NAMIC Wiki - User contributions [en]

2017 Winter Project Week/2017 NVIDIA Demo Contest

2017-01-13T16:32:44Z

Mehrtash:

2017 Winter Project Week/2017 NVIDIA Demo Contest

2017-01-13T16:31:39Z

Mehrtash:

2017 Winter Project Week/2017 NVIDIA Demo Contest

2017-01-13T16:30:02Z

Mehrtash:

2017 Winter Project Week/DeepInfer

2017-01-13T14:56:17Z

Mehrtash:

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

File:Deepinfer arch.png|The initial prototype of the DeepInfer with OpenIGTLink.
</gallery>

==Key Investigators==

* Alireza Mehrtash (BWH, UBC)
* Mehran Pesteie (UBC)
* Yang (Silvia) Yixin (Tianjin University)
* Tina Kapur (BWH)
* Sandy Wells (BWH)
* Purang Abolmaesumi (UBC)
* Andriy Fedorov (BWH)

==Background and References==
Deep learning models have outperformed some of the previous state-of-the-art approaches in medical image analysis. However, utilizing deep models during image-guided therapy procedures requires integration of several software components which is often a tedious taskfor clinical researchers. Hence, there is a gap between the state-of-the-art machine learning research and itsapplication in clinical setup.

DeepInfer enables 3D Slicer to connect to a powerful processing back-end either on the local machine or a remote processing server. Utilizing a repository of pre-trained, task-specific models, DeepInfer allows clinical researchers and biomedical engineers to choose and deploy a model on new data without the need for software development or configuration.

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Redesign the architecture of the toolkit considering Docker as the deep learning model deployment engine.
* Discuss about the implementation details of Slicer side.
* Planning the structure of the cloud model repository.
|

* Study and evaluate different approaches for passing input images and prediction results between Slicer and Docker including CLI.
* Decide about the necessary fields in the metadata of the stored models.
* Implement Slicer side to talk with Docker.
|

* Helpful discussions about the design of Slicer part.
* We will use Github as the repository for storing the metadata information about different trained models. The repository will be the same as Slicer extensions index repository. The maintainers of the models will make pull requests to put their model meta data on the repository.
* The metadata file fields: Author, Institution, Organ, Task, Modality, Accuracy, Training methodology, license, data source, network details, docker image location, version.
* Slicer side scenario for using a deep model:
* Docker generates the XML of CLI
* Slicer reads the XML (using QSlicerCLIModule) and generates the required GUI for the task
* User selects input/output
* The input images would be saved to a temporary directory
* The docker will be run with the parameters on the mounted temporary directory
* Slicer waits for completion of the task.
* Docker saves the results of processing to the temp directory
* Slicer loads the results.
* Next steps
* Implement instantiation of CLI UI from the XML description in Python.
* Test the slicer/docker communication on our prostate-segmenter model.

|}

2017 Winter Project Week/DeepInfer

2017-01-13T14:55:52Z

Mehrtash:

2017 Winter Project Week/DeepInfer

2017-01-13T14:39:45Z

Mehrtash: /* Project Description */

2017 Winter Project Week/DeepInfer

2017-01-13T14:32:30Z

Mehrtash:

2017 Winter Project Week/DeepInfer

2017-01-13T14:32:09Z

Mehrtash:

2017 Winter Project Week/DeepInfer

2017-01-13T14:29:14Z

Mehrtash:

__NOTOC__

==Key Investigators==

* Alireza Mehrtash (BWH, UBC)
* Mehran Pesteie (UBC)
* Yang (Silvia) Yixin (Tianjin University)
* Tina Kapur (BWH)
* Sandy Wells (BWH)
* Purang Abolmaesumi (UBC)
* Andriy Fedorov (BWH)

==Background and References==
Deep learning models have outperformed some of the previous state-of-the-art approaches in medical image analysis. However, utilizing deep models during image-guided therapy procedures requires integration of several software components which is often a tedious taskfor clinical researchers. Hence, there is a gap between the state-of-the-art machine learning research and itsapplication in clinical setup.

DeepInfer enables 3D Slicer to connect to a powerful processing back-end either on the local machine or a remote processing server. Utilizing a repository of pre-trained, task-specific models, DeepInfer allows clinical researchers and biomedical engineers to choose and deploy a model on new data without the need for software development or configuration.

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Redesign the architecture of the toolkit considering Docker as the deep learning model deployment engine.
* Discuss about the implemntation details of Slicer side.
* Planning the structure of the cloud model repository.
|

*
|

*
|}

2017 Winter Project Week/Dinner

2017-01-12T17:11:25Z

Mehrtash: /* RSVPs */

==Dinner Specs==

*Date and Time: Thursday, January 12, 6pm
*Location: Desi Dhaba, 401 Massachusetts Ave, Cambridge (about 10 minute walk from MIT)
*Food: Indian. Menu: Goat curry, chicken tikka masala, chana masala (vegan), saag paneer (veg), naan, rice
*Cost: $25 - CASH ONLY! To be given to Katie Mastrogiacomo (kmast@bwh) during the week. She will provide receipts.
*Drinks: tap water is included in this price. Beyond that each person pays individually for their drinks.

==RSVPs==
# Adam Rankin- pd.
# Andras Lasso
# Curt Lisle- pd.
# Tina Kapur- pd. +7 (Ashley, Ada, Sylvia, Anne, Ziyang, Jerry, Dawai)
# Andrey Fedorov
# Csaba Pinter- pd.
# Simon Drouin- pd.
# Henrik G. Jensen- pd.
# Beatriz Paniagua- pd.
# Beatriz Paniagua's +1 - pd.
# Hans Meine- pd.
# Johan Andruejol- pd.
# Katie Mastrogiacomo- pd.
# Ron Kikinis- pd.
# Zora Kikinis- pd.
# Brian Helba- pd.
# Jennifer Nitsch- pd.
# Jean-Christophe Fillion-Robin- pd.
# Anneke Meyer - pd.
# Erik Ziegler
# Francois Rheault- pd.
# Rebekka Lauer- pd.
# Janne Beate Bakeng- pd.
# Louise Oram- pd.
# Teodora Szasz - pd.
# Danielle Pace- pd.
# David Garcia- pd.
# James Fishbaugh- pd.
# Sungmin Hong- pd.
# Mohsen Ghafoorian
# Alexis Girault- pd.
# Alexis Girault + 1- pd.
# Zhang hongtao
# Sonia Pujol

2017 Winter Project Week/DeepInfer

2017-01-09T18:26:48Z

Mehrtash:

__NOTOC__

==Key Investigators==

* Alireza Mehrtash (BWH, UBC)
* Mehran Pesteie (UBC)
* Yang (Silvia) Yixin (Tianjin University)
* Tina Kapur (BWH)
* Sandy Wells (BWH)
* Purang Abolmaesumi (UBC)
* Andriy Fedorov (BWH)

==Background and References==
Deep learning models have outperformed some of the previous state-of-the-art approaches in medical image analysis. However, utilizing deep models during image-guided therapy procedures requires integration of several software components which is often a tedious taskfor clinical researchers. Hence, there is a gap between the state-of-the-art machine learning research and itsapplication in clinical setup.

