https://www.na-mic.org/w/api.php?action=feedcontributions&feedformat=atom&user=Patmaa 2026-05-20T11:35:40Z User contributions MediaWiki 1.33.0 https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/GeodesicSegmentationandLungtumorAnalysis&diff=95173 2017-01-13T18:56:31Z

<p>Patmaa: /* Project Description */</p> <hr /> <div>__NOTOC__<br /> &lt;gallery&gt;<br /> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br /> &lt;!-- Use the &quot;Upload file&quot; link on the left and then add a line to this list like &quot;File:MyAlgorithmScreenshot.png&quot; --&gt;<br /> &lt;/gallery&gt;<br /> <br /> ==Key Investigators==<br /> * Patmaa Sridharan - UPenn CBICA<br /> * Andras Lasso<br /> * Louise Oram<br /> <br /> ==Project Description==<br /> <br /> {| class=&quot;wikitable&quot;<br /> ! style=&quot;text-align: left; width:27%&quot; | Objective<br /> ! style=&quot;text-align: left; width:27%&quot; | Approach and Plan<br /> ! style=&quot;text-align: left; width:27%&quot; | Progress and Next Steps<br /> |- style=&quot;vertical-align:top;&quot;<br /> |<br /> &lt;!-- Objective bullet points --&gt;<br /> <br /> Integrate two applications listed below with slicer and also focus on interaction between Slicer and CAPTk(our internal tool)<br /> * Geodesic Segmentation<br /> A generic segmentation algorithm that uses geodesic distances.<br /> <br /> * SBRT Lung Tumor segmentation and Analysis<br /> Segmentation of lung tumor from multimodal images- CT and PET using initial seed points. Analyze the segmented region using texture features and predict the nodal failure in lung.<br /> |<br /> &lt;!-- Approach and Plan bullet points --&gt;<br /> <br /> *Analyze the compatibility between the dependencies of our code with that of Slicer and solve it for smooth interaction with our application.<br /> *Enabling Slicer's GUI to provide seed point initialization required for our application. <br /> *Do a code level integration of geodesic segmentation and SBRT with Slicer.<br /> *Investigate on possibility of calling Slicer from CapTk and vice-versa by using pre-populated project files.<br /> |<br /> &lt;!-- Progress and Next steps bullet points --&gt;<br /> * Had discussions on how to get CAPTk and Slicer communicate and get to use some of the applications of Slicer from CapTk<br /> * On process of getting geodesic segmentation into a Slicer plugin.<br /> * Next Steps<br /> * Finish the plugin and submit it for adding as a module<br /> * Finish the OpenIGT linking to CAPTk to enable both applications communicate<br /> <br /> |}<br /> <br /> ==Background and References==<br /> &lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&gt;</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/GeodesicSegmentationandLungtumorAnalysis&diff=95172 2017-01-13T18:48:45Z

<p>Patmaa: </p> <hr /> <div>__NOTOC__<br /> &lt;gallery&gt;<br /> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br /> &lt;!-- Use the &quot;Upload file&quot; link on the left and then add a line to this list like &quot;File:MyAlgorithmScreenshot.png&quot; --&gt;<br /> &lt;/gallery&gt;<br /> <br /> ==Key Investigators==<br /> * Patmaa Sridharan - UPenn CBICA<br /> * Andras Lasso<br /> * Louise Oram<br /> <br /> ==Project Description==<br /> <br /> {| class=&quot;wikitable&quot;<br /> ! style=&quot;text-align: left; width:27%&quot; | Objective<br /> ! style=&quot;text-align: left; width:27%&quot; | Approach and Plan<br /> ! style=&quot;text-align: left; width:27%&quot; | Progress and Next Steps<br /> |- style=&quot;vertical-align:top;&quot;<br /> |<br /> &lt;!-- Objective bullet points --&gt;<br /> <br /> Integrate two applications listed below with slicer and also focus on interaction between Slicer and CAPTk(our internal tool)<br /> * Geodesic Segmentation<br /> A generic segmentation algorithm that uses geodesic distances.<br /> <br /> * SBRT Lung Tumor segmentation and Analysis<br /> Segmentation of lung tumor from multimodal images- CT and PET using initial seed points. Analyze the segmented region using texture features and predict the nodal failure in lung.<br /> |<br /> &lt;!-- Approach and Plan bullet points --&gt;<br /> *Analyze the compatibility between the dependencies of our code with that of Slicer and solve it for smooth interaction with our application.<br /> *Enabling Slicer's GUI to provide seed point initialization required for our application. <br /> *Do a code level integration of geodesic segmentation and SBRT with Slicer.<br /> *Investigate on possibility of calling Slicer from CapTk and vice-versa by using pre-populated project files.<br /> &lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&gt;<br /> * Had discussions on how to get CAPTk and Slicer communicate and get to use some of the applications of Slicer from CapTk<br /> * On process of getting geodesic segmentation into a Slicer plugin.<br /> Next Steps<br /> * Finish the plugin and submit it for adding as a module<br /> * Finish the OpenIGT linking to CAPTk to enable both applications communicate<br /> |}<br /> <br /> ==Background and References==<br /> &lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&gt;</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week&diff=95171 2017-01-13T18:40:06Z

