension to disseminate that methodology<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Data preprocess : Point distribution models (PDM) with 1002 correspondent points constructed using SPHARM-PDM software, features extraction from the shapes<br />
* Implementation of a deep learning network using Tensorflow and create classification using the features extracted before<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
*<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --><br />
[https://github.com/pdedumast/CondylesFeaturesExtractor Features extraction source code]<br><br />
[https://github.com/pdedumast/CondylesClassification Classification source code]</div>Prisgddhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/An_open-source_tool_to_classify_TMJ_OA_condyles&diff=943092017 Winter Project Week/An open-source tool to classify TMJ OA condyles2017-01-04T16:24:31Z<p>Prisgdd: 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..."</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
<!-- Add a bulleted list of investigators and their institutions here --><br />
* Priscille de Dumast (University of Michigan)<br />
* Juan Carlos Prieto (University of North Carolina)<br />
* Beatriz Paniagua (Kitware, Inc.)<br />
<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Develop a Neural Network to classify 3D osteoarthritic morphological variations using 3D models <br />
* Develop a Slicer extension to disseminate that methodology<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Data preprocess : Point distribution models (PDM) with 1002 correspondent points constructed using SPHARM-PDM software, features extraction from the shapes<br />
* Implementation of a deep learning network using Tensorflow and create classification using the features extracted before<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
*<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --><br />
[https://github.com/pdedumast/CondylesFeaturesExtractor]<br><br />
[https://github.com/pdedumast/CondylesClassification]</div>Prisgddhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week&diff=943062017 Winter Project Week2017-01-04T15:08:07Z<p>Prisgdd: /* Learning and GPUs */</p>
<hr />
<div>__NOTOC__<br />
[[image:PW-Winter2017.png|300px]]<br />
<br />
=Welcome to the web page for the 24th Project Week!=<br />
<br />
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].<br />
<br />
==Logistics==<br />
<br />
*'''Dates:''' January 9-13, 2017.<br />
*'''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)<br />
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]<br />
<br />
== Introduction ==<br />
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.<br />
<br />
[[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. <br />
<br />
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.<br />
<br />
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]. <br />
<br />
A summary of all previous Project Events is available [[Project_Events#Past_Project_Weeks|here]].<br />
<br />
Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list]<br />
<br />
==Conference Calls for Preparation==<br />
<br />
Conference call phone number and notes are available [[TCONS:2017_Winter_Project_Week|here]].<br />
<br />
==Calendar==<br />
<br />
'''''<font color="maroon">The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.</font>'''''<br><br />
<br />
<br />
{{#widget:Google Calendar<br />
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com<br />
|timezone=America/New_York&dates=20170108%2F20170114<br />
|title=NAMIC Winter Project Week<br />
|view=WEEK<br />
|dates=20170108/20170114<br />
}}<br />
<br />
iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics<br />
<br />
='''Projects'''=<br />
<br />
*Use this [[2017_Project_Week_Template | Updated Template for project pages]]<br />
<br />
== Learning and GPUs ==<br />
<br />
* [[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Ziyang Wang, Guillaume Pernelle, Tina Kapur)<br />
* [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)<br />
* [[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)<br />
<br />
== Web Technologies ==<br />
* [[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)<br />
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)<br />
* [[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper)<br />
* [[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)<br />
* [[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)<br />
* [[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)<br />
<br />
== Visualization ==<br />
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)<br />
<br />