DeepInfer enables 3D Slicer to connect to a powerful processing back-end either on the local machine or a remote processing server. Utilizing a repository of pre-trained, task-specific models, DeepInfer allows clinical researchers and biomedical engineers to choose and deploy a model on new data without the need for software development or configuration.

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Develop the client side as a Slicer extension.
* Develop the server side.
* Train a diabetic retinopathy classifier and add the model to the DeepInfer model repository.
|

*
|

*
|}

2017 Winter Project Week/DeepInfer

2017-01-09T18:26:32Z

Mehrtash:

__NOTOC__

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

File:Deepinfer_arch.png|DeepInfer Architecture
</gallery>

==Key Investigators==

* Alireza Mehrtash (BWH, UBC)
* Mehran Pesteie (UBC)
* Yang (Silvia) Yixin (Tianjin University)
* Tina Kapur (BWH)
* Sandy Wells (BWH)
* Purang Abolmaesumi (UBC)
* Andriy Fedorov (BWH)

==Background and References==
Deep learning models have outperformed some of the previous state-of-the-art approaches in medical image analysis. However, utilizing deep models during image-guided therapy procedures requires integration of several software components which is often a tedious taskfor clinical researchers. Hence, there is a gap between the state-of-the-art machine learning research and itsapplication in clinical setup.

DeepInfer enables 3D Slicer to connect to a powerful processing back-end either on the local machine or a remote processing server. Utilizing a repository of pre-trained, task-specific models, DeepInfer allows clinical researchers and biomedical engineers to choose and deploy a model on new data without the need for software development or configuration.

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Develop the client side as a Slicer extension.
* Develop the server side.
* Train a diabetic retinopathy classifier and add the model to the DeepInfer model repository.
|

*
|

*
|}

File:Deepinfer arch.png

2017-01-09T18:16:22Z

Mehrtash:

2017 Winter Project Week/DeepInfer

2017-01-09T18:15:47Z

Mehrtash: /* Background and References */

2017 Winter Project Week/Dinner

2017-01-06T17:54:15Z

Mehrtash:

==Dinner Specs==

*Date and Time: Thursday, January 12, 6pm
*Location: Desi Dhaba, 401 Massachusetts Ave, Cambridge (about 10 minute walk from MIT)
*Food: Indian. (Veg and non-veg options, naan, rice)
*Cost: (TBD, last year was $25)
*Drinks: tap water is included in this price. Beyond that each person pays individually for their drinks.

==RSVPs==

#Curt Lisle
#Tina Kapur
# Andrey Fedorov
# Csaba Pinter
# Simon Drouin
# Alireza Mehrtash

2017 Winter Project Week

2017-01-05T00:59:53Z

Mehrtash:

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

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

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

==Logistics==

*'''Dates:''' January 9-13, 2017.
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]

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

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

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

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

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

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

==Conference Calls for Preparation==

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

==Calendar==

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

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

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

='''Projects'''=

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

== Learning and GPUs ==

* [[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Ziyang Wang, Guillaume Pernelle, Paolo Zaffino, Tina Kapur)
* [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)
* [[2017 Winter Project Week/An open-source tool to classify TMJ OA condyles | An open-source tool to classify TMJ OA condyles]] (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)
* [[2017 Winter Project Week/DeepInfer| DeepInfer: Open-source Deep Learning Deployment Toolkit]] (Alireza Mehrtash, Mehran Pesteie, Yang (Silvia) Yixin, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)

== Web Technologies ==
* [[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
* [[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper)
* [[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)
* [[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
* [[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)

== IGT: Navigation, Robotics, Surgical Planning ==
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
* [[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)
* [[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]] (Peter Traneus Anderson)
* [[2017 Winter Project Week/OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab | OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab ]] (Scheherazade Kraß (Shery), Junichi Tokuda, Longquan Chen, )
* [[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
* [[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov)
* [[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)
* [[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)

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

==Quantitative Imaging Infrastructure for Cancer Diagnosis==
* [[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)
* [[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)

== Visualization ==
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)
== Infrastructure ==
* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy refactoring]] (Csaba Pinter)
* [[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
* [[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)
* [[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)

==To be Categorized==

* [[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Piper)
* [[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault, Andras Lasso)
* [[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
* [[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
* [[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)
* [[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
* [[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)

= '''Registrants''' =

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

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

2017 Winter Project Week

2017-01-05T00:56:58Z

Mehrtash:

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

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

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

==Logistics==

*'''Dates:''' January 9-13, 2017.
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]

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

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

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

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

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

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

==Conference Calls for Preparation==

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

==Calendar==

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

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

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

='''Projects'''=

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

== Learning and GPUs ==

* [[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Ziyang Wang, Guillaume Pernelle, Paolo Zaffino, Tina Kapur)
* [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)
* [[2017 Winter Project Week/An open-source tool to classify TMJ OA condyles | An open-source tool to classify TMJ OA condyles]] (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)
* [[2017 Winter Project Week/DeepInfer| Open-source Deep Learning Deployment Toolkit]] (Alireza Mehrtash, Mehran Pesteie, Yang (Silvia) Yixin, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)

== Web Technologies ==
* [[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
* [[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper)
* [[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)
* [[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
* [[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)

== IGT: Navigation, Robotics, Surgical Planning ==
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
* [[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)
* [[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]] (Peter Traneus Anderson)
* [[2017 Winter Project Week/OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab | OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab ]] (Scheherazade Kraß (Shery), Junichi Tokuda, Longquan Chen, )
* [[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
* [[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov)
* [[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)
* [[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)

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

==Quantitative Imaging Infrastructure for Cancer Diagnosis==
* [[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)
* [[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)

== Visualization ==
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)
== Infrastructure ==
* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy refactoring]] (Csaba Pinter)
* [[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
* [[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)
* [[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)

==To be Categorized==

* [[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Piper)
* [[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault, Andras Lasso)
* [[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
* [[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
* [[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)
* [[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
* [[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)

= '''Registrants''' =

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

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

2017 Winter Project Week/DeepInfer

2017-01-05T00:55:49Z

Mehrtash:

2017 Winter Project Week/DeepInfer

2017-01-05T00:44:30Z

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

2017 Winter Project Week

2017-01-05T00:35:43Z

Mehrtash:

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

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

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

==Logistics==

*'''Dates:''' January 9-13, 2017.
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]

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

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

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

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

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

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

==Conference Calls for Preparation==

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

==Calendar==

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

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

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

='''Projects'''=

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

== Learning and GPUs ==

* [[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Ziyang Wang, Guillaume Pernelle, Paolo Zaffino, Tina Kapur)
* [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)
* [[2017 Winter Project Week/An open-source tool to classify TMJ OA condyles | An open-source tool to classify TMJ OA condyles]] (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)
* [[2017 Winter Project Week/DeepInfer| Open-source Deep Learning Deployment Toolkit]] (Alireza Mehrtash, Mehran Pesteie, Silvia, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)

== Web Technologies ==
* [[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)
* [[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper)
* [[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)
* [[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
* [[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)

== IGT: Navigation, Robotics, Surgical Planning ==
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)
* [[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)
* [[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]] (Peter Traneus Anderson)
* [[2017 Winter Project Week/OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab | OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab ]] (Scheherazade Kraß (Shery), Junichi Tokuda, Longquan Chen, )
* [[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)
* [[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov)
* [[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)
* [[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)