<p>Patmaa: Undo revision 95100 by Patmaa (talk)</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&amp;D)<br /> *'''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]<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 /> '''''&lt;font color=&quot;maroon&quot;&gt;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.&lt;/font&gt;'''''&lt;br&gt;<br /> <br /> <br /> {{#widget:Google Calendar<br /> |id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com<br /> |timezone=America/New_York&amp;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 /> == Deep Learning and GPUs ==<br /> #[[2017 Winter Project Week/Deep Learning for Medical Image Computation| Deep Learning for Medical Image Computing]] (Tina Kapur)<br /> #[[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Paolo Zaffino, Ziyang Wang, Guillaume Pernelle, Tina Kapur)<br /> #[[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)<br /> #[[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)<br /> # [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei &quot;Ada&quot; 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 /> #[[2017 Winter Project Week/Evaluate Deep Learning for binary cancer legion classification | Evaluate Deep Learning for binary cancer lesion classification]] (Curt Lisle)<br /> #[[2017 Winter Project Week/Population Based Image Imputation | Population Based Image Imputation]] (Adrian Dalca, Katie Bouman, Mert Sabuncu, Polina Golland)<br /> #[[2017 Winter Project Week/Knee Cartilage Segmentation | Knee Cartilage Segmentation]] (Hans Meine)<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/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper, Satra Ghosh)<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/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 /> #[[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper)<br /> #[[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)<br /> #[[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, Teodora Szasz)<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/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)<br /> #[[2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction| 3D surgical planning solution for autologous breast reconstruction]] (Michael Chae, Andras Lasso, David Garcia, Julian Smith, Warren Rozen, David Hunter-Smith)<br /> #[[2017 Winter Project Week/Intraoperative_Functional_Visualization | Visualization Concept for Intraoperative Use of Functional Mapping Data ]] (Anna Roethe, Rebekka Lauer, Prashin Unadkat, Sarah Frisken)<br /> #[[2017 Winter Project Week/Integrative_Intraoperative_Interface | Integrative Interface for Intraoperative Software Applications ]] (Anna Roethe, Rebekka Lauer, Prashin Unadkat, Sarah Frisken)<br /> <br /> ==dMRI==<br /> #[[2017 Winter Project Week/WhiteMatterAnalysis | Fiber endpoint analysis for neurosurgical planning]] (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-Fredrik Westin)<br /> #[[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Shun Gong, Ye Wu, Isaiah Norton, Fan Zhang, Lauren J. O'Donnell)<br /> #[[2017 Winter Project Week/DiPy_in_Slicer | WMA &amp; 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 /> ==Quantitative Imaging Informatics==<br /> #[[2017 Winter Project Week/dcmqi | dcmqi library]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)<br /> #[[2017 Winter Project Week/QuantitativeReporting | DICOM QuantitativeReporting]] (Christian Herz, Andrey Fedorov, Andras Lasso, Csaba Pinter)<br /> #[[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christophe 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 /> == Shape Analysis, Segmentation ==<br /> #[[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua, Johan Andruejol, JC Fillon-Robin, James Fishbaugh, Priscille de Dumast)<br /> #[[2017 Winter Project Week/MandibularRegression | Mandibular and maxillary Shape Regression ]] (Beatriz Paniagua, Clement Mirabel, Priscille de Dumast, James Fishbaugh, Lucia Cevidanes, Daniella Garib)<br /> #[[2017 Winter Project Week/Slicer_VR | Slicer + VR = &lt;3]] (Adam Rankin, Andras Lasso, Ryan D'Souza (NDI), Matthew Jolley (Children's Hospital of Philadelphia), Kitware+Slicer dev (JC,JFinet,etc...)<br /> #[[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)<br /> #[[2017 Winter Project Week/GeodesicSegmentationandLungtumorAnalysis| Geodesic Segmentation and Lung tumor Analysis]] (Patmaa S,)<br /> #[[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov, Alireza Mehrtash, Christian Hansen, Teodora Szasz)<br /> #[[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)<br /> #[[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Jakub Kaczmarzyk, Satrajit Ghosh, Omar Arnaout)<br /> #[[2017 Winter Project Week/CoronarySegmentationTool| Automatic and Manual Segmentation Tool of Coronary Artery from CTA imaging]] (Haoyin Zhou, Jayender Jagadeesan)<br /> <br /> == Infrastructure ==<br /> #[[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)<br /> #[[2017 Winter Project Week/ImprovementsToSegmentEditor | Improvements to Segment Editor]] (Csaba Pinter, Andras Lasso)<br /> #[[2017 Winter Project Week/Plastimatch19 | Plastimatch multi-planar and multi-metric registration ]] (Greg Sharp)<br /> #[[2017 Winter Project Week/UpdatingCommunityForums | Updating Slicer Community Infrastructure (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)<br /> #[[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)<br /> #[[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Pieper)<br /> #[[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault)<br /> #[[2017 Winter Project Week/Organizations | Slicer* Community Topics, Projects, Flavors: The SLICERVERSE ]] (Beatriz Paniagua, Lauren O'Donnell, Isaiah Norton, Gregory Sharp, Louise Oram)<br /> <br /> ==Training and Dissemination==<br /> #[[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)<br /> #[[2017 Winter Project Week/2017 NVIDIA Demo Contest|NVIDIA Demo Contest]] (Abdul Halabi, Abel Brown)<br /> #[[2017 Winter Project Week/2017 Winter Project Week Surgery|Project Week Survey]] (Krisztina Fischer, Tina Kapur)<br /> #[[2017 Winter Project Week/Next project week| Next project week: PW#25]] (Paolo Zaffino, Maria Francesca Spadea, Tina Kapur)<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 /> # Aman Shboul, Zaina :: Old Dominion University<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 /> # Chen, Longquan :: Surgical Planning Lab<br /> # Dalca, Adrian :: Massachusetts Institute of Technology<br /> # DiPrima, Tammy :: Stony Brook University<br /> # Drouin, Simon :: Montreal Neurological Institute<br /> # Fan, Zhipeng :: Brigham and Women's Hospital<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 /> # Frisken, Sarah :: Brigham and Women's Hospital<br /> # García Mato, David :: Queen´s University / Universidad Carlos III de Madrid<br /> # Ghafoorian, Mohsen :: Brigham and Women's Hospital<br /> # Ghosh, Satrajit :: Massachusetts Institute of Technology<br /> # Girault, Alexis :: Kitware, Inc.<br /> # Golland, Polina :: Massachusetts Institute of Technology<br /> # Gollub, Randy :: Massachusetts General Hospital<br /> # Goncalves, Mathias :: Massachusetts Institute of Technology<br /> # Gong, Shun :: Brigham and Women's Hospital<br /> # Guerrier de Dumast, Priscille :: University of Michigan<br /> # Halle, Michael :: Brigham and Women's Hospital<br /> # Harris, Gordon :: Massachusetts General Hospital<br /> # Helba, Brian :: Kitware, Inc.<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 /> # Jarecka, Dorota :: Massachusetts Institute of Technology<br /> # Jensen, Henrik G. :: University of Copenhagen<br /> # Kaczmarzyk, Jakub :: Massachusetts Institute of Technology<br /> # Kapur, Tina :: Brigham and Women's Hospital<br /> # Kennedy, David :: UMass Medical School<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 /> # Mousavi, Parvin :: Brigham and Women's Hospital<br /> # Nitsch, Jennifer :: University of Bremen<br /> # Norton, Isaiah :: Brigham and Women's Hospital<br /> # O'Donnell, Lauren :: Brigham and Women's Hospital<br /> # Onieva, Jorge :: Brigham and Women's Hospital<br /> # Oram, Louise :: The Intervention Centre-Oslo University Hospital<br /> # Padhy, Smruti :: Massachusetts Institute of Technology<br /> # Paniagua, Beatriz :: Kitware, Inc.<br /> # Parmar, Chintan :: DFCI-Harvard Medical School<br /> # Peled, Sharon :: Brigham and Women's Hospital<br /> # Pienaar, Rudolph :: Boston Children'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 /> # Prieto, Juan :: NIRAL<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 /> # Ross, James :: Brigham and Women's Hospital<br /> # Szczepankiewicz, Filip :: Lund University<br /> # Sharp, Gregory :: Massachusetts General Hospital<br /> # Sridharan, Patmaa :: University of Pennsylvania-CBICA<br /> # Szasz, Teodora :: University of Chicago<br /> # Tokuda, Junichi :: Brigham and Women's Hospital<br /> # Unadkat, Prashin :: Brigham and Women's Hospital<br /> # Van Griethuysen , Joost :: Netherlands Cancer Institute<br /> # Vidyaratne, Lasitha :: Old Dominion University<br /> # Wang, Yaofei :: Brigham and Women's Hospital<br /> # Wang, Ziyang :: Brigham and Women's Hospital<br /> # Wei, Dawei :: Brigham and Women's Hospital<br /> # Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School<br /> # Woo, Jonghye :: Massachusetts General Hospital<br /> # Xu, Wanxin :: Brigham and Women's Hospital<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, Hongtao :: Hebei General Hospital<br /> # Zhang, Miaomiao :: Massachusetts Institute of Technology<br /> # Zhang, Yuqian :: Brigham and Women's Hospital<br /> # Zhou, Haoyin :: Brigham and Women's Hospital<br /> # Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week&diff=95100 2017-01-13T15:48:14Z

