NAMIC Wiki - User contributions [en]

2017 Winter Project Week/OCM-MRI

2017-01-13T15:41:53Z

Frank:

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

</gallery>

==Key Investigators==

* Frank Preiswerk, Brigham and Women's Hospital, Harvard Medical School
* Yaofei Wang (Vivian), Tianjin University, Beijing, China

==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;"
|

* To investigate the use of Deep Learning for the generation of synthetic respiratory MR images.
|

* Look into different software frameworks, choose one
* Investigate generative deep neural network techniques
* Produce preliminary results on hybrid US+MRI data
|

* Discussions
* Installation of and finding our way around Keras and TensorFlow
* Network candidates: CNN with logistic regression output, Generative Adversarial Networks (GAN), Variational Autoencoders
* In particular, Variational Autoencoders are able to model conditional distributions as required here
|}

==Background and References==

* http://link.springer.com/chapter/10.1007%2F978-3-319-24553-9_39#page-1
* http://onlinelibrary.wiley.com/doi/10.1002/mrm.26467/full

2017 Winter Project Week/OCM-MRI

2017-01-10T17:04:29Z

Frank:

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

</gallery>

==Key Investigators==

* Frank Preiswerk, Brigham and Women's Hospital, Harvard Medical School
* Yaofei Wang (Vivian), Tianjin University, Beijing, China

==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;"
|

* To investigate the use of Deep Learning for the generation of synthetic respiratory MR images.
|

* Look into different software frameworks, choose one
* Investigate generative deep neural network techniques
* Produce preliminary results on hybrid US+MRI data
|

* Identified Generative Adversarial Networks (GAN) and Variational Autoencoders as candidates
* In particular, Variational Autoencoders are able to model conditional distributions as required here
|}

==Background and References==

* http://link.springer.com/chapter/10.1007%2F978-3-319-24553-9_39#page-1
* http://onlinelibrary.wiley.com/doi/10.1002/mrm.26467/full

2017 Winter Project Week/OCM-MRI

2017-01-10T17:04:09Z

Frank:

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

</gallery>

==Key Investigators==

* Frank Preiswerk, Brigham and Women's Hospital, Harvard Medical School
* Yaofei Wang (Vivian), Tianjin University, Beijing, China

==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;"
|

* To investigate the use of Deep Learning for the generation of synthetic respiratory MR images.
|

* Look into different software frameworks, choose one
* Investigate generative deep neural network techniques
* Produce preliminary results on hybrid US+MRI data
|

* Identified Generative Adversarial Networks (GAN) and Variational Autoencoders as possible approach
* In particular, Variational Autoencoders are able to model conditional distributions as required here
|}

==Background and References==

* http://link.springer.com/chapter/10.1007%2F978-3-319-24553-9_39#page-1
* http://onlinelibrary.wiley.com/doi/10.1002/mrm.26467/full

2017 Winter Project Week/OCM-MRI

2017-01-10T17:03:35Z

Frank:

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

</gallery>

==Key Investigators==

* Frank Preiswerk, Brigham and Women's Hospital, Harvard Medical School
* Yaofei Wang (Vivian), Tianjin University, Beijing, China

==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;"
|

* To investigate the use of Deep Learning for the generation of synthetic respiratory MR images.
|

* Look into different software frameworks, choose one
* Investigate generative deep neural network techniques
* Produce preliminary results on hybrid US+MRI data
|

* Identified Generative Adversarial Networks (GAN) and Variational Autoencoders as possible approach
|}

==Background and References==

* http://link.springer.com/chapter/10.1007%2F978-3-319-24553-9_39#page-1
* http://onlinelibrary.wiley.com/doi/10.1002/mrm.26467/full

2017 Winter Project Week/OCM-MRI

2017-01-09T18:34:32Z

Frank:

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

</gallery>

==Key Investigators==

* Frank Preiswerk, Brigham and Women's Hospital, Harvard Medical School
* Yaofei Wang (Vivian), Tianjin University, Beijing, China

==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;"
|

* To investigate the use of Deep Learning for the generation of synthetic respiratory MR images.
|

* Look into different software frameworks, choose one
* Investigate generative deep neural network techniques
* Produce preliminary results on hybrid US+MRI data
|

*
|}

==Background and References==

* http://link.springer.com/chapter/10.1007%2F978-3-319-24553-9_39#page-1
* http://onlinelibrary.wiley.com/doi/10.1002/mrm.26467/full

2017 Winter Project Week/OCM-MRI

2017-01-09T18:33:36Z

Frank:

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

</gallery>

==Key Investigators==

* Frank Preiswerk, Brigham and Women's Hospital, Harvard Medical School
* Yaofei Wang (Vivian), Tianjin University, Beijing, China

==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;"
|

* To investigate the use of Deep Learning for the generation of synthetic respiratory MR images.
|

* Look into different software frameworks, choose one
* Investigate generative deep neural networks techniques
* Produce preliminary results on hybrid US+MRI data
|