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

==Quantitative Imaging Infrastructure for Cancer Diagnosis==
* [[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)
* [[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)

== Visualization ==
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)
== Infrastructure ==
* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy refactoring]] (Csaba Pinter)
* [[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)
* [[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)
* [[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)

==To be Categorized==

* [[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Piper)
* [[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault, Andras Lasso)
* [[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)
* [[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)
* [[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)
* [[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
* [[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)

= '''Registrants''' =

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

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

2015 Winter Project Week:DICOM Module Improvements

2015-01-09T16:41:18Z

Mehrtash: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Alireza Mehrtash, BWH
* Andrey Fedorov, BWH
* Ron Kikinis, BWH
* Steve Pieper, Isomics

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Study and try to fix some of the known bugs in Slicer DICOM Module to improve usability of DICOM browser.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

* Sort order for DICOM browser content by most recent [1]
* Populating of DICOM browser tables after start-up [2]
* Remove single series of an exam in the DICOM browser [3]

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* We took a look at the ctkDICOMDatabase schema. The schema organized according the the DICOM standard hierarchy Patient/ Study/ Series/ Images. On event of adding dicom object to database for every image object insertTimeStamp is stored in the database. One suggested design would be to assign the insertTimeStamp of the first image of a specific series to the whole correspondent series and add a column to the series table which provides the option for user to sort the table based on the insert time. For studies and patients tables columns can be add that shows the latest time instance of the last added series and study respectively. This probably requires changing the database schema and changes in ctkDICOMBrowser.

</div>
</div>
===References===
* [1] [http://na-mic.org/Mantis/view.php?id=3770 3770: Sort order for DICOM browser content by most recent]
* [2] [http://na-mic.org/Mantis/view.php?id=3769 3769: All series are shown when DICOM browser is launched for the first time ... ]
* [3] [http://na-mic.org/Mantis/view.php?id=3792 3792: Remove one series of an exam in the dicom menu]

2015 Winter Project Week:Slice View Annotations

2015-01-09T16:36:24Z

Mehrtash:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
File:Colorbar.PNG|colorbar fixed for small ranges.

</gallery>

==Key Investigators==
* Alireza Mehrtash, BWH
* Andrey Fedorov, BWH
* Steve Pieper, Isomics

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improve usability of Slice view annotations.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

* Color bar issue in displaying window/level in the range of [0,1]
* Studying the option for moving slice view annotation settings from Data-probe module to slice view controller widget and to invoke configuration dialog per slice view.
* Adding the feature of orientation marker to slice view annotations [1].

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Issue #3881 for displaying small window width values in color bar [2] was resolved and the fix is merged into slicer.
* After reviewing code and discussions with Steve and Andriy, we decided to move the slice view annotations settings to applications settings instead of slice view controller.
</div>
</div>
===References===
* [1] [https://github.com/mehrtash/OrientationFigure Orientation Figure Github page]
* [2] http://na-mic.org/Mantis/view.php?id=3881

2015 Winter Project Week:Bolus Arrival Time Estimation in PK Modelling

2015-01-09T16:34:37Z

Mehrtash:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
File:Peak-gradient.png|[Peak gradient method on one of the prostate cases (whole gland)]

</gallery>

==Key Investigators==
* Alireza Mehrtash, BWH
* Andrey Fedorov, BWH
* Jim Miller, GE Global Research
* Sandeep Gupta, GE Global Research

==Project Description==
<div style="margin: 20px;">
PharmacoKinetics (PK) analysis of DCE-MRI images requires estimation of bolus arrival time (BAT). Inaccuracies in estimation of BAT can affect the results of derived PK metrics. The goal of this project is to improve the current implementation of BAT estimation in Slicer's PK Modelling extension [1]. The current implemented method in Slicer measures the time point before the peak gradient arrival and set it as BAT.
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Study current implementation of BAT detection in PK Modelling software in available clinical data for prostate and breast cancers.
* Investigate possible solutions to improve the robustness of BAT detection in PK Modelling.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Add option for manual assignment of BAT separately for AIF (Arterial Input Function) and TRF (Tissue Residual Function).
* Compare different bat detection methods: LL ([1]), PL ([2]) and slicer's methods (PG) in detection of AIF BAT and TRF BAT in whole prostate gland [3].

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* PG method was used to detect BAT in QIN Prostate and OHSU Breast DCE-MRI data sets.
* On prostate data sets we extracted the AIF from the left femoral artery and then we used LL, PL and PG methods to detect BAT. Due to the sharp rise in AIF curve all three methods successfully detect BAT in AIF signal (%100 agreement on 9 cases).
* By studying BAT maps for the whole prostate gland we observed that for tissue residual function (TRF) concentration curves in areas with slower uptake curves, there is higher chance that PG method trapping in local minima. However some of the curves in which PG fails are voxels which are not good candidates for Tofts modelling (This could include necrotic ROIs). For future improvement of PG method Jim suggested to inpaint the false BATs by using the neighborhood information.
* Since PG works correctly on AIF detection, we are going to use manual assignment for TRF only and use automatic bat detection for AIF.

</div>
</div>
===References===
* [1] [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/PkModeling PK Modelling extension documentation page]
* [2] [http://www.ncbi.nlm.nih.gov/pubmed/12696805 An automatic approach for estimating bolus arrival time in dynamic contrastMRI using piecewise continuous regression models]
* [3] [http://www.ncbi.nlm.nih.gov/pubmed/19097111 Improved bolus arrival time and arterial input function estimation for tracer kinetic analysis in DCE-MRI.]
* [4] [http://www.ncbi.nlm.nih.gov/pubmed/24772219 Variations of dynamic contrast-enhanced magnetic resonance imaging in evaluation of breast cancer therapy response: a multicenter data analysis challenge.]

File:Peak-gradient.png

2015-01-09T16:33:15Z

Mehrtash:

2015 Winter Project Week:Bolus Arrival Time Estimation in PK Modelling

2015-01-09T16:30:52Z

Mehrtash:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Alireza Mehrtash, BWH
* Andrey Fedorov, BWH
* Jim Miller, GE Global Research
* Sandeep Gupta, GE Global Research

==Project Description==
<div style="margin: 20px;">
PharmacoKinetics (PK) analysis of DCE-MRI images requires estimation of bolus arrival time (BAT). Inaccuracies in estimation of BAT can affect the results of derived PK metrics. The goal of this project is to improve the current implementation of BAT estimation in Slicer's PK Modelling extension [1]. The current implemented method in Slicer measures the time point before the peak gradient arrival and set it as BAT.
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Study current implementation of BAT detection in PK Modelling software in available clinical data for prostate and breast cancers.
* Investigate possible solutions to improve the robustness of BAT detection in PK Modelling.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Add option for manual assignment of BAT separately for AIF (Arterial Input Function) and TRF (Tissue Residual Function).
* Compare different bat detection methods: LL ([1]), PL ([2]) and slicer's methods (PG) in detection of AIF BAT and TRF BAT in whole prostate gland [3].