<p>Patmaa: </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&amp;D)<br /> *'''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]<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 /> '''''&lt;font color=&quot;maroon&quot;&gt;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.&lt;/font&gt;'''''&lt;br&gt;<br /> <br /> <br /> {{#widget:Google Calendar<br /> |id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com<br /> |timezone=America/New_York&amp;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 /> == Deep Learning and GPUs ==<br /> #[[2017 Winter Project Week/Deep Learning for Medical Image Computation| Deep Learning for Medical Image Computing]] (Tina Kapur)<br /> #[[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Paolo Zaffino, Ziyang Wang, Guillaume Pernelle, Tina Kapur)<br /> #[[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)<br /> #[[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)<br /> # [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei &quot;Ada&quot; 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 /> #[[2017 Winter Project Week/Evaluate Deep Learning for binary cancer legion classification | Evaluate Deep Learning for binary cancer lesion classification]] (Curt Lisle)<br /> #[[2017 Winter Project Week/Population Based Image Imputation | Population Based Image Imputation]] (Adrian Dalca, Katie Bouman, Mert Sabuncu, Polina Golland)<br /> #[[2017 Winter Project Week/Knee Cartilage Segmentation | Knee Cartilage Segmentation]] (Hans Meine)<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/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper, Satra Ghosh)<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/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 /> #[[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper)<br /> #[[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)<br /> #[[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, Teodora Szasz)<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/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)<br /> #[[2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction| 3D surgical planning solution for autologous breast reconstruction]] (Michael Chae, Andras Lasso, David Garcia, Julian Smith, Warren Rozen, David Hunter-Smith)<br /> #[[2017 Winter Project Week/Intraoperative_Functional_Visualization | Visualization Concept for Intraoperative Use of Functional Mapping Data ]] (Anna Roethe, Rebekka Lauer, Prashin Unadkat, Sarah Frisken)<br /> #[[2017 Winter Project Week/Integrative_Intraoperative_Interface | Integrative Interface for Intraoperative Software Applications ]] (Anna Roethe, Rebekka Lauer, Prashin Unadkat, Sarah Frisken)<br /> <br /> ==dMRI==<br /> #[[2017 Winter Project Week/WhiteMatterAnalysis | Fiber endpoint analysis for neurosurgical planning]] (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-Fredrik Westin)<br /> #[[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Shun Gong, Ye Wu, Isaiah Norton, Fan Zhang, Lauren J. O'Donnell)<br /> #[[2017 Winter Project Week/DiPy_in_Slicer | WMA &amp; 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 /> ==Quantitative Imaging Informatics==<br /> #[[2017 Winter Project Week/dcmqi | dcmqi library]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)<br /> #[[2017 Winter Project Week/QuantitativeReporting | DICOM QuantitativeReporting]] (Christian Herz, Andrey Fedorov, Andras Lasso, Csaba Pinter)<br /> #[[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christophe 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 /> == Shape Analysis, Segmentation ==<br /> #[[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)<br /> #[[2017 Winter Project Week/MandibularRegression | Mandibular and maxillary Shape Regression ]] (Beatriz Paniagua, Clement Mirabel, Priscille de Dumast, James Fishbaugh, Lucia Cevidanes, Daniella Garib)<br /> #[[2017 Winter Project Week/Slicer_VR | Slicer + VR = &lt;3]] (Adam Rankin, Andras Lasso, Ryan D'Souza (NDI), Matthew Jolley (Children's Hospital of Philadelphia), Kitware+Slicer dev (JC,JFinet,etc...)<br /> #[[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)<br /> #[[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov, Alireza Mehrtash, Christian Hansen, Teodora Szasz)<br /> #[[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)<br /> #[[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Jakub Kaczmarzyk, Satrajit Ghosh, Omar Arnaout)<br /> #[[2017 Winter Project Week/CoronarySegmentationTool| Automatic and Manual Segmentation Tool of Coronary Artery from CTA imaging]] (Haoyin Zhou, Jayender Jagadeesan)<br /> <br /> == Infrastructure ==<br /> #[[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)<br /> #[[2017 Winter Project Week/ImprovementsToSegmentEditor | Improvements to Segment Editor]] (Csaba Pinter, Andras Lasso)<br /> #[[2017 Winter Project Week/Plastimatch19 | Plastimatch multi-planar and multi-metric registration ]] (Greg Sharp)<br /> #[[2017 Winter Project Week/UpdatingCommunityForums | Updating Slicer Community Infrastructure (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)<br /> #[[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)<br /> #[[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Pieper)<br /> #[[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault)<br /> #[[2017 Winter Project Week/Organizations | Slicer* Community Topics, Projects, Flavors: The SLICERVERSE ]] (Beatriz Paniagua, Lauren O'Donnell, Isaiah Norton, Gregory Sharp, Louise Oram)<br /> <br /> ==Training and Dissemination==<br /> #[[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)<br /> #[[2017 Winter Project Week/2017 NVIDIA Demo Contest|NVIDIA Demo Contest]] (Abdul Halabi, Abel Brown)<br /> #[[2017 Winter Project Week/2017 Winter Project Week Surgery|Project Week Survey]] (Krisztina Fischer, Tina Kapur)<br /> #[[2017 Winter Project Week/Next project week| Next project week: PW#25]] (Paolo Zaffino, Maria Francesca Spadea, Tina Kapur)<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 /> # Aman Shboul, Zaina :: Old Dominion University<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 /> # Chen, Longquan :: Surgical Planning Lab<br /> # Dalca, Adrian :: Massachusetts Institute of Technology<br /> # DiPrima, Tammy :: Stony Brook University<br /> # Drouin, Simon :: Montreal Neurological Institute<br /> # Fan, Zhipeng :: Brigham and Women's Hospital<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 /> # Frisken, Sarah :: Brigham and Women's Hospital<br /> # García Mato, David :: Queen´s University / Universidad Carlos III de Madrid<br /> # Ghafoorian, Mohsen :: Brigham and Women's Hospital<br /> # Ghosh, Satrajit :: Massachusetts Institute of Technology<br /> # Girault, Alexis :: Kitware, Inc.<br /> # Golland, Polina :: Massachusetts Institute of Technology<br /> # Gollub, Randy :: Massachusetts General Hospital<br /> # Goncalves, Mathias :: Massachusetts Institute of Technology<br /> # Gong, Shun :: Brigham and Women's Hospital<br /> # Guerrier de Dumast, Priscille :: University of Michigan<br /> # Halle, Michael :: Brigham and Women's Hospital<br /> # Harris, Gordon :: Massachusetts General Hospital<br /> # Helba, Brian :: Kitware, Inc.<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 /> # Jarecka, Dorota :: Massachusetts Institute of Technology<br /> # Jensen, Henrik G. :: University of Copenhagen<br /> # Kaczmarzyk, Jakub :: Massachusetts Institute of Technology<br /> # Kapur, Tina :: Brigham and Women's Hospital<br /> # Kennedy, David :: UMass Medical School<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 /> # Mousavi, Parvin :: Brigham and Women's Hospital<br /> # Nitsch, Jennifer :: University of Bremen<br /> # Norton, Isaiah :: Brigham and Women's Hospital<br /> # O'Donnell, Lauren :: Brigham and Women's Hospital<br /> # Onieva, Jorge :: Brigham and Women's Hospital<br /> # Oram, Louise :: The Intervention Centre-Oslo University Hospital<br /> # Padhy, Smruti :: Massachusetts Institute of Technology<br /> # Paniagua, Beatriz :: Kitware, Inc.<br /> # Parmar, Chintan :: DFCI-Harvard Medical School<br /> # Peled, Sharon :: Brigham and Women's Hospital<br /> # Pienaar, Rudolph :: Boston Children'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 /> # Prieto, Juan :: NIRAL<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 /> # Ross, James :: Brigham and Women's Hospital<br /> # Szczepankiewicz, Filip :: Lund University<br /> # Sharp, Gregory :: Massachusetts General Hospital<br /> # Sridharan, Patmaa :: University of Pennsylvania-CBICA<br /> # Szasz, Teodora :: University of Chicago<br /> # Tokuda, Junichi :: Brigham and Women's Hospital<br /> # Unadkat, Prashin :: Brigham and Women's Hospital<br /> # Van Griethuysen , Joost :: Netherlands Cancer Institute<br /> # Vidyaratne, Lasitha :: Old Dominion University<br /> # Wang, Yaofei :: Brigham and Women's Hospital<br /> # Wang, Ziyang :: Brigham and Women's Hospital<br /> # Wei, Dawei :: Brigham and Women's Hospital<br /> # Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School<br /> # Woo, Jonghye :: Massachusetts General Hospital<br /> # Xu, Wanxin :: Brigham and Women's Hospital<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, Hongtao :: Hebei General Hospital<br /> # Zhang, Miaomiao :: Massachusetts Institute of Technology<br /> # Zhang, Yuqian :: Brigham and Women's Hospital<br /> # Zhou, Haoyin :: Brigham and Women's Hospital<br /> # Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/GeodesicSegmentationandLungtumorAnalysis&diff=94711 2017-01-09T19:32:43Z

<p>Patmaa: </p> <hr /> <div>__NOTOC__<br /> &lt;gallery&gt;<br /> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br /> &lt;!-- Use the &quot;Upload file&quot; link on the left and then add a line to this list like &quot;File:MyAlgorithmScreenshot.png&quot; --&gt;<br /> &lt;/gallery&gt;<br /> <br /> ==Key Investigators==<br /> * Patmaa Sridharan - UPenn CBICA<br /> <br /> <br /> ==Project Description==<br /> <br /> {| class=&quot;wikitable&quot;<br /> ! style=&quot;text-align: left; width:27%&quot; | Objective<br /> ! style=&quot;text-align: left; width:27%&quot; | Approach and Plan<br /> ! style=&quot;text-align: left; width:27%&quot; | Progress and Next Steps<br /> |- style=&quot;vertical-align:top;&quot;<br /> |<br /> &lt;!-- Objective bullet points --&gt;<br /> <br /> Integrate two applications listed below with slicer and also focus on interaction between Slicer and CAPTk(our internal tool)<br /> * Geodesic Segmentation<br /> A generic segmentation algorithm that uses geodesic distances.<br /> <br /> * SBRT Lung Tumor segmentation and Analysis<br /> Segmentation of lung tumor from multimodal images- CT and PET using initial seed points. Analyze the segmented region using texture features and predict the nodal failure in lung.<br /> |<br /> &lt;!-- Approach and Plan bullet points --&gt;<br /> *Analyze the compatibility between the dependencies of our code with that of Slicer and solve it for smooth interaction with our application.<br /> *Enabling Slicer's GUI to provide seed point initialization required for our application. <br /> *Do a code level integration of geodesic segmentation and SBRT with Slicer.<br /> *Investigate on possibility of calling Slicer from CapTk and vice-versa by using pre-populated project files.<br /> &lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&gt;<br /> *<br /> |}<br /> <br /> ==Background and References==<br /> &lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&gt;</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week&diff=94707 2017-01-09T19:28:42Z