== IGT: Navigation, Robotics, Surgical Planning ==<br />
* [[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)<br />
* [[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)<br />
* [[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]] (Peter Traneus Anderson)<br />
* [[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, )<br />
* [[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)<br />
* [[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov)<br />
* [[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)<br />
<br />
==dMRI==<br />
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (Fan Zhang, Shun Gong, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)<br />
* [[2017 Winter Project Week/LORDWI | Density-based DMRI registration ]] (Henrik Groenholt Jensen, Lauren J. O'Donnell, Tina Kapur, Fan Zhang, Carl-Frederik Westin)<br />
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)<br />
* [[2017 Winter Project Week/DiPy_in_Slicer | DiPy integration in Slicer]] (Isaiah Norton, Lauren J. O'Donnell)<br />
* [[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)<br />
<br />
== Infrastructure ==<br />
<br />
* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy refactoring]] (Csaba Pinter)<br />
* [[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)<br />
* [[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)<br />
<br />
==To be Categorized==<br />
<br />
* [[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)<br />
* [[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)<br />
* [[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)<br />
* [[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)<br />
* [[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)<br />
* [[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)<br />
* [[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)<br />
<br />
= '''Registrants''' =<br />
<br />
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].<br />
<br />
# A, Zeina :: SHBOUL<br />
# Aerts, Hugo :: DFCI-Harvard<br />
# Alam, Mahbubul :: Old Dominion University<br />
# Anderson, Peter :: Retired<br />
# Andruejol, Johan :: Kitware, Inc.<br />
# Bakeng, Janne Beate :: SINTEF<br />
# Beers, Andrew :: Massachusetts General Hospital<br />
# Bernal Rusiel, Jorge Luis :: Boston Children's Hospital<br />
# Bremer, Erich :: Stony Brook University<br />
# Burke, Brice :: American University of Antigua College of Medicine<br />
# Cetin Karayumak, Suheyla :: Brigham and Women's Hospital<br />
# Chae, Michael :: Monash University<br />
# Chauvin, Laurent :: ETS<br />
# Dalca, Adrian :: Massachusetts Institute of Technology<br />
# Fedorov, Andriy :: Brigham and Women's Hospital<br />
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.<br />
# Fishbaugh, James :: New York University<br />
# Frank, Tobias :: Leibniz Universität Hannover<br />
# García Mato, David :: Queen´s University / Universidad Carlos III de Madrid<br />
# Girault, Alexis :: Kitware, Inc.<br />
# Golland, Polina :: Massachusetts Institute of Technology<br />
# Gollub, Randy :: Massachusetts General Hospital<br />
# Gong, Shun :: Brigham and Women's Hospital<br />
# Guerrier de Dumast, Priscille :: University of Michigan<br />
# Harris, Gordon :: Massachusetts General Hospital<br />
# Herz, Christian :: Brigham and Women's Hospital<br />
# Hong, Sungmin :: New York University<br />
# Hosny, Ahmed :: Dana-Farber<br />
# Jagadeesan, Jayender :: Brigham and Women's Hospital<br />
# Jensen, Henrik G. :: University of Copenhagen<br />
# Kapur, Tina :: Brigham and Women's Hospital<br />
# Kikinis, Ron :: Brigham and Women's Hospital<br />
# Lasso, Andras :: PerkLab, Queen's University<br />
# Lauer, Rebekka :: Humboldt University Berlin<br />
# Lisle, Curtis :: KnowledgeVis, LLC<br />
# Mastrogiacomo, Katie :: Brigham and Women's Hospital<br />
# Mateus, D. :: TUM<br />
# Mehrtash, Alireza :: Brigham and Women's Hospital<br />
# Meine, Hans :: University of Bremen<br />
# Meyer, Anneke :: University of Magdeburg<br />
# Miller, James :: GE Research<br />
# Mirabel, Clement :: University of Michigan<br />
# Nitsch, Jennifer :: University of Bremen<br />
# Norton, Isaiah :: Brigham and Women's Hospital<br />
# O'Donnell, Lauren :: Brigham and Women's Hospital<br />
# Oram, Louise :: The Intervention Centre-Oslo University Hospital<br />
# Paniagua, Beatriz :: Kitware, Inc.<br />
# Parmar, Chintan :: DFCI-Harvard Medical School<br />
# Peled, Sharon :: Brigham and Women's Hospital<br />
# Pieper, Steve :: Isomics, Inc.<br />
# Pinter, Csaba :: Queen's University<br />
# Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School<br />