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* PG method was used to detect BAT in QIN Prostate and OHSU Breast DCE-MRI data sets.
* On prostate data sets we extracted the AIF from the left femoral artery and then we used LL, PL and PG methods to detect BAT. Due to the sharp rise in AIF curve all three methods successfully detect BAT in AIF signal (%100 agreement on 9 cases).
* By studying BAT maps for the whole prostate gland we observed that for tissue residual function (TRF) concentration curves in areas with slower uptake curves, there is higher chance that PG method trapping in local minima. However some of the curves in which PG fails are voxels which are not good candidates for Tofts modelling (This could include necrotic ROIs). For future improvement of PG method Jim suggested to inpaint the false BATs by using the neighborhood information.
* Since PG works correctly on AIF detection, we are going to use manual assignment for TRF only and use automatic bat detection for AIF.

</div>
</div>
===References===
* [1] [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/PkModeling PK Modelling extension documentation page]
* [2] [http://www.ncbi.nlm.nih.gov/pubmed/12696805 An automatic approach for estimating bolus arrival time in dynamic contrastMRI using piecewise continuous regression models]
* [3] [http://www.ncbi.nlm.nih.gov/pubmed/19097111 Improved bolus arrival time and arterial input function estimation for tracer kinetic analysis in DCE-MRI.]
* [4] [http://www.ncbi.nlm.nih.gov/pubmed/24772219 Variations of dynamic contrast-enhanced magnetic resonance imaging in evaluation of breast cancer therapy response: a multicenter data analysis challenge.]

2015 Winter Project Week:Bolus Arrival Time Estimation in PK Modelling

2015-01-09T16:30:34Z

Mehrtash:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Alireza Mehrtash, BWH
* Andrey Fedorov, BWH
* Jim Miller, GE Global Research
* Sandeep Gupta, GE Global Research

==Project Description==
<div style="margin: 20px;">
PharmacoKinetics (PK) analysis of DCE-MRI images requires estimation of bolus arrival time (BAT). Inaccuracies in estimation of BAT can affect the results of derived PK metrics. The goal of this project is to improve the current implementation of BAT estimation in Slicer's PK Modelling extension [1]. The current implemented method in Slicer measures the time point before the peak gradient arrival and set it as BAT.
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Study current implementation of BAT detection in PK Modelling software in available clinical data for prostate and breast cancers.
* Investigate possible solutions to improve the robustness of BAT detection in PK Modelling.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Add option for manual assignment of BAT separately for AIF (Arterial Input Function) and TRF (Tissue Residual Function).
* Compare different bat detection methods: LL ([1]), PL ([2]) and slicer's methods (PG) in detection of AIF BAT and TRF BAT in whole prostate gland [3].

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* PG method was used to detect BAT in QIN Prostate and OHSU Breast DCE-MRI data sets.
* On prostate data sets we extracted the AIF from the left femoral artery and then we used LL, PL and PG methods to detect BAT. Due to the sharp rise in AIF curve all three methods successfully detect BAT in AIF signal (%100 agreement on 9 cases).
* By studying BAT maps for the whole prostate gland we observed that for tissue residual function (TRF) concentration curves in areas with slower uptake curves, there is higher chance that PG method trapping in local minima. However some of the curves in which PG fails are voxels which are not good candidates for Tofts modelling (This could include necrotic ROIs). For future improvement of PG method Jim suggested to inpaint the false BATs by using the neighborhood information.
* Since PG works correctly on AIF detection, we are going to use manual assignment for TRF only and use automatic bat detection for AIF.

</div>
</div>
===References===
* [1] [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/PkModeling PK Modelling extension documentation page]
* [3] [http://www.ncbi.nlm.nih.gov/pubmed/19097111 Improved bolus arrival time and arterial input function estimation for tracer kinetic analysis in DCE-MRI.]
* [2] [http://www.ncbi.nlm.nih.gov/pubmed/12696805 An automatic approach for estimating bolus arrival time in dynamic contrastMRI using piecewise continuous regression models]
* [4] [http://www.ncbi.nlm.nih.gov/pubmed/24772219 Variations of dynamic contrast-enhanced magnetic resonance imaging in evaluation of breast cancer therapy response: a multicenter data analysis challenge.]

2015 Winter Project Week:Bolus Arrival Time Estimation in PK Modelling

2015-01-09T16:28:05Z

Mehrtash:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Alireza Mehrtash, BWH
* Andrey Fedorov, BWH
* Jim Miller, GE Global Research
* Sandeep Gupta, GE Global Research

==Project Description==
<div style="margin: 20px;">
PharmacoKinetics (PK) analysis of DCE-MRI images requires estimation of bolus arrival time (BAT). Inaccuracies in estimation of BAT can affect the results of derived PK metrics. The goal of this project is to improve the current implementation of BAT estimation in Slicer's PK Modelling extension [1]. The current implemented method in Slicer measures the time point before the peak gradient arrival and set it as BAT.
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Study current implementation of BAT detection in PK Modelling software in available clinical data for prostate and breast cancers.
* Investigate possible solutions to improve the robustness of BAT detection in PK Modelling.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Add option for manual assignment of BAT separately for AIF (Arterial Input Function) and TRF (Tissue Residual Function).
* Compare different bat detection methods: LL ([1]), PL ([2]) and slicer's methods (PG) in detection of AIF BAT and TRF BAT in whole prostate gland [3].

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* PG method was used to detect BAT in QIN Prostate and OHSU Breast DCE-MRI data sets.
* On prostate data sets we extracted the AIF from the left femoral artery and then we used LL, PL and PG methods to detect BAT. Due to the sharp rise in AIF curve all three methods successfully detect BAT in AIF signal (%100 agreement on 9 cases).
* By studying BAT maps for the whole prostate gland we observed that for tissue residual function (TRF) concentration curves in areas with slower uptake curves, there is higher chance that PG method trapping in local minima. However some of the curves in which PG fails are voxels which are not good candidates for Tofts modelling (This could include necrotic ROIs). For future improvement of PG method Jim suggested to inpaint the false BATs by using the neighborhood information.
* Since PG works correctly on AIF detection, we are going to use manual assignment for TRF only and use automatic bat detection for AIF.

</div>
</div>
===References===
* [1] [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/PkModeling PK Modelling extension documentation page]
* [2] [http://www.ncbi.nlm.nih.gov/pubmed/19097111 Improved bolus arrival time and arterial input function estimation for tracer kinetic analysis in DCE-MRI.]
* [3]
* [4] [http://www.ncbi.nlm.nih.gov/pubmed/24772219 Variations of dynamic contrast-enhanced magnetic resonance imaging in evaluation of breast cancer therapy response: a multicenter data analysis challenge.]