<p>Patmaa: /* Shape Analysis, Segmentation */</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&amp;D)<br /> *'''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]<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 /> '''''&lt;font color=&quot;maroon&quot;&gt;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.&lt;/font&gt;'''''&lt;br&gt;<br /> <br /> <br /> {{#widget:Google Calendar<br /> |id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com<br /> |timezone=America/New_York&amp;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 /> == Deep Learning and GPUs ==<br /> #[[2017 Winter Project Week/Deep Learning for Medical Image Computation| Deep Learning for Medical Image Computing]] (Tina Kapur)<br /> #[[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Tina Kapur, Ziyang Wang, Guillaume Pernelle, Paolo Zaffino)<br /> #[[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)<br /> #[[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)<br /> # [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei &quot;Ada&quot; 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 /> #[[2017 Winter Project Week/Evaluate Deep Learning for binary cancer legion classification | Evaluate Deep Learning for binary cancer lesion classification]] (Curt Lisle)<br /> #[[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)<br /> #[[2017 Winter Project Week/Population Based Image Imputation | Population Based Image Imputation]] (Adrian Dalca, Katie Bouman, Mert Sabuncu, Polina Golland)<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/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, 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/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 /> #[[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper, Teodora Szasz)<br /> #[[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)<br /> #[[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)<br /> #[[2017_Winter_Project_Week/MedicalVisualizerUsingParaViewWeb | Medical Visualizer using ParaViewWeb]] (Teodora Szasz)<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/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)<br /> #[[2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction| 3D surgical planning solution for autologous breast reconstruction]] (Michael Chae, Andras Lasso, David Garcia, Julian Smith, Warren Rozen, David Hunter-Smith)<br /> #[[2017 Winter Project Week/Intraoperative_Functional_Visualization | Visualization Concept for Intraoperative Use of Functional Mapping Data ]] (Anna Roethe, Rebekka Lauer, Prashin Unadkat, Sarah Frisken)<br /> <br /> ==dMRI==<br /> #[[2017 Winter Project Week/WhiteMatterAnalysis | Fiber endpoint analysis for neurosurgical planning]] (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-Fredrik Westin)<br /> #[[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Shun Gong, Ye Wu, Isaiah Norton, Fan Zhang, Lauren J. O'Donnell)<br /> #[[2017 Winter Project Week/DiPy_in_Slicer | WMA &amp; 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 /> ==Quantitative Imaging Informatics==<br /> #[[2017 Winter Project Week/dcmqi | dcmqi library]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)<br /> #[[2017 Winter Project Week/QuantitativeReporting | DICOM QuantitativeReporting]] (Christian Herz, Andrey Fedorov, Andras Lasso, Csaba Pinter)<br /> #[[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christophe 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 /> == Shape Analysis, Segmentation ==<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/Slicer_HoloLens | Slicer &amp; HoloLens]] (Adam Rankin, Andras Lasso)<br /> #[[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)<br /> #[[2017 Winter Project Week/GeodesicSegmentationandLungtumorAnalysis| Geodesic Segmentation and Lung tumor Analysis]] (Patmaa S,)<br /> #[[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov, Alireza Mehrtash, Christian Hansen, Teodora Szasz)<br /> #[[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)<br /> #[[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)<br /> #[[2017 Winter Project Week/CoronarySegmentationTool| Automatic and Manual Segmentation Tool of Coronary Artery from CTA imaging]] (Haoyin Zhou, Jayender Jagadeesan)<br /> <br /> == Infrastructure ==<br /> #[[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)<br /> #[[2017 Winter Project Week/ImprovementsToSegmentEditor | Improvements to Segment Editor]] (Csaba Pinter, Andras Lasso)<br /> #[[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)<br /> #[[2017 Winter Project Week/UpdatingCommunityForums | Updating Slicer Community Infrastructure (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)<br /> #[[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)<br /> #[[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Pieper)<br /> #[[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault)<br /> #[[2017 Winter Project Week/Integrative_Intraoperative_Interface | Integrative Interface for Intraoperative Software Applications ]] (Anna Roethe, Rebekka Lauer, Prashin Unadkat, Sarah Frisken)<br /> <br /> ==Training and Dissemination==<br /> #[[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)<br /> #[[2017 Winter Project Week/2017 NVIDIA Demo Contest|NVIDIA Demo Contest]] (Abdul Halabi, Abel Brown)<br /> <br /> ==Next project week==<br /> #[[2017 Winter Project Week/Next project week| Next project week]] (Paolo Zaffino, Maria Francesca Spadea, Tina Kapur)<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 /> # Aman Shboul, Zaina :: Old Dominion University<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 /> # DiPrima, Tammy :: Stony Brook University<br /> # Drouin, Simon :: Montreal Neurological Institute<br /> # Fan, Zhipeng :: Brigham and Women's Hospital<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 /> # Frisken, Sarah :: Brigham and Women's Hospital<br /> # García Mato, David :: Queen´s University / Universidad Carlos III de Madrid<br /> # Ghafoorian, Mohsen :: Brigham and Women's Hospital<br /> # Ghosh, Satrajit :: Massachusetts Institute of Technology<br /> # Girault, Alexis :: Kitware, Inc.<br /> # Golland, Polina :: Massachusetts Institute of Technology<br /> # Gollub, Randy :: Massachusetts General Hospital<br /> # Goncalves, Mathias :: Massachusetts Institute of Technology<br /> # Gong, Shun :: Brigham and Women's Hospital<br /> # Guerrier de Dumast, Priscille :: University of Michigan<br /> # Halle, Michael :: Brigham and Women's Hospital<br /> # Harris, Gordon :: Massachusetts General Hospital<br /> # Helba, Brian :: Kitware, Inc.<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 /> # Jarecka, Dorota :: Massachusetts Institute of Technology<br /> # Jensen, Henrik G. :: University of Copenhagen<br /> # Kaczmarzyk, Jakub :: Massachusetts Institute of Technology<br /> # Kapur, Tina :: Brigham and Women's Hospital<br /> # Kennedy, David :: UMass Medical School<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 /> # Padhy, Smruti :: Massachusetts Institute of Technology<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 /> # Prieto, Juan :: NIRAL<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 /> # Szczepankiewicz, Filip :: Lund University<br /> # Sharp, Gregory :: Massachusetts General Hospital<br /> # Sridharan, Patmaa :: University of Pennsylvania-CBICA<br /> # Szasz, Teodora :: University of Chicago<br /> # Unadkat, Prashin :: Brigham and Women's Hospital<br /> # Van Griethuysen , Joost :: Netherlands Cancer Institute<br /> # Vidyaratne, Lasitha :: Old Dominion University<br /> # Wang, Yaofei :: Brigham and Women's Hospital<br /> # Wang, Ziyang :: Brigham and Women's Hospital<br /> # Wei, Dawei :: Brigham and Women's Hospital<br /> # Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School<br /> # Xu, Wanxin :: Brigham and Women's Hospital<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 /> # Zhou, Haoyin :: Brigham and Women's Hospital<br /> # Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/GeodesicSegmentationandLungtumorAnalysis&diff=94655 2017-01-09T18:28:48Z

<p>Patmaa: </p> <hr /> <div>__NOTOC__<br /> &lt;gallery&gt;<br /> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br /> &lt;!-- Use the &quot;Upload file&quot; link on the left and then add a line to this list like &quot;File:MyAlgorithmScreenshot.png&quot; --&gt;<br /> &lt;/gallery&gt;<br /> <br /> ==Key Investigators==<br /> * Patmaa Sridharan (MS)<br /> <br /> <br /> ==Project Description==<br /> <br /> {| class=&quot;wikitable&quot;<br /> ! style=&quot;text-align: left; width:27%&quot; | Objective<br /> ! style=&quot;text-align: left; width:27%&quot; | Approach and Plan<br /> ! style=&quot;text-align: left; width:27%&quot; | Progress and Next Steps<br /> |- style=&quot;vertical-align:top;&quot;<br /> |<br /> &lt;!-- Objective bullet points --&gt;<br /> <br /> Integrate two applications listed below with slicer and also focus on interaction between Slicer and CAPTk(our internal tool)<br /> * Geodesic Segmentation<br /> A generic segmentation algorithm that uses geodesic distances.<br /> <br /> * SBRT Lung Tumor segmentation and Analysis<br /> Segmentation of lung tumor from multimodal images- CT and PET using initial seed points. Analyze the segmented region using texture features and predict the nodal failure in lung.<br /> |<br /> &lt;!-- Approach and Plan bullet points --&gt;<br /> *Analyze the compatibility between the dependencies of our code with that of Slicer and solve it for smooth interaction with our application.<br /> *Enabling Slicer's GUI to provide seed point initialization required for our application. <br /> *Do a code level integration of geodesic segmentation and SBRT with Slicer.<br /> *Investigate on possibility of calling Slicer from CapTk and vice-versa by using pre-populated project files.<br /> &lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&gt;<br /> *<br /> |}<br /> <br /> ==Background and References==<br /> &lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&gt;</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week&diff=94654 2017-01-09T18:28:19Z