*
|}

==Background and References==

* http://link.springer.com/chapter/10.1007%2F978-3-319-24553-9_39#page-1
* http://onlinelibrary.wiley.com/doi/10.1002/mrm.26467/full

2017 Winter Project Week/OCM-MRI

2017-01-09T18:32:29Z

Frank:

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

</gallery>

==Key Investigators==

* Frank Preiswerk, Brigham and Women's Hospital, Harvard Medical School
* Yaofei Wang (Vivian), Tianjin University, Beijing, China

==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;"
|

* To investigate the use of Deep Learning for the generation of synthetic respiratory MR images.
|

* Look into different frameworks
* Investigate generative deep neural networks techniques
* Produce preliminary results
|

*
|}

==Background and References==

* http://link.springer.com/chapter/10.1007%2F978-3-319-24553-9_39#page-1
* http://onlinelibrary.wiley.com/doi/10.1002/mrm.26467/full

2017 Winter Project Week/OCM-MRI

2017-01-02T16:08:21Z

Frank: 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..."

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

</gallery>

==Key Investigators==

* Frank Preiswerk, Brigham and Women's Hospital, Harvard Medical School
* Yaofei Wang (Vivian), Tianjin University, Beijing, China

==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;"
|

* To investigate the use of Deep Learning for the generation of synthetic respiratory MR images.
|

*
|

*
|}

==Background and References==

* http://link.springer.com/chapter/10.1007%2F978-3-319-24553-9_39#page-1
* http://onlinelibrary.wiley.com/doi/10.1002/mrm.26467/full

2017 Winter Project Week

2017-01-02T16:03:48Z

Frank: Added link to my project summary page

__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.

== 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]].

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

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

==Conference Calls for Preparation==

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

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 9
!style="width:18%" |Tuesday, January 10
!style="width:18%" |Wednesday, January 11
!style="width:18%" |Thursday, January 12
!style="width:18%" |Friday, January 13
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#faedb6"| '''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|rowspan="2"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-10:30am'''
|bgcolor="#88aaae"|[http://www.spl.harvard.edu/pages/People/ctempany Clare Tempany] led Image-Guided Therapy Discussion
|bgcolor="#88aaae"|9:00am-10:00am: Shape Analysis Breakout<br>---- ---- ---- ---- ---- ----<br>10:00am-12:00pm: Luis Ibanez TensorFlow Workshop
|bgcolor="#88aaae"|Fiona Fennessy led Quantitative Imaging for Prostate Cancer Discussion
|bgcolor="#88aaae"|
|-
|bgcolor="#ffffdd"|'''10:30am-12pm:'''
|'''[http://cmictig.cs.ucl.ac.uk/people/academic-staff/1-sourselin Sebastien Ourselin, PhD, UCL] Talk'''
|
|
|
|Project Reporting
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1:00-5:30pm'''
|'''1:00pm-2:30pm:''' Project Presentations
|
|
|
|'''1:30-2:30pm:''' [[AMIGO_TourPW2017Winter|AMIGO Tour]]
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day <br> [[2017_Winter_Project_Week/Dinner|Dinner on Thursday Night]] (Optional)
|
|}

==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, Tina Kapur)
* [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei Wang (Vivian))

== Web Technologies ==
* [[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer)

== Visualization ==
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin)

== IGT ==
* [[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/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (Fan Zhang, Shun Gong, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)
* [[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)

== Robotics in IGT ==
* [[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, )

== Craniofacial ==
* [[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)

== Infrastructure ==
* [[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/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)
* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy refactoring]] (Csaba Pinter)
* [[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)
* [[2017 Winter Project Week/DiPy_in_Slicer | DiPy integration in Slicer]] (Isaiah Norton, Lauren J. O'Donnell)

== DICOM ==
* [[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)

==To be Categorized==

* [[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/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua)
* [[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)
* [[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)
* [[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/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram)

= '''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
# 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.
# 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
# Kapur, Tina :: Brigham and Women's Hospital
# Kikinis, Ron :: Brigham and Women's Hospital
# 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
# Sharp, Gregory :: Massachusetts General Hospital
# Sridharan, Patmaa :: University of Pennsylvania-CBICA
# Vidyaratne, Lasitha :: Old Dominion University
# Ye, Wu :: Brigham and Women's Hospital
# Zeleznik, Roman :: DFCI
# Zhang, Fan :: Brigham and Women's Hospital
# Zhang, Miaomiao :: Massachusetts Institute of Technology
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital

2015 Summer Project Week:USReconstruction

2015-06-24T15:07:55Z

Frank: /* Key Investigators */

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Frank Preiswerk
* Laurent Chauvin
* Andras Lasso
* Tamas Ungi
* Adam Rankin (observer)
* Robert Owen, BK