2015 Winter Project Week:DICOM Module Improvements

2015-01-09T16:11:37Z

Mehrtash:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Alireza Mehrtash, BWH
* Andrey Fedorov, BWH
* Ron Kikinis, BWH
* Steve Pieper, Isomics

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Study and try to fix some of the known bugs in Slicer DICOM Module to improve usability of DICOM browser.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

* Sort order for DICOM browser content by most recent [1]
* Populating of DICOM browser tables after start-up [2]
* Remove single series of an exam in the DICOM browser [3]

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* For issue #3770: We took a look at the ctkDICOMDatabase schema. The schema organized according the the DICOM standard hierarchy Patient/ Study/ Series/ Images. On event of adding dicom object to database for every image object insertTimeStamp is stored in the database. One suggested design would be to assign the insertTimeStamp of the first image of a specific series to the whole correspondent series and add a column to the series table which provides the option for user to sort the table based on the insert time. For studies and patients tables columns can be add that shows the latest time instance of the last added series and study respectively. This probably requires changing the database schema and changes in ctkDICOMBrowser.
*
*
</div>
</div>
===References===
* [1] [http://na-mic.org/Mantis/view.php?id=3770 3770: Sort order for DICOM browser content by most recent]
* [2] [http://na-mic.org/Mantis/view.php?id=3769 3769: All series are shown when DICOM browser is launched for the first time ... ]
* [3] [http://na-mic.org/Mantis/view.php?id=3792 3792: Remove one series of an exam in the dicom menu]

2015 Winter Project Week:Slice View Annotations

2015-01-09T15:50:41Z

Mehrtash:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
File:Colorbar.PNG|[colorbar fixed for small ranges.]

</gallery>

==Key Investigators==
* Alireza Mehrtash, BWH
* Andrey Fedorov, BWH
* Steve Pieper, Isomics

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improve usability of Slice view annotations.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

* Color bar issue in displaying window/level in the range of [0,1]
* Studying the option for moving slice view annotation settings from Data-probe module to slice view controller widget and to invoke configuration dialog per slice view.
* Adding the feature of orientation marker to slice view annotations [1].

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Issue #3881 for displaying small window width values in color bar [2] was resolved and the fix is merged into slicer.
* After reviewing code and discussions with Steve and Andriy, we decided to move the slice view annotations settings to applications settings instead of slice view controller.
</div>
</div>
===References===
* [1] [https://github.com/mehrtash/OrientationFigure Orientation Figure Github page]
* [2] http://na-mic.org/Mantis/view.php?id=3881

2015 Winter Project Week:Slice View Annotations

2015-01-09T15:38:46Z

Mehrtash:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
File:Colorbar.PNG|[colorbar fixed for small ranges.]

</gallery>

==Key Investigators==
* Alireza Mehrtash, BWH
* Andrey Fedorov, BWH
* Steve Pieper, Isomics

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improve usability of Slice view annotations.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

* Color bar issue (regarding to vtkPVScalarBarActor) in displaying window/level in the range of [0,1]
* Studying the option for moving slice view annotation settings from Data-probe module to slice view controller widget and to invoke configuration dialog per slice view.
* Adding the feature of orientation marker to slice view annotations [1].

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
*
</div>
</div>
===References===
* [1] [https://github.com/mehrtash/OrientationFigure Orientation Figure Github page]

File:Colorbar.PNG

2015-01-09T15:37:05Z

Mehrtash:

2015 Winter Project Week:Bolus Arrival Time Estimation in PK Modelling

2015-01-09T15:10:02Z

Mehrtash:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Alireza Mehrtash, BWH
* Andrey Fedorov, BWH
* Jim Miller, GE Global Research
* Sandeep Gupta, GE Global Research

==Project Description==
<div style="margin: 20px;">
PharmacoKinetics (PK) analysis of DCE-MRI images requires estimation of bolus arrival time (BAT). Inaccuracies in estimation of BAT can affect the results of derived PK metrics. The goal of this project is to improve the current implementation of BAT estimation in Slicer's PK Modelling extension [1]. The current implemented method in Slicer measures the time point before the peak gradient arrival and set it as BAT.
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Study current implementation of BAT detection in PK Modelling software in available clinical data for prostate and breast cancers.
* Investigate possible solutions to improve the robustness of BAT detection in PK Modelling.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Add option for manual assignment of BAT separately for AIF (Arterial Input Function) and TRF (Tissue Residual Function).
* Compare different bat detection methods: LL ([1]), PL ([2]) and slicer's methods (PG) in detection of AIF BAT and TRF BAT in whole prostate gland [3].

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* PG method was used to detect BAT in QIN Prostate and OHSU Breast DCE-MRI data sets.
* On prostate data sets we extracted the AIF from the left femoral artery and then we used LL, PL and PG methods to detect BAT. Due to the sharp rise in AIF curve all three methods successfully detect BAT in AIF signal (%100 agreement on 9 cases).
* By studying BAT maps for the whole prostate gland we observed that for tissue residual function (TRF) concentration curves in areas with slower uptake curves, there is higher chance that PG method trapping in local minima. However some of the curves in which PG fails are voxels which are not good candidates for Tofts modelling (This could include necrotic ROIs). For future improvement of PG method Jim suggested to inpaint the false BATs by using the neighborhood information.
* Since PG works correctly on AIF detection, we are going to use manual assignment for TRF only and use automatic bat detection for AIF.

</div>
</div>
===References===
* [1] [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/PkModeling PK Modelling extension documentation page]
* [2] [http://www.ncbi.nlm.nih.gov/pubmed/19097111 Improved bolus arrival time and arterial input function estimation for tracer kinetic analysis in DCE-MRI.]
* [3]

2015 Winter Project Week:Bolus Arrival Time Estimation in PK Modelling

2015-01-05T22:48:19Z

Mehrtash: /* References */

2015 Winter Project Week:Bolus Arrival Time Estimation in PK Modelling

2015-01-05T22:47:53Z

Mehrtash:

2015 Winter Project Week: Registration of preop and intraop DTI to correlate parameters with postop prognosis

2015-01-05T14:02:45Z

Mehrtash: Created page with '__NOTOC__ <gallery> Image:PW-2015SLC.png|Projects List </gallery> ==Key Investigators== * Yi Le, BWH * Steve Pieper, Isomics * Alireza Mehr…'

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Yi Le, BWH
* Steve Pieper, Isomics
* Alireza Mehrtash, BWH
* Lauren O'Donnell, BWH

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* to test whether FA/MD alternation of CST after surgery could predict the patients motor strength change
** without taking the voxel-based FA/MD calculation, we want to test the feasibility of the FA/MD value of a whole tract
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* the registration of pre-op DTI to post-op DTI
* convert DTI tractography models to label-map
* evaluate the changes of FA/MD after surgery and the correlation with patients' motor strength
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>
===References===
* [1]

2015 Winter Project Week

2015-01-05T14:02:24Z

Mehrtash: /* Image-Guided Therapy */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

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

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

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 2015.