<p>Patmaa: Undo revision 94652 by Patmaa (talk)</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&amp;D)<br /> *'''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]<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 /> '''''&lt;font color=&quot;maroon&quot;&gt;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.&lt;/font&gt;'''''&lt;br&gt;<br /> <br /> <br /> {{#widget:Google Calendar<br /> |id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com<br /> |timezone=America/New_York&amp;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 /> == Deep Learning and GPUs ==<br /> #[[2017 Winter Project Week/Deep Learning for Medical Image Computation| Deep Learning for Medical Image Computing]] (Tina Kapur)<br /> #[[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Tina Kapur, Ziyang Wang, Guillaume Pernelle, Paolo Zaffino)<br /> #[[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)<br /> #[[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)<br /> # [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei &quot;Ada&quot; 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 /> #[[2017 Winter Project Week/Evaluate Deep Learning for binary cancer legion classification | Evaluate Deep Learning for binary cancer lesion classification]] (Curt Lisle)<br /> #[[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)<br /> #[[2017 Winter Project Week/Population Based Image Imputation | Population Based Image Imputation]] (Adrian Dalca, Katie Bouman, Mert Sabuncu, Polina Golland)<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/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, 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/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 /> #[[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper, Teodora Szasz)<br /> #[[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)<br /> #[[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)<br /> #[[2017_Winter_Project_Week/MedicalVisualizerUsingParaViewWeb | Medical Visualizer using ParaViewWeb]] (Teodora Szasz)<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/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)<br /> #[[2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction| 3D surgical planning solution for autologous breast reconstruction]] (Michael Chae, Andras Lasso, Julian Smith, Warren Rozen, David Hunter-Smith)<br /> #[[2017 Winter Project Week/Intraoperative_Functional_Visualization | Visualization Concept for Intraoperative Use of Functional Mapping Data ]] (Rebekka Lauer, Anna Roethe, Prashin Unadkat, Sarah Frisken)<br /> <br /> ==dMRI==<br /> #[[2017 Winter Project Week/WhiteMatterAnalysis | Fiber endpoint analysis for neurosurgical planning]] (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-Fredrik Westin)<br /> #[[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Shun Gong, Ye Wu, Isaiah Norton, Fan Zhang, Lauren J. O'Donnell)<br /> #[[2017 Winter Project Week/DiPy_in_Slicer | WMA &amp; 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 /> ==Quantitative Imaging Informatics==<br /> #[[2017 Winter Project Week/dcmqi | dcmqi library]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)<br /> #[[2017 Winter Project Week/QuantitativeReporting | DICOM QuantitativeReporting]] (Christian Herz, Andrey Fedorov, Andras Lasso, Csaba Pinter)<br /> #[[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christophe 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 /> == Shape Analysis, Segmentation ==<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/Slicer_HoloLens | Slicer &amp; HoloLens]] (Adam Rankin, Andras Lasso)<br /> #[[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)<br /> #[[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)<br /> #[[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov, Alireza Mehrtash, Christian Hansen)<br /> #[[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)<br /> #[[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)<br /> #[[2017 Winter Project Week/CoronarySegmentationTool| Automatic and Manual Segmentation Tool of Coronary Artery from CTA imaging]] (Haoyin Zhou, Jayender Jagadeesan)<br /> <br /> == Infrastructure ==<br /> #[[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)<br /> #[[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)<br /> #[[2017 Winter Project Week/UpdatingCommunityForums | Updating Community Forums (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)<br /> #[[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)<br /> #[[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Pieper)<br /> #[[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault, Andras Lasso)<br /> #[[2017 Winter Project Week/Integrative_Intraoperative_Interface | Integrative Interface for Intraoperative Software Applications ]] (Rebekka Lauer, Anna Roethe, Prashin Unadkat, Sarah Frisken)<br /> <br /> ==Training and Dissemination==<br /> #[[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)<br /> #[[2017 Winter Project Week/2017 NVIDIA Demo Contest|NVIDIA Demo Contest]] (Abdul Halabi, Abel Brown)<br /> <br /> ==Next project week==<br /> #[[2017 Winter Project Week/Next project week| Next project week]] (Paolo Zaffino, Maria Francesca Spadea, Tina Kapur)<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 /> # Aman Shboul, Zaina :: Old Dominion University<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 /> # DiPrima, Tammy :: Stony Brook University<br /> # Drouin, Simon :: Montreal Neurological Institute<br /> # Fan, Zhipeng :: Brigham and Women's Hospital<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 /> # Frisken, Sarah :: Brigham and Women's Hospital<br /> # García Mato, David :: Queen´s University / Universidad Carlos III de Madrid<br /> # Ghafoorian, Mohsen :: Brigham and Women's Hospital<br /> # Ghosh, Satrajit :: Massachusetts Institute of Technology<br /> # Girault, Alexis :: Kitware, Inc.<br /> # Golland, Polina :: Massachusetts Institute of Technology<br /> # Gollub, Randy :: Massachusetts General Hospital<br /> # Goncalves, Mathias :: Massachusetts Institute of Technology<br /> # Gong, Shun :: Brigham and Women's Hospital<br /> # Guerrier de Dumast, Priscille :: University of Michigan<br /> # Halle, Michael :: Brigham and Women's Hospital<br /> # Harris, Gordon :: Massachusetts General Hospital<br /> # Helba, Brian :: Kitware, Inc.<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 /> # Jarecka, Dorota :: Massachusetts Institute of Technology<br /> # Jensen, Henrik G. :: University of Copenhagen<br /> # Kaczmarzyk, Jakub :: Massachusetts Institute of Technology<br /> # Kapur, Tina :: Brigham and Women's Hospital<br /> # Kennedy, David :: UMass Medical School<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 /> # Padhy, Smruti :: Massachusetts Institute of Technology<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 /> # Prieto, Juan :: NIRAL<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 /> # Szczepankiewicz, Filip :: Lund University<br /> # Sharp, Gregory :: Massachusetts General Hospital<br /> # Sridharan, Patmaa :: University of Pennsylvania-CBICA<br /> # Szasz, Teodora :: University of Chicago<br /> # Unadkat, Prashin :: Brigham and Women's Hospital<br /> # Van Griethuysen , Joost :: Netherlands Cancer Institute<br /> # Vidyaratne, Lasitha :: Old Dominion University<br /> # Wang, Yaofei :: Brigham and Women's Hospital<br /> # Wang, Ziyang :: Brigham and Women's Hospital<br /> # Wei, Dawei :: Brigham and Women's Hospital<br /> # Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School<br /> # Xu, Wanxin :: Brigham and Women's Hospital<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 /> # Zhou, Haoyin :: Brigham and Women's Hospital<br /> # Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week&diff=94652 2017-01-09T18:27:24Z