# Pujol, Sonia :: Brigham and Women's Hospital/Harvard Medical School<br />
# Rankin, Adam :: Robarts Research Institute<br />
# Rheault, Francois :: Université de Sherbrooke<br />
# Roethe, Anna :: Humboldt University / Charité University Hospital Berlin<br />
# Sharp, Gregory :: Massachusetts General Hospital<br />
# Sridharan, Patmaa :: University of Pennsylvania-CBICA<br />
# Vidyaratne, Lasitha :: Old Dominion University<br />
# Wang, Yaofei :: Brigham and Women's Hospital<br />
# Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School<br />
# Yang, Yixin :: Brigham and Women's Hospital<br />
# Ye, Wu :: Brigham and Women's Hospital<br />
# Zaffino, Paolo :: Magna Graecia University of Catanzaro, Italy<br />
# Zeleznik, Roman :: DFCI<br />
# Zhang, Fan :: Brigham and Women's Hospital<br />
# Zhang, Miaomiao :: Massachusetts Institute of Technology<br />
# Zhang, Yuqian :: Brigham and Women's Hospital<br />
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital</div>Prisgddhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week&diff=943042017 Winter Project Week2017-01-04T15:02:34Z<p>Prisgdd: /* Learning and GPUs */</p>
<hr />
<div>__NOTOC__<br />
[[image:PW-Winter2017.png|300px]]<br />
<br />
=Welcome to the web page for the 24th Project Week!=<br />
<br />
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].<br />
<br />
==Logistics==<br />
<br />
*'''Dates:''' January 9-13, 2017.<br />
*'''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)<br />
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]<br />
<br />
== Introduction ==<br />
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.<br />
<br />
[[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. <br />
<br />
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.<br />
<br />
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]. <br />
<br />
A summary of all previous Project Events is available [[Project_Events#Past_Project_Weeks|here]].<br />
<br />
Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list]<br />
<br />
==Conference Calls for Preparation==<br />
<br />
Conference call phone number and notes are available [[TCONS:2017_Winter_Project_Week|here]].<br />
<br />
==Calendar==<br />
<br />
'''''<font color="maroon">The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.</font>'''''<br><br />
<br />
<br />
{{#widget:Google Calendar<br />
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com<br />
|timezone=America/New_York&dates=20170108%2F20170114<br />
|title=NAMIC Winter Project Week<br />
|view=WEEK<br />
|dates=20170108/20170114<br />
}}<br />
<br />
iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics<br />
<br />
='''Projects'''=<br />
<br />
*Use this [[2017_Project_Week_Template | Updated Template for project pages]]<br />
<br />
== Learning and GPUs ==<br />
<br />
* [[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Ziyang Wang, Guillaume Pernelle, Tina Kapur)<br />
* [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)<br />
* [[2017 Winter Project Week/An open-source tool to classify shapes | An open-source tool to classify shapes]] (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)<br />
<br />
== Web Technologies ==<br />
* [[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)<br />
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)<br />
* [[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper)<br />
* [[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)<br />
* [[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)<br />
* [[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)<br />
<br />
== Visualization ==<br />
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)<br />
<br />
== IGT: Navigation, Robotics, Surgical Planning ==<br />
* [[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)<br />
* [[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)<br />
* [[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]] (Peter Traneus Anderson)<br />
* [[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, )<br />
* [[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)<br />
* [[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov)<br />
* [[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)<br />
<br />
==dMRI==<br />
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (Fan Zhang, Shun Gong, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)<br />
* [[2017 Winter Project Week/LORDWI | Density-based DMRI registration ]] (Henrik Groenholt Jensen, Lauren J. O'Donnell, Tina Kapur, Fan Zhang, Carl-Frederik Westin)<br />
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)<br />