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

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

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

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| <br><font color="#9966cc"></font>
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
|
|
| [[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
| style="background:#dbf3ff; color:#522200"| [http://ferenc.jolesz.muchloved.com/frame.aspx? A tribute to Ferenc Jolesz] <br> [[2015_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|
| <font color="#44AA88">''(Olympus B)''</font>
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] <br><font color="#44AA88">''(Amethyst 1)'' <br> 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
* [[2015_Winter_Project_Week:_Registration_of_preop_and_intraop_DTI_to_correlate_parameters_with_postop_prognosis|Registration of pre-op and intra-op DTI to correlate parameters with post-op prognosis]] (Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)
* [[New Distance|A new modified Frechet distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)
* [[ProstateSegmentation | Prostate segmentation and biopsy]] (Peter Behringer, Andriy Fedorov)
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[Needle Finder Tutorial | Needle Finder Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*[[VR Radiology | Application of consumer virtual reality devices in creating environments for diagnostic radiology]] (Franklin King, Steve Pieper)
*[[Distribution modeling | Summary statistics versus distributions: evaluating improved ability to detect clinical differences using DTI]] (Anuja Sharma, Guido Gerig)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Fissure Enhancement | Supervised fissure enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)
== Lung ==

*Small lung nodule differential diagnosis using 3D Slicer (Li Ming, Jay Jagadeesan)

==[http://qiicr.org QIICR]==
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* [[2015_Winter_Project_Week:_DICOM_representation_of_QIICR_Iowa_DBP_data|Representation of Iowa QIN data using DICOM]] (Andrey, Christian Bauer, Steve Pieper)
* [[Whole Body PET/CT Reference Region segmentation]] (Christian Bauer)
* [[2015_Winter_Project_Week:Bolus_Arrival_Time_Estimation_in_PK_Modelling|Bolus Arrival Time (BAT) Estimation in PK Modelling]] (Alireza Mehrtash, Andriy Fedorov, Jim Miller)
* [[2015_Winter_Project_Week:DICOM_Module_Improvements|DICOM Module Improvements]] (Alireza Mehrtash, Andriy Fedorov, Ron Kikinis, Steve Pieper)
* [[2015_Winter_Project_Week:Slice_View_Annotations|Slice View Annotations]] (Alireza Mehrtash, Andriy Fedorov, Steve Pieper)

==Feature Extraction==
* [[3D_SIFT_VIEW| 3D SIFT Feature Visualization in Slicer]] (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)

==Slicer4 Extensions==
* [[PET Tumor Segmentation]] (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* Improved model display (Francois Boudin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Bradley Lowenkamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter, ?)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)
* [[2015_Winter_Project_Week:RemoveITKv3Compatibility|Remove ITKv3 Compatibility for 64-bit image support]] (Bradley Lowekamp, Hans Johnson?, ?)
* [[2015_Winter_Project_Week:VersorTransforms|ITK Composed Versor Transforms]] (Bradley Lowekamp, Hans Johnson?, ?)

== '''Registrants''' ==

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

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

2015 Winter Project Week: Registration of preop and intraop DTI

2015-01-05T14:01:15Z

Mehrtash: Created page with '__NOTOC__ <gallery> Image:PW-2015SLC.png|Projects List </gallery> ==Key Investigators== * Yi Le, BWH * Steve Pieper, Isomics * Alireza Mehr…'

2015 Winter Project Week

2015-01-05T13:57:13Z

Mehrtash: /* Image-Guided Therapy */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

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

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

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 2015.

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

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

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

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| <br><font color="#9966cc"></font>
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
|
|
| [[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
| style="background:#dbf3ff; color:#522200"| [http://ferenc.jolesz.muchloved.com/frame.aspx? A tribute to Ferenc Jolesz] <br> [[2015_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|
| <font color="#44AA88">''(Olympus B)''</font>
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] <br><font color="#44AA88">''(Amethyst 1)'' <br> 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
* [[2015_Winter_Project_Week:_Registration_of_preop_and_intraop_DTI|Registration of pre-op and intra-op DTI to correlate parameters with post-op prognosis]] (Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)
* [[New Distance|A new modified Frechet distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)
* [[ProstateSegmentation | Prostate segmentation and biopsy]] (Peter Behringer, Andriy Fedorov)
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[Needle Finder Tutorial | Needle Finder Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*[[VR Radiology | Application of consumer virtual reality devices in creating environments for diagnostic radiology]] (Franklin King, Steve Pieper)
*[[Distribution modeling | Summary statistics versus distributions: evaluating improved ability to detect clinical differences using DTI]] (Anuja Sharma, Guido Gerig)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Fissure Enhancement | Supervised fissure enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)
== Lung ==

*Small lung nodule differential diagnosis using 3D Slicer (Li Ming, Jay Jagadeesan)

==[http://qiicr.org QIICR]==
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* [[2015_Winter_Project_Week:_DICOM_representation_of_QIICR_Iowa_DBP_data|Representation of Iowa QIN data using DICOM]] (Andrey, Christian Bauer, Steve Pieper)
* [[Whole Body PET/CT Reference Region segmentation]] (Christian Bauer)
* [[2015_Winter_Project_Week:Bolus_Arrival_Time_Estimation_in_PK_Modelling|Bolus Arrival Time (BAT) Estimation in PK Modelling]] (Alireza Mehrtash, Andriy Fedorov, Jim Miller)
* [[2015_Winter_Project_Week:DICOM_Module_Improvements|DICOM Module Improvements]] (Alireza Mehrtash, Andriy Fedorov, Ron Kikinis, Steve Pieper)
* [[2015_Winter_Project_Week:Slice_View_Annotations|Slice View Annotations]] (Alireza Mehrtash, Andriy Fedorov, Steve Pieper)

==Feature Extraction==
* [[3D_SIFT_VIEW| 3D SIFT Feature Visualization in Slicer]] (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)

==Slicer4 Extensions==
* [[PET Tumor Segmentation]] (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* Improved model display (Francois Boudin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Bradley Lowenkamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter, ?)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)
* [[2015_Winter_Project_Week:RemoveITKv3Compatibility|Remove ITKv3 Compatibility for 64-bit image support]] (Bradley Lowekamp, Hans Johnson?, ?)
* [[2015_Winter_Project_Week:VersorTransforms|ITK Composed Versor Transforms]] (Bradley Lowekamp, Hans Johnson?, ?)

== '''Registrants''' ==

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

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

2015 Winter Project Week:Slice View Annotations

2015-01-02T23:45:33Z

Mehrtash: Created page with '__NOTOC__ <gallery> Image:PW-2015SLC.png|Projects List </gallery> ==Key Investigators== * Alireza Mehrtash, BWH * Andrey Fedorov, BWH * Ste…'

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Alireza Mehrtash, BWH
* Andrey Fedorov, BWH
* Steve Pieper, Isomics

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improve usability of Slice view annotations.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

* Color bar issue (regarding to vtkPVScalarBarActor) in displaying window/level in the range of [0,1]
* Studying the option for moving slice view annotation settings from Data-probe module to slice view controller widget and to invoke configuration dialog per slice view.
* Adding the feature of orientation marker to slice view annotations [1].

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
*
</div>
</div>
===References===
* [1] [https://github.com/mehrtash/OrientationFigure Orientation Figure Github page]

2015 Winter Project Week:DICOM Module Improvements

2015-01-02T23:14:07Z

Mehrtash: Created page with '__NOTOC__ <gallery> Image:PW-2015SLC.png|Projects List </gallery> ==Key Investigators== * Alireza Mehrtash, BWH * Andrey Fedorov, BWH * Ron…'

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Alireza Mehrtash, BWH
* Andrey Fedorov, BWH
* Ron Kikinis, BWH
* Steve Pieper, Isomics

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Fix some of the known bugs in Slicer DICOM Module to improve usability of DICOM browser.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

* Sort order for DICOM browser content by most recent [1]
* Populating of DICOM browser tables after start-up [2]
* Remove single series of an exam in the DICOM browser [3]

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
*
</div>
</div>
===References===
* [1] [http://na-mic.org/Mantis/view.php?id=3770 3770: Sort order for DICOM browser content by most recent]
* [2] [http://na-mic.org/Mantis/view.php?id=3769 3769: All series are shown when DICOM browser is launched for the first time ... ]
* [3] [http://na-mic.org/Mantis/view.php?id=3792 3792: Remove one series of an exam in the dicom menu]