<p>Patmaa: </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&amp;D)<br /> *'''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]<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 /> '''''&lt;font color=&quot;maroon&quot;&gt;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.&lt;/font&gt;'''''&lt;br&gt;<br /> <br /> <br /> {{#widget:Google Calendar<br /> |id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com<br /> |timezone=America/New_York&amp;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 /> == Deep Learning and GPUs ==<br /> #[[2017 Winter Project Week/Deep Learning for Medical Image Computation| Deep Learning for Medical Image Computing]] (Tina Kapur)<br /> #[[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Tina Kapur, Ziyang Wang, Guillaume Pernelle, Paolo Zaffino)<br /> #[[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)<br /> #[[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)<br /> # [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei &quot;Ada&quot; 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 /> #[[2017 Winter Project Week/Evaluate Deep Learning for binary cancer legion classification | Evaluate Deep Learning for binary cancer lesion classification]] (Curt Lisle)<br /> #[[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)<br /> #[[2017 Winter Project Week/Population Based Image Imputation | Population Based Image Imputation]] (Adrian Dalca, Katie Bouman, Mert Sabuncu, Polina Golland)<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/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, 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/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 /> #[[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper, Teodora Szasz)<br /> #[[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)<br /> #[[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)<br /> #[[2017_Winter_Project_Week/MedicalVisualizerUsingParaViewWeb | Medical Visualizer using ParaViewWeb]] (Teodora Szasz)<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/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)<br /> #[[2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction| 3D surgical planning solution for autologous breast reconstruction]] (Michael Chae, Andras Lasso, Julian Smith, Warren Rozen, David Hunter-Smith)<br /> #[[2017 Winter Project Week/Intraoperative_Functional_Visualization | Visualization Concept for Intraoperative Use of Functional Mapping Data ]] (Rebekka Lauer, Anna Roethe, Prashin Unadkat, Sarah Frisken)<br /> <br /> ==dMRI==<br /> #[[2017 Winter Project Week/WhiteMatterAnalysis | Fiber endpoint analysis for neurosurgical planning]] (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-Fredrik Westin)<br /> #[[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Shun Gong, Ye Wu, Isaiah Norton, Fan Zhang, Lauren J. O'Donnell)<br /> #[[2017 Winter Project Week/DiPy_in_Slicer | WMA &amp; 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 /> ==Quantitative Imaging Informatics==<br /> #[[2017 Winter Project Week/dcmqi | dcmqi library]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)<br /> #[[2017 Winter Project Week/QuantitativeReporting | DICOM QuantitativeReporting]] (Christian Herz, Andrey Fedorov, Andras Lasso, Csaba Pinter)<br /> #[[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christophe 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 /> == Shape Analysis, Segmentation ==<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/Slicer_HoloLens | Slicer &amp; HoloLens]] (Adam Rankin, Andras Lasso)<br /> #[[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)<br /> #[[2017 Winter Project Week/IntegrationwithSlicer-GeodesicSegmentationandLungtumorAnalysis| Integration with Slicer-Geodesic Segmentation and Lung tumor Analysis]] (Patmaa S, Sarthak Pati, Ratheesh k, Mark B, Yong F, Despina K, Ragini V, Christos D)<br /> #[[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov, Alireza Mehrtash, Christian Hansen)<br /> #[[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)<br /> #[[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)<br /> #[[2017 Winter Project Week/CoronarySegmentationTool| Automatic and Manual Segmentation Tool of Coronary Artery from CTA imaging]] (Haoyin Zhou, Jayender Jagadeesan)<br /> <br /> == Infrastructure ==<br /> #[[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)<br /> #[[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)<br /> #[[2017 Winter Project Week/UpdatingCommunityForums | Updating Community Forums (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)<br /> #[[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)<br /> #[[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Pieper)<br /> #[[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault, Andras Lasso)<br /> #[[2017 Winter Project Week/Integrative_Intraoperative_Interface | Integrative Interface for Intraoperative Software Applications ]] (Rebekka Lauer, Anna Roethe, Prashin Unadkat, Sarah Frisken)<br /> <br /> ==Training and Dissemination==<br /> #[[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)<br /> #[[2017 Winter Project Week/2017 NVIDIA Demo Contest|NVIDIA Demo Contest]] (Abdul Halabi, Abel Brown)<br /> <br /> ==Next project week==<br /> #[[2017 Winter Project Week/Next project week| Next project week]] (Paolo Zaffino, Maria Francesca Spadea, Tina Kapur)<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 /> # Aman Shboul, Zaina :: Old Dominion University<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 /> # DiPrima, Tammy :: Stony Brook University<br /> # Drouin, Simon :: Montreal Neurological Institute<br /> # Fan, Zhipeng :: Brigham and Women's Hospital<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 /> # Frisken, Sarah :: Brigham and Women's Hospital<br /> # García Mato, David :: Queen´s University / Universidad Carlos III de Madrid<br /> # Ghafoorian, Mohsen :: Brigham and Women's Hospital<br /> # Ghosh, Satrajit :: Massachusetts Institute of Technology<br /> # Girault, Alexis :: Kitware, Inc.<br /> # Golland, Polina :: Massachusetts Institute of Technology<br /> # Gollub, Randy :: Massachusetts General Hospital<br /> # Goncalves, Mathias :: Massachusetts Institute of Technology<br /> # Gong, Shun :: Brigham and Women's Hospital<br /> # Guerrier de Dumast, Priscille :: University of Michigan<br /> # Halle, Michael :: Brigham and Women's Hospital<br /> # Harris, Gordon :: Massachusetts General Hospital<br /> # Helba, Brian :: Kitware, Inc.<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 /> # Jarecka, Dorota :: Massachusetts Institute of Technology<br /> # Jensen, Henrik G. :: University of Copenhagen<br /> # Kaczmarzyk, Jakub :: Massachusetts Institute of Technology<br /> # Kapur, Tina :: Brigham and Women's Hospital<br /> # Kennedy, David :: UMass Medical School<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 /> # Padhy, Smruti :: Massachusetts Institute of Technology<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 /> # Prieto, Juan :: NIRAL<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 /> # Szczepankiewicz, Filip :: Lund University<br /> # Sharp, Gregory :: Massachusetts General Hospital<br /> # Sridharan, Patmaa :: University of Pennsylvania-CBICA<br /> # Szasz, Teodora :: University of Chicago<br /> # Unadkat, Prashin :: Brigham and Women's Hospital<br /> # Van Griethuysen , Joost :: Netherlands Cancer Institute<br /> # Vidyaratne, Lasitha :: Old Dominion University<br /> # Wang, Yaofei :: Brigham and Women's Hospital<br /> # Wang, Ziyang :: Brigham and Women's Hospital<br /> # Wei, Dawei :: Brigham and Women's Hospital<br /> # Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School<br /> # Xu, Wanxin :: Brigham and Women's Hospital<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 /> # Zhou, Haoyin :: Brigham and Women's Hospital<br /> # Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/GeodesicSegmentationandLungtumorAnalysis&diff=94645 2017-01-09T18:26:02Z

<p>Patmaa: </p> <hr /> <div>__NOTOC__<br /> &lt;gallery&gt;<br /> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br /> &lt;!-- Use the &quot;Upload file&quot; link on the left and then add a line to this list like &quot;File:MyAlgorithmScreenshot.png&quot; --&gt;<br /> &lt;/gallery&gt;<br /> <br /> ==Key Investigators==<br /> * Patmaa Sridharan (MS), <br /> <br /> <br /> ==Project Description==<br /> <br /> {| class=&quot;wikitable&quot;<br /> ! style=&quot;text-align: left; width:27%&quot; | Objective<br /> ! style=&quot;text-align: left; width:27%&quot; | Approach and Plan<br /> ! style=&quot;text-align: left; width:27%&quot; | Progress and Next Steps<br /> |- style=&quot;vertical-align:top;&quot;<br /> |<br /> &lt;!-- Objective bullet points --&gt;<br /> <br /> Integrate two applications listed below with slicer and also focus on interaction between Slicer and CAPTk(our internal tool)<br /> * Geodesic Segmentation<br /> A generic segmentation algorithm that uses geodesic distances.<br /> <br /> * SBRT Lung Tumor segmentation and Analysis<br /> Segmentation of lung tumor from multimodal images- CT and PET using initial seed points. Analyze the segmented region using texture features and predict the nodal failure in lung.<br /> |<br /> &lt;!-- Approach and Plan bullet points --&gt;<br /> *Analyze the compatibility between the dependencies of our code with that of Slicer and solve it for smooth interaction with our application.<br /> *Enabling Slicer's GUI to provide seed point initialization required for our application. <br /> *Do a code level integration of geodesic segmentation and SBRT with Slicer.<br /> *Investigate on possibility of calling Slicer from CapTk and vice-versa by using pre-populated project files.<br /> &lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&gt;<br /> *<br /> |}<br /> <br /> ==Background and References==<br /> &lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&gt;</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/GeodesicSegmentationandLungtumorAnalysis&diff=94440 2017-01-06T20:47:30Z

<p>Patmaa: </p> <hr /> <div>__NOTOC__<br /> &lt;gallery&gt;<br /> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br /> &lt;!-- Use the &quot;Upload file&quot; link on the left and then add a line to this list like &quot;File:MyAlgorithmScreenshot.png&quot; --&gt;<br /> &lt;/gallery&gt;<br /> <br /> ==Key Investigators==<br /> * Sarthak Pati (MS),<br /> * Saima Rathore (PhD),<br /> * Ratheesh Kalarot (PhD),<br /> * Patmaa Sridharan (MS), <br /> * Mark Bergman (BA), <br /> * Ragini Verma (PhD),<br /> * Despina Kontos (PhD),<br /> * Yong Fan (PhD), <br /> * Paul Yushkevich (PhD),<br /> * Taki Shinohara (PhD),<br /> * Christos Davatzikos (PhD)<br /> <br /> ==Project Description==<br /> <br /> {| class=&quot;wikitable&quot;<br /> ! style=&quot;text-align: left; width:27%&quot; | Objective<br /> ! style=&quot;text-align: left; width:27%&quot; | Approach and Plan<br /> ! style=&quot;text-align: left; width:27%&quot; | Progress and Next Steps<br /> |- style=&quot;vertical-align:top;&quot;<br /> |<br /> &lt;!-- Objective bullet points --&gt;<br /> <br /> Integrate two applications listed below with slicer and also focus on interaction between Slicer and CAPTk(our internal tool)<br /> * Geodesic Segmentation<br /> A generic segmentation algorithm that uses geodesic distances.<br /> <br /> * SBRT Lung Tumor segmentation and Analysis<br /> Segmentation of lung tumor from multimodal images- CT and PET using initial seed points. Analyze the segmented region using texture features and predict the nodal failure in lung.<br /> |<br /> &lt;!-- Approach and Plan bullet points --&gt;<br /> *Analyze the compatibility between the dependencies of our code with that of Slicer and solve it for smooth interaction with our application.<br /> *Enabling Slicer's GUI to provide seed point initialization required for our application. <br /> *Do a code level integration of geodesic segmentation and SBRT with Slicer.<br /> *Investigate on possibility of calling Slicer from CapTk and vice-versa by using pre-populated project files.<br /> &lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&gt;<br /> *<br /> |}<br /> <br /> ==Background and References==<br /> &lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&gt;</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/GeodesicSegmentationandLungtumorAnalysis&diff=94439 2017-01-06T20:05:45Z