==Project Description==

[[File:Usrd_2dus.png]]
[[File:Usrd_setup.jpg]]
[[File:Usrd_reconstruction.png]]
[[File:Usrd_usrd.png]]
[[File:Usrd_respsig.png]]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* This project will investigate the use of a single-element ultrasound transducer for 2D image reconstruction from navigated 2D ultrasound images.
* Technology: invariant feature extraction, descriptor representation.
* Application domains: registration, respiratory motion compensation
* Image domains: Ultrasound.
* Clinical use case scenarios: Establishment of a 4D motion atlas from 2D ultrasound data.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discussion and documentation
* Algorithms: fast KNN methods, binning.
* Mathematical formalisms: Correlation, similarity measures.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Learned how to perform volume reconstruction from tracked 2D ultrasound in plus
* Implemented a binning algorithm for the USrd signal using Principal Component Analysis (PCA)
* Had very insightful discussions with the PLUS developers including the idea of potentially updating older, depreciated functionality in PLUS for gated acquisitions (originally developed for ECG-based gating).

</div>
</div>
<br/>

==References==

Hybrid Utrasound and MRI Acquisitions for High-Speed Imaging of Respiratory Organ Motion<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, L.P. Panych, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Scanner-less High-Speed MR-Imaging of Repetitive Organ Motion for Image-Guided Therapy<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Detecting Rapid Organ Motion using a Hybrid MR-Ultrasound Setup and Bayesian Data Processing.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2014, pp. 7309<br/>
PDF © ISMRM, 2014.<br/>

Boosting MR Temporal Resolution using Rapid Ultrasound Measurements, for Motion-Tracking Purposes.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, B. M. Schwartz, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2013, pp. 478. Oral Presentation<br/>
PDF © ISMRM, 2013.<br/>

2015 Summer Project Week:USReconstruction

2015-06-24T14:58:34Z

Frank: /* Project Description */

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Frank Preiswerk
* Laurent Chauvin
* Andras Lasso
* Adam Rankin (observer)
* Robert Owen, BK

==Project Description==

[[File:Usrd_2dus.png]]
[[File:Usrd_setup.jpg]]
[[File:Usrd_reconstruction.png]]
[[File:Usrd_usrd.png]]
[[File:Usrd_respsig.png]]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* This project will investigate the use of a single-element ultrasound transducer for 2D image reconstruction from navigated 2D ultrasound images.
* Technology: invariant feature extraction, descriptor representation.
* Application domains: registration, respiratory motion compensation
* Image domains: Ultrasound.
* Clinical use case scenarios: Establishment of a 4D motion atlas from 2D ultrasound data.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discussion and documentation
* Algorithms: fast KNN methods, binning.
* Mathematical formalisms: Correlation, similarity measures.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Learned how to perform volume reconstruction from tracked 2D ultrasound in plus
* Implemented a binning algorithm for the USrd signal using Principal Component Analysis (PCA)
* Had very insightful discussions with the PLUS developers including the idea of potentially updating older, depreciated functionality in PLUS for gated acquisitions (originally developed for ECG-based gating).

</div>
</div>
<br/>

==References==

Hybrid Utrasound and MRI Acquisitions for High-Speed Imaging of Respiratory Organ Motion<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, L.P. Panych, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Scanner-less High-Speed MR-Imaging of Repetitive Organ Motion for Image-Guided Therapy<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Detecting Rapid Organ Motion using a Hybrid MR-Ultrasound Setup and Bayesian Data Processing.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2014, pp. 7309<br/>
PDF © ISMRM, 2014.<br/>

Boosting MR Temporal Resolution using Rapid Ultrasound Measurements, for Motion-Tracking Purposes.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, B. M. Schwartz, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2013, pp. 478. Oral Presentation<br/>
PDF © ISMRM, 2013.<br/>

2015 Summer Project Week:USReconstruction

2015-06-24T14:57:39Z

Frank: /* Project Description */

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Frank Preiswerk
* Laurent Chauvin
* Andras Lasso
* Adam Rankin (observer)
* Robert Owen, BK

==Project Description==

[[File:Usrd_2dus.png]]
[[File:Usrd_setup.jpg]]
[[File:Usrd_reconstruction.png]]
[[File:Usrd_usrd.png]]
[[File:Usrd_respsig.png]]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* This project will investigate the use of a single-element ultrasound transducer for 2D image reconstruction from navigated 2D ultrasound images.
* Technology: invariant feature extraction, descriptor representation.
* Application domains: registration, respiratory motion compensation
* Image domains: Ultrasound.
* Clinical use case scenarios: Establishment of a 4D motion atlas from 2D ultrasound data.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discussion and documentation
* Algorithms: fast KNN methods, binning.
* Mathematical formalisms: Correlation, similarity measures.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Learned how to perform volume reconstruction from tracked 2D ultrasound in plus
* Implemented a binning algorithm for the USrd signal using Principal Component Analysis (PCA)
* Had very insightful discussions with the PLUS developers including the idea of potentially updating older, depreciated functionality in PLUS for gated acquisitions (originally developed for ECG).