2015 Winter Project Week:Bolus Arrival Time Estimation in PK Modelling

2015-01-02T18:42:06Z

Mehrtash: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Alireza Mehrtash, BWH
* Andrey Fedorov, BWH
* Jim Miller, GE

==Project Description==
<div style="margin: 20px;">
PharmacoKinetics (PK) analysis of DCE-MRI images requires estimation of bolus arrival time (BAT). Inaccuracies in estimation of BAT can affect the results of derived PK metrics. The goal of this project is to improve the current implementation of BAT estimation in Slicer's PK Modelling extension [1]. The current implemented method in Slicer measures the time point before the peak gradient arrival and set it as BAT.
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Investigate options for improving current implementation in case of noisy data by adding a low pass filter (e.g. savitzky golay filter).
* Adding option for manual assignment of BAT separately for AIF (Arterial Input Function) and TRF (Tissue Residual Function).
* Adding three segments piecewise continous regression model (PL Method) [2] for bat estimation to PK Modelling module.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
*
</div>
</div>
===References===
* [1] [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/PkModeling| PK Modelling extension documentation page]
* [2] [http://www.ncbi.nlm.nih.gov/pubmed/19097111| Improved bolus arrival time and arterial input function estimation for tracer kinetic analysis in DCE-MRI.]

2015 Winter Project Week:Bolus Arrival Time Estimation in PK Modelling

2015-01-02T18:41:43Z

Mehrtash: Created page with '__NOTOC__ <gallery> Image:PW-2015SLC.png|Projects List </gallery> ==Key Investigators== * Alireza Mehrtash, BWH * Andrey Fedorov, BWH * Jim…'

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Alireza Mehrtash, BWH
* Andrey Fedorov, BWH
* Jim Miller, GE

==Project Description==
<div style="margin: 20px;">
PharmacoKinetics (PK) analysis of DCE-MRI images requires estimation of bolus arrival time (BAT). Inaccuracies in estimation of BAT can affect the results of derived PK metrics. The goal of this project is to improve the current implementation of BAT estimation in Slicer's PK Modelling extension [1]. The current implemented method in Slicer measures the time point before the peak gradient arrival and set it as BAT.
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Investigate options for improving current implementation in case of noisy data by adding a low pass filter (e.g. savitzky golay filter).
* Adding option for manual assignment of BAT separately for AIF (Arterial Input Function) and TRF (Tissue Residual Function).
* Adding three segments piecewise continous regression model (PL Method) for bat estimation to PK Modelling module.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
*
</div>
</div>
===References===
* [1] [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/PkModeling| PK Modelling extension documentation page]
* [2] [http://www.ncbi.nlm.nih.gov/pubmed/19097111| Improved bolus arrival time and arterial input function estimation for tracer kinetic analysis in DCE-MRI.]

2015 Winter Project Week

2015-01-02T18:07:21Z

Mehrtash: /* QIICR */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

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

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

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 2015.

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

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

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

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| <br><font color="#9966cc"></font>
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
|
|
| [[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''l
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_SLC_Training_Workshop|Slicer Workshop (Ron Kikinis)]]
| <font color="#44AA88">''(Olympus B)''</font>
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] <br><font color="#44AA88">''(Amethyst 2)'' <br> 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*Registration of pre-op and intra-op DTI to correlate parameters with post-op prognosis(Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)
* [[ProstateSegmentation | Prostate segmentation and biopsy]] (Peter Behringer, Andriy Fedorov)
* [[Needle Detection Tutorial | Needle Detection Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
* [[New Distance|A new modified Frechet distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

==TBI==

==Stroke==

==Cardiac==

== Lung ==

*Small lung nodule differential diagnosis using 3D Slicer (Li Ming, Jay Jagadeesan, Jim Miller)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Feature Enhancement | Supervised feature enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)

==Head and Neck Cancer / Radiotherapy ==

==[http://qiicr.org QIICR]==
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* [[2015_Winter_Project_Week:_DICOM_representation_of_QIICR_Iowa_DBP_data|Representation of Iowa QIN data using DICOM]] (Andrey, Christian Bauer)
* [[Whole Body PET/CT Reference Region segmentation]] (Christian Bauer)
* [[2015_Winter_Project_Week:Bolus_Arrival_Time_Estimation_in_PK_Modelling|Bolus Arrival Time (BAT) Estimation in PK Modelling]] (Alireza Mehrtash, Andriy Fedrov, Jim Miller)
* [[2015_Winter_Project_Week:DICOM_Module_Improvements|DICOM Module Improvements]] (Alireza Mehrtash, Andriy Fedorov, Ron Kikinis, Steve Pieper)
* [[2015_Winter_Project_Week:Slice_View_Annotations|Slice View Annotations]] (Alireza Mehrtash, Andriy Fedorov, Steve Pieper)

==Feature Extraction==

==Additional Brain Image Analysis==

==Slicer4 Extensions==
* [[PET Tumor Segmentation]] (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* Improved model display (Francois Boudin, Steve Pieper)

==Infrastructure==

* [[2015_Winter_Project_Week:SlicerMicroMacroScale | Micro and Macro Scale in Slicer]] (Nicole Aucoin, Bradley Lowenkamp)
* [[2015_Winter_Project_Week:Markups | Markups]] (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter, ?)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)

== '''Registrants''' ==

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

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

2014 Summer Project Week: ColorBar support

2014-06-27T14:34:34Z

Mehrtash:

__NOTOC__

<gallery>
Image:PW-SLC2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

[[Image:ColorSclarBar.gif|500px|thumb|right|Demo of Color Scalar Bar]]
==Key Investigators==
* BWH: Alireza Mehrtash, Andrey Fedorov
* Isomics: Steve Pieper
* Princess Margaret Cancer Centre: Kevin Wang
* Kitware: JC

==Project Description==
Support for color scale bar in slice views can be very helpful in many cases such as when 3D Slicer is used to create figures for academic publications ([1] and [2]). Currently color scale visualization is only available in 3D viewer and it is not very useful as the numbers associated with colors are not the actual image pixel values but they are numbers of the individual colors in the lookup table (LUT).
There was a previous effort to include color scale bar in SlicerRT [3]. The goal of this project is to add the support of color bar for 2D slice views in 3D Slicer Core.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Support of color scale bar for 2D slice views.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Study the latest related changes and improvements in VTK6.
* Discuss about the functionality and UI design.
* Add color scalar bar widget to 2D sliceview.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* We added the support for color scalar bar to the slice view annotations script.
* The color scalar bar is sensitive to window/level changes and update the color lookup table range based on W/L of the current slice node.
* We are going to migrate and refactor the code from slice view annotations script to vtkMRMLSliceNode class.
</div>
</div>

==References==
*[1] Mantis Bug #1918: http://na-mic.org/Mantis/view.php?id=1918
*[2] Mantis Bug #3575: http://na-mic.org/Mantis/view.php?id=3575
*[3] Color Scalar bar for SlicerRT (2013 Project Week): http://www.na-mic.org/Wiki/index.php/2013_Project_Week:ScalarBar

2014 Summer Project Week: Slicer DICOM

2014-06-27T14:28:29Z

Mehrtash:

__NOTOC__



==Key Investigators==
* BWH: Alireza Mehrtash, Andrey Fedorov, Ron Kikinis
* Isomics: Steve Pieper

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Continue the work on fixing known bugs and also adding new features to Slicer DICOM module.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Add Export Support
** Add the functionality at CTK level
** Add support to Slicer
* Add the combobox for changing the density of DICOM table views
** This is already available in CTK but has not imported to Slicer.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* We discussed in detail the current status of DICOM module in Slicer at DICOM breakout session and got feedback from community.
* We added the feature for changing the density of the DICOM table views to Slicer. It is going to be merged into Slicer hopefully within the next week.