<p>Patmaa: </p> <hr /> <div>__NOTOC__<br /> &lt;gallery&gt;<br /> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br /> &lt;!-- Use the &quot;Upload file&quot; link on the left and then add a line to this list like &quot;File:MyAlgorithmScreenshot.png&quot; --&gt;<br /> &lt;/gallery&gt;<br /> <br /> ==Key Investigators==<br /> * Sarthak.P, CBICA, UPenn<br /> * Saima.R, CBICA, UPenn<br /> * Ratheesh.K CBICA, UPenn<br /> * Patmaa.S CBICA,UPenn<br /> * Mark.B , CBICA, UPenn<br /> * Ragini.V CBICA, UPenn<br /> * Despina k, CBICA, UPenn<br /> * Yong F, CBICA, UPenn<br /> * Christos.D, CBICA, UPenn<br /> <br /> ==Project Description==<br /> <br /> {| class=&quot;wikitable&quot;<br /> ! style=&quot;text-align: left; width:27%&quot; | Objective<br /> ! style=&quot;text-align: left; width:27%&quot; | Approach and Plan<br /> ! style=&quot;text-align: left; width:27%&quot; | Progress and Next Steps<br /> |- style=&quot;vertical-align:top;&quot;<br /> |<br /> &lt;!-- Objective bullet points --&gt;<br /> <br /> Integrate two applications listed below with slicer and also focus on interaction between Slicer and CAPTk(our internal tool)<br /> * Geodesic Segmentation<br /> A generic segmentation algorithm that uses geodesic distances.<br /> <br /> * SBRT Lung Tumor segmentation and Analysis<br /> Segmentation of lung tumor from multimodal images- CT and PET using initial seed points. Analyze the segmented region using texture features and predict the nodal failure in lung.<br /> |<br /> &lt;!-- Approach and Plan bullet points --&gt;<br /> *Analyze the compatibility between the dependencies of our code with that of Slicer and solve it for smooth interaction with our application.<br /> *Enabling Slicer's GUI to provide seed point initialization required for our application. <br /> *Do a code level integration of geodesic segmentation and SBRT with Slicer.<br /> *Investigate on possibility of calling Slicer from CapTk and vice-versa by using pre-populated project files.<br /> &lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&gt;<br /> *<br /> |}<br /> <br /> ==Background and References==<br /> &lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&gt;</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/GeodesicSegmentationandLungtumorAnalysis&diff=94380 2017-01-06T09:52:59Z

<p>Patmaa: </p> <hr /> <div>__NOTOC__<br /> &lt;gallery&gt;<br /> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br /> &lt;!-- Use the &quot;Upload file&quot; link on the left and then add a line to this list like &quot;File:MyAlgorithmScreenshot.png&quot; --&gt;<br /> &lt;/gallery&gt;<br /> <br /> ==Key Investigators==<br /> * Sarthak.P, CBICA, UPenn<br /> * Saima.R, CBICA, UPenn<br /> * Ratheesh.K CBICA, UPenn<br /> * Patmaa.S CBICA,UPenn<br /> * Mark.B , CBICA, UPenn<br /> * Ragini.V CBICA, UPenn<br /> * Despina k, CBICA, UPenn<br /> * Yong F, CBICA, UPenn<br /> * Christos.D, CBICA, UPenn<br /> <br /> ==Project Description==<br /> <br /> {| class=&quot;wikitable&quot;<br /> ! style=&quot;text-align: left; width:27%&quot; | Objective<br /> ! style=&quot;text-align: left; width:27%&quot; | Approach and Plan<br /> ! style=&quot;text-align: left; width:27%&quot; | Progress and Next Steps<br /> |- style=&quot;vertical-align:top;&quot;<br /> |<br /> &lt;!-- Objective bullet points --&gt;<br /> <br /> Integrate two algorthims with slicer and also focus on getting some applications available in Slicer to be callable from CapTk(out internal tool).<br /> * Geodesic Segmentation<br /> A generic segmentation algorithm that uses geodesic distances.<br /> <br /> * SBRT Lung Tumor segmentation and Analysis<br /> Segmentation of lung tumor from multimodal images- CT and PET using initial seed points. Analyze the segmented region using texture features and predict the nodal failure in lung.<br /> |<br /> &lt;!-- Approach and Plan bullet points --&gt;<br /> *Do a code level integration of this application with Slicer <br /> *Enabling Slicer's GUI to provide seed point intializations and to display the algorithm output. <br /> <br /> <br /> &lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&gt;<br /> *<br /> |}<br /> <br /> ==Background and References==<br /> &lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&gt;</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/GeodesicSegmentationandLungtumorAnalysis&diff=94379 2017-01-06T09:44:26Z

<p>Patmaa: </p> <hr /> <div>__NOTOC__<br /> &lt;gallery&gt;<br /> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br /> &lt;!-- Use the &quot;Upload file&quot; link on the left and then add a line to this list like &quot;File:MyAlgorithmScreenshot.png&quot; --&gt;<br /> &lt;/gallery&gt;<br /> <br /> ==Key Investigators==<br /> * Sarthak.P, CBICA, UPenn<br /> * Saima.R, CBICA, UPenn<br /> * Ratheesh.K CBICA, UPenn<br /> * Patmaa.S CBICA,UPenn<br /> * Mark.B , CBICA, UPenn<br /> * Ragini.V CBICA, UPenn<br /> * Despina k, CBICA, UPenn<br /> * Yong F, CBICA, UPenn<br /> * Christos.D, CBICA, UPenn<br /> <br /> ==Project Description==<br /> <br /> {| class=&quot;wikitable&quot;<br /> ! style=&quot;text-align: left; width:27%&quot; | Objective<br /> ! style=&quot;text-align: left; width:27%&quot; | Approach and Plan<br /> ! style=&quot;text-align: left; width:27%&quot; | Progress and Next Steps<br /> |- style=&quot;vertical-align:top;&quot;<br /> |<br /> &lt;!-- Objective bullet points --&gt;<br /> <br /> Integrate two algorthims with slicer and also focus on getting some applications available in Slicer to be callable from CapTk(out internal tool).<br /> * Geodesic Segmentation<br /> A generic segmentation algorithm that uses geodesic distances.<br /> <br /> * SBRT Lung Tumor segmentation and Analysis<br /> Segmentation of lung tumor from multimodal images- CT and PET using initial seed points. Analyze the segmented region using texture features and predict the nodal failure in lung.<br /> |<br /> &lt;!-- Approach and Plan bullet points --&gt;<br /> *Do a code level integration of this application with Slicer <br /> *Enabling Slicer's GUI to provide seed point intializations and to display the algorithm output. <br /> <br /> &lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&gt;<br /> *<br /> |}<br /> <br /> ==Background and References==<br /> &lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&gt;</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/GeodesicSegmentationandLungtumorAnalysis&diff=94378 2017-01-06T09:40:33Z