</div>
</div>
<br/>

==References==

Hybrid Utrasound and MRI Acquisitions for High-Speed Imaging of Respiratory Organ Motion<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, L.P. Panych, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Scanner-less High-Speed MR-Imaging of Repetitive Organ Motion for Image-Guided Therapy<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Detecting Rapid Organ Motion using a Hybrid MR-Ultrasound Setup and Bayesian Data Processing.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2014, pp. 7309<br/>
PDF © ISMRM, 2014.<br/>

Boosting MR Temporal Resolution using Rapid Ultrasound Measurements, for Motion-Tracking Purposes.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, B. M. Schwartz, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2013, pp. 478. Oral Presentation<br/>
PDF © ISMRM, 2013.<br/>

2015 Summer Project Week:USReconstruction

2015-06-24T14:56:29Z

Frank: /* Project Description */

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Frank Preiswerk
* Laurent Chauvin
* Andras Lasso
* Adam Rankin (observer)
* Robert Owen, BK

==Project Description==

[[File:Usrd_2dus.png]]
[[File:Usrd_setup.jpg]]
[[File:Usrd_reconstruction.png]]
[[File:Usrd_usrd.png]]
[[File:Usrd_respsig.png]]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* This project will investigate the use of a single-element ultrasound transducer for 2D image reconstruction from navigated 2D ultrasound images.
* Technology: invariant feature extraction, descriptor representation.
* Application domains: registration, respiratory motion compensation
* Image domains: Ultrasound.
* Clinical use case scenarios: Establishment of a 4D motion atlas from 2D ultrasound data.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discussion and documentation
* Algorithms: fast KNN methods, binning.
* Mathematical formalisms: Correlation, similarity measures.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Learning how to do volume reconstruction from tracked 2D ultrasound in plus
* Implementation of a binning algorithm for the USrd signal using Principal Component Analysis (PCA)
* Discussions with the PLUS developers about potentially updating older, depreciated functionality in PLUS for gated acquisitions (originally developed for ECG).

</div>
</div>
<br/>

==References==

Hybrid Utrasound and MRI Acquisitions for High-Speed Imaging of Respiratory Organ Motion<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, L.P. Panych, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Scanner-less High-Speed MR-Imaging of Repetitive Organ Motion for Image-Guided Therapy<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Detecting Rapid Organ Motion using a Hybrid MR-Ultrasound Setup and Bayesian Data Processing.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2014, pp. 7309<br/>
PDF © ISMRM, 2014.<br/>

Boosting MR Temporal Resolution using Rapid Ultrasound Measurements, for Motion-Tracking Purposes.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, B. M. Schwartz, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2013, pp. 478. Oral Presentation<br/>
PDF © ISMRM, 2013.<br/>

2015 Summer Project Week:USReconstruction

2015-06-24T14:49:41Z

Frank: /* Project Description */

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Frank Preiswerk
* Laurent Chauvin
* Andras Lasso
* Adam Rankin (observer)
* Robert Owen, BK

==Project Description==

[[File:Usrd_2dus.png]]
[[File:Usrd_setup.jpg]]
[[File:Usrd_reconstruction.png]]
[[File:Usrd_usrd.png]]
[[File:Usrd_respsig.png]]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* This project will investigate the use of a single-element ultrasound transducer for 2D image reconstruction from navigated 2D ultrasound images.
* Technology: invariant feature extraction, descriptor representation.
* Application domains: registration, respiratory motion compensation
* Image domains: Ultrasound.
* Clinical use case scenarios: Establishment of a 4D motion atlas from 2D ultrasound data.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discussion and documentation
* Algorithms: fast KNN methods, binning.
* Mathematical formalisms: Correlation, similarity measures.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>
<br/>

==References==

Hybrid Utrasound and MRI Acquisitions for High-Speed Imaging of Respiratory Organ Motion<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, L.P. Panych, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Scanner-less High-Speed MR-Imaging of Repetitive Organ Motion for Image-Guided Therapy<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Detecting Rapid Organ Motion using a Hybrid MR-Ultrasound Setup and Bayesian Data Processing.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2014, pp. 7309<br/>
PDF © ISMRM, 2014.<br/>

Boosting MR Temporal Resolution using Rapid Ultrasound Measurements, for Motion-Tracking Purposes.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, B. M. Schwartz, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2013, pp. 478. Oral Presentation<br/>
PDF © ISMRM, 2013.<br/>

2015 Summer Project Week:USReconstruction

2015-06-24T14:47:13Z

Frank: /* Project Description */

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Frank Preiswerk
* Laurent Chauvin
* Andras Lasso
* Adam Rankin (observer)
* Robert Owen, BK