* [[2017 Winter Project Week/DiPy_in_Slicer | DiPy integration in Slicer]] (Isaiah Norton, Lauren J. O'Donnell)<br />
* [[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)<br />
<br />
== Infrastructure ==<br />
<br />
* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy refactoring]] (Csaba Pinter)<br />
* [[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)<br />
* [[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)<br />
<br />
==To be Categorized==<br />
<br />
* [[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)<br />
* [[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)<br />
* [[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)<br />
* [[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)<br />
* [[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)<br />
* [[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)<br />
* [[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)<br />
<br />
= '''Registrants''' =<br />
<br />
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].<br />
<br />
# A, Zeina :: SHBOUL<br />
# Aerts, Hugo :: DFCI-Harvard<br />
# Alam, Mahbubul :: Old Dominion University<br />
# Anderson, Peter :: Retired<br />
# Andruejol, Johan :: Kitware, Inc.<br />
# Bakeng, Janne Beate :: SINTEF<br />
# Beers, Andrew :: Massachusetts General Hospital<br />
# Bernal Rusiel, Jorge Luis :: Boston Children's Hospital<br />
# Bremer, Erich :: Stony Brook University<br />
# Burke, Brice :: American University of Antigua College of Medicine<br />
# Cetin Karayumak, Suheyla :: Brigham and Women's Hospital<br />
# Chae, Michael :: Monash University<br />
# Chauvin, Laurent :: ETS<br />
# Dalca, Adrian :: Massachusetts Institute of Technology<br />
# Fedorov, Andriy :: Brigham and Women's Hospital<br />
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.<br />
# Fishbaugh, James :: New York University<br />
# Frank, Tobias :: Leibniz Universität Hannover<br />
# García Mato, David :: Queen´s University / Universidad Carlos III de Madrid<br />
# Girault, Alexis :: Kitware, Inc.<br />
# Golland, Polina :: Massachusetts Institute of Technology<br />
# Gollub, Randy :: Massachusetts General Hospital<br />
# Gong, Shun :: Brigham and Women's Hospital<br />
# Guerrier de Dumast, Priscille :: University of Michigan<br />
# Harris, Gordon :: Massachusetts General Hospital<br />
# Herz, Christian :: Brigham and Women's Hospital<br />
# Hong, Sungmin :: New York University<br />
# Hosny, Ahmed :: Dana-Farber<br />
# Jagadeesan, Jayender :: Brigham and Women's Hospital<br />
# Jensen, Henrik G. :: University of Copenhagen<br />
# Kapur, Tina :: Brigham and Women's Hospital<br />
# Kikinis, Ron :: Brigham and Women's Hospital<br />
# Lasso, Andras :: PerkLab, Queen's University<br />
# Lauer, Rebekka :: Humboldt University Berlin<br />
# Lisle, Curtis :: KnowledgeVis, LLC<br />
# Mastrogiacomo, Katie :: Brigham and Women's Hospital<br />
# Mateus, D. :: TUM<br />
# Mehrtash, Alireza :: Brigham and Women's Hospital<br />
# Meine, Hans :: University of Bremen<br />
# Meyer, Anneke :: University of Magdeburg<br />
# Miller, James :: GE Research<br />
# Mirabel, Clement :: University of Michigan<br />
# Nitsch, Jennifer :: University of Bremen<br />
# Norton, Isaiah :: Brigham and Women's Hospital<br />
# O'Donnell, Lauren :: Brigham and Women's Hospital<br />
# Oram, Louise :: The Intervention Centre-Oslo University Hospital<br />
# Paniagua, Beatriz :: Kitware, Inc.<br />
# Parmar, Chintan :: DFCI-Harvard Medical School<br />
# Peled, Sharon :: Brigham and Women's Hospital<br />
# Pieper, Steve :: Isomics, Inc.<br />
# Pinter, Csaba :: Queen's University<br />
# Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School<br />
# Pujol, Sonia :: Brigham and Women's Hospital/Harvard Medical School<br />
# Rankin, Adam :: Robarts Research Institute<br />
# Rheault, Francois :: Université de Sherbrooke<br />
# Roethe, Anna :: Humboldt University / Charité University Hospital Berlin<br />
# Sharp, Gregory :: Massachusetts General Hospital<br />
# Sridharan, Patmaa :: University of Pennsylvania-CBICA<br />
# Vidyaratne, Lasitha :: Old Dominion University<br />
# Wang, Yaofei :: Brigham and Women's Hospital<br />
# Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School<br />
# Yang, Yixin :: Brigham and Women's Hospital<br />
# Ye, Wu :: Brigham and Women's Hospital<br />
# Zaffino, Paolo :: Magna Graecia University of Catanzaro, Italy<br />
# Zeleznik, Roman :: DFCI<br />
# Zhang, Fan :: Brigham and Women's Hospital<br />
# Zhang, Miaomiao :: Massachusetts Institute of Technology<br />
# Zhang, Yuqian :: Brigham and Women's Hospital<br />
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital</div>Prisgdd