<p>Patmaa: </p> <hr /> <div>__NOTOC__<br /> &lt;gallery&gt;<br /> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br /> &lt;!-- Use the &quot;Upload file&quot; link on the left and then add a line to this list like &quot;File:MyAlgorithmScreenshot.png&quot; --&gt;<br /> &lt;/gallery&gt;<br /> <br /> ==Key Investigators==<br /> * Sarthak.P, CBICA, UPenn<br /> * Saima.R, CBICA, UPenn<br /> * Ratheesh.K CBICA, UPenn<br /> * Patmaa.S CBICA,UPenn<br /> * Mark.B , CBICA, UPenn<br /> * Ragini.V CBICA, UPenn<br /> * Despina k, CBICA, UPenn<br /> * Yong F, CBICA, UPenn<br /> * Christos.D, CBICA, UPenn<br /> <br /> ==Project Description==<br /> <br /> {| class=&quot;wikitable&quot;<br /> ! style=&quot;text-align: left; width:27%&quot; | Objective<br /> ! style=&quot;text-align: left; width:27%&quot; | Approach and Plan<br /> ! style=&quot;text-align: left; width:27%&quot; | Progress and Next Steps<br /> |- style=&quot;vertical-align:top;&quot;<br /> |<br /> &lt;!-- Objective bullet points --&gt;<br /> * Geodesic Segmentation<br /> A generic segmentation algorithm that uses geodesic distances.<br /> <br /> * SBRT Lung Tumor segmentation and Analysis<br /> Segmentation of lung tumor from multimodal images- CT and PET using initial seed points. Analyze the segmented region using texture features and predict the nodal failure in lung.<br /> |<br /> &lt;!-- Approach and Plan bullet points --&gt;<br /> *Do a code level integration of this application with Slicer <br /> *Enabling Slicer's GUI to provide seed point intializations and to display the algorithm output <br /> <br /> &lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&gt;<br /> *<br /> |}<br /> <br /> ==Background and References==<br /> &lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&gt;</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/GeodesicSegmentationandLungtumorAnalysis&diff=94377 2017-01-06T09:32:54Z

<p>Patmaa: Created page with &quot;__NOTOC__ &lt;gallery&gt; Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|Projects List &lt;!-- Use the &quot;Upload file&quot; link on the l...&quot;</p> <hr /> <div>__NOTOC__<br /> &lt;gallery&gt;<br /> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br /> &lt;!-- Use the &quot;Upload file&quot; link on the left and then add a line to this list like &quot;File:MyAlgorithmScreenshot.png&quot; --&gt;<br /> &lt;/gallery&gt;<br /> <br /> ==Key Investigators==<br /> * Sarthak.P, CBICA, UPenn<br /> * Saima.R, CBICA, UPenn<br /> * Ratheesh.K CBICA, UPenn<br /> * Patmaa.S CBICA,UPenn<br /> * Mark.B , CBICA, UPenn<br /> * Ragini.V CBICA, UPenn<br /> * Despina k, CBICA, UPenn<br /> * Yong F, CBICA, UPenn<br /> * Christos.D, CBICA, UPenn<br /> <br /> ==Project Description==<br /> <br /> {| class=&quot;wikitable&quot;<br /> ! style=&quot;text-align: left; width:27%&quot; | Objective<br /> ! style=&quot;text-align: left; width:27%&quot; | Approach and Plan<br /> ! style=&quot;text-align: left; width:27%&quot; | Progress and Next Steps<br /> |- style=&quot;vertical-align:top;&quot;<br /> |<br /> &lt;!-- Objective bullet points --&gt;<br /> * Geodesic Segmentation<br /> A generic segmentation algorithm that uses geodesic distances.<br /> <br /> * SBRT Lung Tumor segmentation and Analysis<br /> Segmentation of lung tumor from multimodal images- CT and PET using initial seed points. Analyze the segmented region using texture features and predict the nodal failure in lung.<br /> |<br /> &lt;!-- Approach and Plan bullet points --&gt;<br /> * Geodesic Segmentation<br /> <br /> * SBRT Lung Tumor segmentation and Analysis<br /> <br /> |<br /> &lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&gt;<br /> *<br /> |}<br /> <br /> ==Background and References==<br /> &lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&gt;</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week&diff=94376 2017-01-06T09:27:07Z

<p>Patmaa: </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&amp;D)<br /> *'''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]]<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 /> '''''&lt;font color=&quot;maroon&quot;&gt;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.&lt;/font&gt;'''''&lt;br&gt;<br /> <br /> <br /> {{#widget:Google Calendar<br /> |id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com<br /> |timezone=America/New_York&amp;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, Paolo Zaffino, Tina Kapur)<br /> * [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei &quot;Ada&quot; 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 /> * [[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)<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 /> *[[2017 Winter Project Week/Electron App to add, navigate and visualize DICOM images | Electron App to add, navigate and visualize DICOM images<br /> ]] (Smruti Padhy, Satrajit Ghosh, Mathias Goncalves)<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 /> * [[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)<br /> * [[2017 Winter Project Week/CoronarySegmentationTool| Automatic and Manual Segmentation Tool of Coronary Artery from CTA imaging]] (Haoyin Zhou, Jayender Jagadeesan)<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 /> ==Quantitative Imaging Informatics==<br /> * [[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)<br /> * [[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)<br /> <br /> == Visualization ==<br /> * [[2017 Winter Project Week/Slicer_HoloLens | Slicer &amp; HoloLens]] (Adam Rankin, Andras Lasso)<br /> == Infrastructure ==<br /> * [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)<br /> * [[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)<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 /> * [[2017 Winter Project Week/UpdatingCommunityForums | Updating Community Forums (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)<br /> <br /> ==To be Categorized==<br /> <br /> * [[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Piper)<br /> * [[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault, Andras Lasso)<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/2017TutorialContest| Tutorial contest]] (Sonia Pujol)<br /> * [[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)<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>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Project_Week_Template&diff=94375 2017-01-06T09:22:00Z

<p>Patmaa: Undo revision 94374 by Patmaa (talk)</p> <hr /> <div>__NOTOC__<br /> &lt;gallery&gt;<br /> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br /> &lt;!-- Use the &quot;Upload file&quot; link on the left and then add a line to this list like &quot;File:MyAlgorithmScreenshot.png&quot; --&gt;<br /> &lt;/gallery&gt;<br /> <br /> ==Key Investigators==<br /> &lt;!-- Add a bulleted list of investigators and their institutions here --&gt;<br /> <br /> ==Project Description==<br /> {| class=&quot;wikitable&quot;<br /> ! style=&quot;text-align: left; width:27%&quot; | Objective<br /> ! style=&quot;text-align: left; width:27%&quot; | Approach and Plan<br /> ! style=&quot;text-align: left; width:27%&quot; | Progress and Next Steps<br /> |- style=&quot;vertical-align:top;&quot;<br /> |<br /> &lt;!-- Objective bullet points --&gt;<br /> * <br /> |<br /> &lt;!-- Approach and Plan bullet points --&gt;<br /> * <br /> |<br /> &lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&gt;<br /> *<br /> |}<br /> <br /> ==Background and References==<br /> &lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&gt;</div>

Patmaa https://www.na-mic.org/w/index.php?title=2017_Project_Week_Template&diff=94374 2017-01-06T09:14:30Z

<p>Patmaa: </p> <hr /> <div>__NOTOC__<br /> &lt;gallery&gt;<br /> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br /> &lt;!-- Use the &quot;Upload file&quot; link on the left and then add a line to this list like &quot;File:MyAlgorithmScreenshot.png&quot; --&gt;<br /> &lt;/gallery&gt;<br /> <br /> ==Key Investigators==<br /> * Sarthak.P, CBICA, UPenn<br /> * Saima.R, CBICA, UPenn<br /> * Ratheesh.K CBICA, UPenn<br /> * Patmaa.S CBICA,UPenn<br /> * Mark.B , CBICA, UPenn<br /> * Ragini.V CBICA, UPenn<br /> * Despina k, CBICA, UPenn<br /> * Yong F, CBICA, UPenn<br /> * Christos.D, CBICA, UPenn<br /> <br /> ==Project Description==<br /> <br /> {| class=&quot;wikitable&quot;<br /> ! style=&quot;text-align: left; width:27%&quot; | Objective<br /> ! style=&quot;text-align: left; width:27%&quot; | Approach and Plan<br /> ! style=&quot;text-align: left; width:27%&quot; | Progress and Next Steps<br /> |- style=&quot;vertical-align:top;&quot;<br /> |<br /> &lt;!-- Objective bullet points --&gt;<br /> * Geodesic Segmentation<br /> A generic segmentation algorithm that uses geodesic distances <br /> <br /> * SBRT Lung Tumor segmentation and Analysis<br /> |<br /> &lt;!-- Approach and Plan bullet points --&gt;<br /> * Geodesic Segmentation<br /> <br /> * SBRT Lung Tumor segmentation and Analysis<br /> <br /> |<br /> &lt;!-- Progress and Next steps bullet points (fill out at the end of project week) --&gt;<br /> *<br /> |}<br /> <br /> ==Background and References==<br /> &lt;!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --&gt;</div>

Patmaa