==Project Description==

[[File:Usrd_2dus.png]]
[[File:Usrd_setup.jpg]]
[[File:Usrd_usrd.png]]
[[File:Usrd_respsig.png]]
[[File:Usrd_reconstruction.png]]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* This project will investigate the use of a single-element ultrasound transducer for 2D image reconstruction from navigated 2D ultrasound images.
* Technology: invariant feature extraction, descriptor representation.
* Application domains: registration, respiratory motion compensation
* Image domains: Ultrasound.
* Clinical use case scenarios: Establishment of a 4D motion atlas from 2D ultrasound data.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discussion and documentation
* Algorithms: fast KNN methods, binning.
* Mathematical formalisms: Correlation, similarity measures.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>
<br/>

==References==

Hybrid Utrasound and MRI Acquisitions for High-Speed Imaging of Respiratory Organ Motion<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, L.P. Panych, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Scanner-less High-Speed MR-Imaging of Repetitive Organ Motion for Image-Guided Therapy<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Detecting Rapid Organ Motion using a Hybrid MR-Ultrasound Setup and Bayesian Data Processing.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2014, pp. 7309<br/>
PDF © ISMRM, 2014.<br/>

Boosting MR Temporal Resolution using Rapid Ultrasound Measurements, for Motion-Tracking Purposes.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, B. M. Schwartz, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2013, pp. 478. Oral Presentation<br/>
PDF © ISMRM, 2013.<br/>

File:Usrd setup.jpg

2015-06-24T14:46:50Z

Frank: uploaded a new version of "File:Usrd setup.jpg"

2015 Summer Project Week:USReconstruction

2015-06-24T14:45:19Z

Frank: /* Project Description */

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Frank Preiswerk
* Laurent Chauvin
* Andras Lasso
* Adam Rankin (observer)
* Robert Owen, BK

==Project Description==

[[File:Usrd_2dus.png]]
[[File:Usrd_setup.jpg]]
[[File:Usrd_usrd.png]]
[[File:Usrd_respsig.png]]
[[File:Usrd_reconstruction.png]]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* This project will investigate the use of a single-element ultrasound transducer for 2D image reconstruction from navigated 2D ultrasound images.
* Technology: invariant feature extraction, descriptor representation.
* Application domains: registration, respiratory motion compensation
* Image domains: Ultrasound.
* Clinical use case scenarios: Establishment of a 4D motion atlas from 2D ultrasound data.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discussion and documentation
* Algorithms: fast KNN methods, binning.
* Mathematical formalisms: Correlation, similarity measures.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>
<br/>

==References==

Hybrid Utrasound and MRI Acquisitions for High-Speed Imaging of Respiratory Organ Motion<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, L.P. Panych, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Scanner-less High-Speed MR-Imaging of Repetitive Organ Motion for Image-Guided Therapy<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Detecting Rapid Organ Motion using a Hybrid MR-Ultrasound Setup and Bayesian Data Processing.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2014, pp. 7309<br/>
PDF © ISMRM, 2014.<br/>

Boosting MR Temporal Resolution using Rapid Ultrasound Measurements, for Motion-Tracking Purposes.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, B. M. Schwartz, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2013, pp. 478. Oral Presentation<br/>
PDF © ISMRM, 2013.<br/>

2015 Summer Project Week:USReconstruction

2015-06-24T14:43:21Z

Frank: /* Project Description */

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Frank Preiswerk
* Laurent Chauvin
* Andras Lasso
* Adam Rankin (observer)
* Robert Owen, BK

==Project Description==

[[File:Usrd_2dus.png]]
[[File:Usrd_setup.png]]
[[File:Usrd_usrd.png]]
[[File:Usrd_respsig.png]]
[[File:Usrd_reconstruction.png]]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* This project will investigate the use of a single-element ultrasound transducer for 2D image reconstruction from navigated 2D ultrasound images.
* Technology: invariant feature extraction, descriptor representation.
* Application domains: registration, respiratory motion compensation
* Image domains: Ultrasound.
* Clinical use case scenarios: Establishment of a 4D motion atlas from 2D ultrasound data.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discussion and documentation
* Algorithms: fast KNN methods, binning.
* Mathematical formalisms: Correlation, similarity measures.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>
<br/>

==References==

Hybrid Utrasound and MRI Acquisitions for High-Speed Imaging of Respiratory Organ Motion<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, L.P. Panych, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Scanner-less High-Speed MR-Imaging of Repetitive Organ Motion for Image-Guided Therapy<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Detecting Rapid Organ Motion using a Hybrid MR-Ultrasound Setup and Bayesian Data Processing.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2014, pp. 7309<br/>
PDF © ISMRM, 2014.<br/>

Boosting MR Temporal Resolution using Rapid Ultrasound Measurements, for Motion-Tracking Purposes.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, B. M. Schwartz, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2013, pp. 478. Oral Presentation<br/>
PDF © ISMRM, 2013.<br/>

File:Usrd reconstruction.png

2015-06-24T14:42:20Z

Frank:

File:Usrd setup.jpg

2015-06-24T14:40:33Z

Frank:

File:Usrd usrd.png

2015-06-24T14:40:13Z

Frank:

File:Usrd respsig.png

2015-06-24T14:38:14Z

Frank:

2015 Summer Project Week:USReconstruction

2015-06-22T08:14:56Z

Frank:

==Key Investigators==
* Frank Preiswerk
* Laurent Chauvin
* Andras Lasso

==Project Description==

[[File:Usrd_2dus.png]]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* This project will investigate the use of a single-element ultrasound transducer for 2D image reconstruction from navigated 2D ultrasound images.
* Technology: invariant feature extraction, descriptor representation.
* Application domains: registration, respiratory motion compensation
* Image domains: Ultrasound.
* Clinical use case scenarios: Establishment of a 4D motion atlas from 2D ultrasound data.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discussion and documentation
* Algorithms: fast KNN methods, binning.
* Mathematical formalisms: Correlation, similarity measures.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>
<br/>

==References==

Hybrid Utrasound and MRI Acquisitions for High-Speed Imaging of Respiratory Organ Motion<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, L.P. Panych, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Scanner-less High-Speed MR-Imaging of Repetitive Organ Motion for Image-Guided Therapy<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Detecting Rapid Organ Motion using a Hybrid MR-Ultrasound Setup and Bayesian Data Processing.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2014, pp. 7309<br/>
PDF © ISMRM, 2014.<br/>

Boosting MR Temporal Resolution using Rapid Ultrasound Measurements, for Motion-Tracking Purposes.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, B. M. Schwartz, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2013, pp. 478. Oral Presentation<br/>
PDF © ISMRM, 2013.<br/>

2015 Summer Project Week:USReconstruction

2015-06-22T08:14:24Z

Frank: /* Project Description */

2015 Summer Project Week:USReconstruction

2015-06-22T08:11:10Z

Frank: /* References */

==Key Investigators==
* Frank Preiswerk
* Laurent Chauvin
* Andras Lasso

==Project Description==

[[File:Usrd_2dus.png]]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* This project will investigate the use of a single-element ultrasound transducer for 2D image reconstruction from navigated 2D ultrasound images.
* Technology: invariant feature extraction, descriptor representation.
* Application domains: registration, respiratory motion compensation
* Image domains: Ultrasound.
* Clinical use case scenarios: Establishment of a 4D motion atlas from 2D ultrasound data.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discussion and documentation
* Algorithms: fast KNN methods, binning.
* Mathematical formalisms: Correlation, similarity measures.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==

Hybrid Utrasound and MRI Acquisitions for High-Speed Imaging of Respiratory Organ Motion<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, L.P. Panych, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Scanner-less High-Speed MR-Imaging of Repetitive Organ Motion for Image-Guided Therapy<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Detecting Rapid Organ Motion using a Hybrid MR-Ultrasound Setup and Bayesian Data Processing.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2014, pp. 7309<br/>
PDF © ISMRM, 2014.<br/>

Boosting MR Temporal Resolution using Rapid Ultrasound Measurements, for Motion-Tracking Purposes.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, B. M. Schwartz, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2013, pp. 478. Oral Presentation<br/>
PDF © ISMRM, 2013.<br/>

2015 Summer Project Week:USReconstruction

2015-06-22T08:10:32Z

Frank: /* References */

==Key Investigators==
* Frank Preiswerk
* Laurent Chauvin
* Andras Lasso

==Project Description==

[[File:Usrd_2dus.png]]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* This project will investigate the use of a single-element ultrasound transducer for 2D image reconstruction from navigated 2D ultrasound images.
* Technology: invariant feature extraction, descriptor representation.
* Application domains: registration, respiratory motion compensation
* Image domains: Ultrasound.
* Clinical use case scenarios: Establishment of a 4D motion atlas from 2D ultrasound data.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discussion and documentation
* Algorithms: fast KNN methods, binning.
* Mathematical formalisms: Correlation, similarity measures.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==

Hybrid Utrasound and MRI Acquisitions for High-Speed Imaging of Respiratory Organ Motion<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, L.P. Panych, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Scanner-less High-Speed MR-Imaging of Repetitive Organ Motion for Image-Guided Therapy<br/>
F. Preiswerk, M. Toews, W.S. Hoge, J.G. Chiou, W.M. Wells III, B. Madore.<br/>
Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.<br/>
PDF © Springer, 2015.<br/>

Detecting Rapid Organ Motion using a Hybrid MR-Ultrasound Setup and Bayesian Data Processing.<br/>
M. Toews, C.S. Mei, R. Chu, W. S. Hoge, L. P. Panych, B. Madore<br/>
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2014, pp. 7309<br/>
PDF © ISMRM, 2014.<br/>

2015 Summer Project Week:USReconstruction

2015-06-22T08:08:28Z

Frank:

File:1.png

2015-06-10T15:34:53Z

Frank: uploaded a new version of "File:1.png": Reverted to version as of 16:37, 17 June 2013

2015 Summer Project Week:USReconstruction

2015-06-10T15:34:02Z

Frank:

File:Usrd 2dus.png

2015-06-10T15:33:00Z

Frank:

File:1.png

2015-06-10T15:30:38Z

Frank: uploaded a new version of "File:1.png"

2015 Summer Project Week:USReconstruction

2015-06-10T15:27:05Z

Frank: /* Key Investigators */

==Key Investigators==
* Frank Preiswerk
* Laurent Chauvin
* Andras Lasso

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* This project will investigate the use of a single-element ultrasound transducer for 2D image reconstruction from navigated 2D ultrasound images.
* Technology: invariant feature extraction, descriptor representation.
* Application domains: registration, respiratory motion compensation
* Image domains: Ultrasound.
* Clinical use case scenarios: Establishment of a 4D motion atlas from 2D ultrasound data.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discussion and documentation
* Algorithms: fast KNN methods, binning.
* Mathematical formalisms: Correlation, similarity measures.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2015 Summer Project Week:USReconstruction

2015-06-08T14:28:39Z

Frank: /* Key Investigators */

==Key Investigators==
* Frank Preiswerk
* Laurent Chauvin

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* This project will investigate the use of a single-element ultrasound transducer for 2D image reconstruction from navigated 2D ultrasound images.
* Technology: invariant feature extraction, descriptor representation.
* Application domains: registration, respiratory motion compensation
* Image domains: Ultrasound.
* Clinical use case scenarios: Establishment of a 4D motion atlas from 2D ultrasound data.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discussion and documentation
* Algorithms: fast KNN methods, binning.
* Mathematical formalisms: Correlation, similarity measures.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2015 Summer Project Week:USReconstruction

2015-06-08T14:23:51Z

Frank: Created page with '==Key Investigators== * Frank Preiswerk * Laurent Chauvin'

==Key Investigators==
* Frank Preiswerk
* Laurent Chauvin

2015 Summer Project Week

2015-06-08T14:23:36Z

Frank: /* Feature Based Image Analysis */

__NOTOC__

[[image:PW-Summer2015.png|300px]]
<br>

'''Welcome to the web page for the 21st Project Week! This is the first Project Week that is being held in conjunction with the [http://www.cars-int.org/ CARS conference].'''

==Logistics==

*'''Dates:''' June 21-24, 2015.
*'''Location:''' [http://www.nh-collection.com/hotel/nh-collection-barcelona-constanza NH Collection Constanza Hotel, Barcelona, Spain]
*'''REGISTRATION:''' Please register by adding your name to the list at the end of this page
*'''Registration Fee:''' None. The organizers will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.
*'''Hotel:''' You are welcome to book a room using the CARS 2015 conference services ([http://www.cars-int.org/fileadmin/templates/download/2015/CARS_2015_accomondation.pdf Click here for form])
*To attend the CARS meeting, please visit [http://www.cars-int.org/ http://www.cars-int.org/]

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Sunday, June 21
!style="width:18%" |Monday, June 22
!style="width:18%" |Tuesday, June 23
!style="width:18%" |Wednesday, June 24
|-
|bgcolor="#ffffdd"|'''10:00am-3:00pm:'''
|rowspan=3 valign=bottom|<hr>'''6pm''' Meeting with All Participants in Hotel Constanza Lobby
|'''10:00-11am:''' <font color="#503020">Rapid Introduction of all Projects and Teams <br>
'''11am-3pm''' <font color="#503020">Work <br>

|
'''10:00am-11am:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis) <br>
'''11am-3pm''' <font color="#503020">Work
|'''10am-3pm''' <font color="#503020">Work <br>
|-
|bgcolor="#ffffdd"|'''3:00pm-5:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|-
|bgcolor="#ffffdd"|'''5:00-7:00pm'''
|'''5:00-7pm:''' <font color="#503020"> Work
|'''5:00-7:00pm:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2015_Summer_Project_Week/SoftwareStack| Open Software Stack]] (Steve Pieper)
|'''5:00-6pm:''' <font color="#503020"> Work <br>
'''6:00-7pm:''' Report Progress
|-
|bgcolor="#ffffdd"|'''7:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|}

== '''Background''' ==

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

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

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

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

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.

The 21st Project Week is being held on conjunction with the [http://www.cars-int.org/ CARS conference].