</div>
</div>

==References==
*[1] [https://github.com/QIICR/ProjectIssuesAndWiki/wiki/Slicer-Infrastructure-Projects QIICR Page for DICOM Improvements]

2014 Summer Project Week: Slicer DICOM

2014-06-27T14:20:21Z

Mehrtash:

__NOTOC__



==Key Investigators==
* BWH: Alireza Mehrtash, Andrey Fedorov, Ron Kikinis
* Isomics: Steve Pieper

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Continue the work on fixing known bugs and also adding new features to Slicer DICOM module.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Add Export Support
** Add the functionality at CTK level
** Add support to Slicer
* Add the combobox for changing the density of DICOM table views
** This is already available in CTK but has not imported to Slicer.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*

</div>
</div>

==References==
*[1] [https://github.com/QIICR/ProjectIssuesAndWiki/wiki/Slicer-Infrastructure-Projects QIICR Page for DICOM Improvements]

2014 Summer Project Week: ColorBar support

2014-06-27T14:09:13Z

Mehrtash:

__NOTOC__

<gallery>
Image:PW-SLC2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

[[Image:ColorSclarBar.gif|500px|thumb|right|Demo of Color Scalar Bar]]
==Key Investigators==
* BWH: Alireza Mehrtash, Andrey Fedorov
* Isomics: Steve Pieper
* Princess Margaret Cancer Centre: Kevin Wang

==Project Description==
Support for color scale bar in slice views can be very helpful in many cases such as when 3D Slicer is used to create figures for academic publications ([1] and [2]). Currently color scale visualization is only available in 3D viewer and it is not very useful as the numbers associated with colors are not the actual image pixel values but they are numbers of the individual colors in the lookup table (LUT).
There was a previous effort to include color scale bar in SlicerRT [3]. The goal of this project is to add the support of color bar for 2D slice views in 3D Slicer Core.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Support of color scale bar for 2D slice views.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Study the latest related changes and improvements in VTK6.
* Discuss about the functionality and UI design.
* Add color scalar bar widget to 2D sliceview.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* We added the support for color scalar bar to the slice view annotations script.
* The color scalar bar is sensitive to window/level changes and update the color lookup table range based on W/L of the current slice node.
* We are going to migrate and refactor the code from slice view annotations script to vtkMRMLSliceNode class.
</div>
</div>

==References==
*[1] Mantis Bug #1918: http://na-mic.org/Mantis/view.php?id=1918
*[2] Mantis Bug #3575: http://na-mic.org/Mantis/view.php?id=3575
*[3] Color Scalar bar for SlicerRT (2013 Project Week): http://www.na-mic.org/Wiki/index.php/2013_Project_Week:ScalarBar

2014 Summer Project Week:Visual Guidance for Neurosurgery US Recording

2014-06-27T14:01:27Z

Mehrtash:

__NOTOC__

<gallery>
Image:PW-SLC2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

[[Image:Neuro_us_visual_feedback.gif|500px|thumb|right|Real Time Ultrasound Reconstruction]]

==Key Investigators==
* BWH: Alireza Mehrtash, Isaiah Norton,Rahul Sastry, Matthew Toews, Tina Kapur, Sandy Wells
* Queen's: Andras Lasso

==Project Description==
Intraoperative ultrasound is a safe and cost-effective tool that provides useful information about the localization of the brain tumors and also targeting residual tumor. 3D reconstruction of intra-operative US can be obtained by recording tracked 2D US data and can be visualized in conjunction with pre-operative MRI scans. Recording appropriate 2D US slices can have a direct affect on the output of 3D reconstructed volume. The goal of this project is to develop a visual guidance tool to aid neurosurgeons in the process of recording US data.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* To develop a visual guidance tool to aid neurosurgeons in the process of recording US data.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Create scripted module in 3D Slicer for guiding recording process.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* We added the functionality of real-time reconstruction of volumes to PlusRemote module from Slicer through an active PLUS Server connection.
* We tested the real-time reconstruction on the existing available AMIGO neurosurgery data.

</div>
</div>

==References==
*[1] Preliminary test and presentation video: http://youtu.be/fGkG6LTWn6g

2014 Summer Project Week:Visual Guidance for Neurosurgery US Recording

2014-06-27T13:57:03Z

Mehrtash:

__NOTOC__

<gallery>
Image:PW-SLC2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

[[Image:Neuro_us_visual_feedback.gif|500px|thumb|right|Real Time Ultrasound Reconstruction]]

==Key Investigators==
* BWH: Alireza Mehrtash, Isaiah Norton,Rahul Sastry, Matthew Toews, Tina Kapur, Sandy Wells

==Project Description==
Intraoperative ultrasound is a safe and cost-effective tool that provides useful information about the localization of the brain tumors and also targeting residual tumor. 3D reconstruction of intra-operative US can be obtained by recording tracked 2D US data and can be visualized in conjunction with pre-operative MRI scans. Recording appropriate 2D US slices can have a direct affect on the output of 3D reconstructed volume. The goal of this project is to develop a visual guidance tool to aid neurosurgeons in the process of recording US data.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* To develop a visual guidance tool to aid neurosurgeons in the process of recording US data.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Create scripted module in 3D Slicer for guiding recording process.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* We added the functionality of real-time reconstruction of volumes to PlusRemote module from Slicer through an active PLUS Server connection.

</div>
</div>

==References==
*[1] Preliminary test and presentation video: http://youtu.be/fGkG6LTWn6g

2014 Summer Project Week:Visual Guidance for Neurosurgery US Recording

2014-06-27T03:57:44Z

Mehrtash:

__NOTOC__

<gallery>
Image:PW-SLC2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

[[Image:Neuro_us_visual_feedback.gif|500px|thumb|right|Real Time Ultrasound Reconstruction]]

==Key Investigators==
* BWH: Alireza Mehrtash, Isaiah Norton,Rahul Sastry, Matthew Toews, Tina Kapur, Sandy Wells

==Project Description==
Intraoperative ultrasound is a safe and cost-effective tool that provides useful information about the localization of the brain tumors and also targeting residual tumor. 3D reconstruction of intra-operative US can be obtained by recording tracked 2D US data and can be visualized in conjunction with pre-operative MRI scans. Recording appropriate 2D US slices can have a direct affect on the output of 3D reconstructed volume. The goal of this project is to develop a visual guidance tool to aid neurosurgeons in the process of recording US data.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* To develop a visual guidance tool to aid neurosurgeons in the process of recording US data.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Create scripted module in 3D Slicer for guiding recording process.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*

</div>
</div>

==References==
*[1] Preliminary test and presentation video: http://youtu.be/fGkG6LTWn6g