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

=Projects=
* [[2015_Summer_Project_Week_Template | Template for project pages]]

==Image-Guided Therapy==
*[[2015 Orthognatic Surgery|Orthognatic Surgery]] (Dženan Zukić, Kitware)
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]
*[[2015_pilot trajectory planning | Pilot Trajectory Planning(Caroline Essert, Sonia Pujol)]]
*[http://www.na-mic.org/Wiki/index.php/2015_Multi_atlas_based_prostate_segmentation Multi atlas based prostate segmentation] (Paolo Zaffino, Giampaolo Pileggi, Salvatore Scaramuzzino, Peter Behringer, Andrey Fedorov, Maria Francesca Spadea)
*[[2015_Summer_Project_Week:SlicerIGT|SlicerIGT tutorials for use cases]] (Tamas Ungi)
*[http://www.na-mic.org/Wiki/index.php/2015_Refinement_Registration_Module Refinement of RegistrationModule] (Peter Behringer, Andrey Fedorov)
*[http://www.na-mic.org/Wiki/index.php/2015_BRAINSFit_registration_in_SimpleITK BRAINSFit registration in SimpleITK] (Peter Behringer, Andrey Fedorov)

==Feature Based Image Analysis==
*[[2015_Summer_Project_Week:LungCAD| LungCAD]] (Jayender Jagadeesan)
*[[2015_Summer_Project_Week:QuantitativeProstate | Texture Analysis for Prostate Imaging]] (Tobias Penzkofer, Jay Jagadeesan, Tina Kapur)
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells, Tina Kapur)
*[[2015_Summer_Project_Week:USReconstruction | Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer ]] (Frank Preiswerk, Laurent Chauvin)

==Astronomy==
*[[2015_Summer_Project_Week:Astronomy | visualization of HI in galaxies]] (Davide Punzo)

==Infrastructure==
*[[2015_Summer_Project_Week:DCMTK| Integration and testing of new DCMTK with Slicer]] (Michael Onken, Andrey Fedorov)
*[[2015_Summer_Project_Week:Python_scripts_from_command_line|Simplify use of python scripts from the command line]] (Andrey Fedorov, Steve Pieper, Robin Weiss, Artem Mamonov)
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC)
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, ??)
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with "interesting" CLI modules (BRAINSFit, CIP, UKFTractography?) in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin, Jim Miller)
*[[2015_Summer_Project_Week:Update Checker | Update Checker]] (Frankling King, BWH)
*[[2015_Summer_Project_Week:Integrated Virtual Reality Viewer | Integrated Virtual Reality Viewer]] (Frankling King, BWH)
*[[2015_Summer_Project_Week:SegmentationNode| Use new Segmentation node in Editor]] (Andras Lasso, Steve Pieper)
*[[2015_Summer_Project_Week:IGTSliceletBase| Create base classes for IGT slicelet]] (Andras Lasso, Andrey Fedorov)

==Web / DCMJS==
*[[2015_Summer_Project_Week:Dicom parsing with DCMJS | Dicom parsing with DCMJS]] (Nicolas Rannou, Steve Pieper)
*[[2015_Summer_Project_Week:Volume rendering with DCMJS and THREEJS | Volume Rendering with DCMJS and THREEJS]] (Nicolas Rannou, Steve Pieper)

== '''Registrants''' ==

Please add your name to the list. This is the registration mechanism for this project week.
#Tina Kapur, BWH
#Ron Kikinis, BWH & Fraunhofer
#Steve Pieper, Isomics
#Tamas Ungi, Queen's University, Canada
#Andras Lasso, Queen's University, Canada
#Paolo Zaffino, ImagEngLab, Magna Graecia University, Italy
#Salvatore Scaramuzzino, ImagEngLab, Magna Graecia University, Italy
#Giampaolo Pileggi, ImagEngLab, Magna Graecia University, Italy
#Hans Meine, Fraunhofer MEVIS, Bremen, Germany
#Nicole Aucoin, BWH
#Sonia Pujol, BWH
#Dženan Zukić, Kitware, Carrboro, NC
#Jayender Jagadeesan, BWH
#Guido Gerig, Utah
#Sandy Wells, BWH
#Matthew Toews, École de Technologie Supérieure, Montreal, Canada
#Frank Preiswerk, BWH
#Junichi Tokuda, BWH
#Raul San Jose, BWH
#Jorge Onieva, BWH
#Yulong Zhao, Université de Rennes
#Laurent Chauvin, BWH
#Michael Onken, Open Connections
#Tobias Penzkofer, Department of Radiology, Charité Berlin, Germany
#Javier Pascau, Universidad Carlos III de Madrid, Spain
#Angel Torrado-Carvajal, Universidad Rey Juan Carlos, Madrid, Spain
#Nobuhiko Hata, BWH
#Robert H. Owen, BK Medical ApS, Denmark
#Clare Tempany, BWH
#Adam Rankin, Robarts
#Utsav Pardasani, Robarts
#Marcelo Romero, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#J. Jesus Montufar, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
#Andrey Fedorov, BWH
#Nicolas Rannou, BCH
#Mikael Brudfors, Universidad Carlos III de Madrid, Spain
#Laura Sanz, Universidad Carlos III de Madrid, Spain
#Eugenio Marinetto, Universidad Carlos III de Madrid, Spain
#David García, Universidad Carlos III de Madrid, Spain
#Franklin King, Queen's University / BWH
#Jorge García, Universidad Politécnica de Madrid, Spain
#Peter Behringer, BWH
#Caroline Essert, University of Strasbourg
#Pradyumna Reddy, Birla Institute of Technology and Science, Goa-Campus, India.