NAMIC Wiki - User contributions [en]

2017 Winter Project Week/Dinner

2017-01-09T16:58:14Z

Dpace: /* 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==

#Andras Lasso
#Curt Lisle
#Tina Kapur
# Andrey Fedorov
# Csaba Pinter
# Simon Drouin
# Alireza Mehrtash
# Henrik G. Jensen
# Beatriz Paniagua
# Beatriz Paniagua's +1
# Hans Meine
# Johan Andruejol
# Katie Mastrogiacomo
# Ron Kikinis
# Zora Kikinis
# Brian Helba
# Jennifer Nitsch
# Jean-Christophe Fillion-Robin
# Anneke Meyer
# Erik Ziegler
# Francois Rheault
# Rebekka Lauer
# Janne Beate Bakeng
# Louise Oram
# Teodora Szasz
# Danielle Pace

2016 Winter Project Week

2016-01-08T15:13:08Z

Dpace:

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

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

'''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/namic16 here].
<br>

== 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 [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|here]].

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

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

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 4
!style="width:18%" |Tuesday, January 5
!style="width:18%" |Wednesday, January 6
!style="width:18%" |Thursday, January 7
!style="width:18%" |Friday, January 8
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-12:00pm'''
|'''10:30am-12pm:''' [Tutorial] Diffeomorphic registration and geodesic shooting methods (I). (Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10:00-11:30am:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/NewSlicerExtensions | Slicer Extensions Birds of a Feather]]
|
'''10:00-11:30am:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/SlicerForMedicalRoboticsResearch| Slicer for Medical Robotics Research]]
<br>
|'''8:30-9:30am''' MR, US, Mass Spect guided Breast Surgery (Melissa Mallory, Nathalie Agar, Gabrielle Gauvin, Andras Lasso) <br>
'''9:30-10:30am''' Clinical perspective on Image Guided Neurosurgery (Alexandra Golby) <br>
'''10:30-11:30am''' Clinical perspective on Multiparametric MRI (Fiona Fennessy)<br>
'''11:30am-12pm''' Drug Delivery to Brain (Jason White) <br>
|'''10:00am-12:00pm:''' [[#Projects|Project Progress Updates]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''12pm:''' [[Winter2016TutorialContest|Tutorial Contest Winner Announcement]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|-
|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-1:05pm: <font color="#503020">Welcome</font>'''<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''2:45-4:00pm:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Ultrasound]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>

'''4:00-5:30pm:''' [Tutorial] Diffeomorphic registration geodesic shooting methods (II). (Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|
|'''1:00-2:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/DiffusionMRI| Diffusion MRI]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br>
'''3:00-4:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/QIICRTools| QIICR Tools]]
|'''1:00-3:00pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Session/What's_Planned_for_Slicer_Core|What's Planned for Slicer Core]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br>
'''3:30-5:00pm:''' Breakout Session: [[Events:TutorialContestJanuary2016 |2016 Tutorial Contest Review (Kiva)]]
| [[AMIGO Tours#Project Week 22|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> (Optional) [[2016_Winter_Project_Week/Dinner|Dinner on Thursday Night]]
|
|}

==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20160103%2F20160110
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20160103/20160110
}}

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

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

== IGT ==
* [[2016_Winter_Project_Week/Projects/SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard, Jayender Jagadeesan)
* [[2016_Winter_Project_Week/Projects/External_beam_planning | External Beam Radiotherapy Planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week/Projects/CryoPlanningSlicerModule | CryoPlanning Module in Slicer]] (Jayender Jagadeesan, Steve Pieper, Sandy Wells)
* [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin, Thomas Kirchner, Janek Groehl)
*[[2016_Winter_Project_Week/Projects/IntegrationCustusX|Integration of CustusX with PLUS on BK System]] (Christian A, Andras Lasso, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
*[[2016_Winter_Project_Week/Projects/IntegrationImFusion| Integration of ImFusion MR-US Registration with BWH AMIGO Neurosurgery Setup]] (Sarah Frisken, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso, Christian Askelan)
* [[2016_Winter_Project_Week/Projects/PLUS | Improvement of PLUS communication with Slicer (skip, see US standardization)]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/SliceTracker | Prostate motion tracking and navigation in Slicer ]] (Christian Herz, Andrey Fedorov, Andras Lasso)
* [[2016_Winter_Project_Week/Projects/EVD |Measuring Anatomic Factors for Extraventricular Drain Placement]] (Kirby Vosburgh, P. Jason White)
* [[2016_Winter_Project_Week/Projects/GABA_Delivery |Localized GABA delivery via BBB disruption]] (Nick Todd)
* [[2016_Winter_Project_Week/Projects/3DNrrdSequences | Sequences extension support for 3D+t NRRD]] (Adam Rankin)

== Tractography ==
* [[2016_Winter_Project_Week/Projects/Tractography_format_interoperability | Tractography Format Interoperability]] (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/SlicerDMRI_documentation | Slicer Diffusion MR / tractography workflow documentation]] (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/TractographyModuleDevelop&Test | Tractography Analysis Module Development and Testing]] (Fan Zhang, Pegah Kahaliardabili, Isaiah Norton, Lauren O'Donnell, others)

==Image Analysis==
* [[2016_Winter_Project_Week/Projects/CongenitalHeart | Interactive patch-based segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)
* [[2016_Winter_Project_Week/Projects/ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week/Projects/PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week/Projects/SphericalWaveletShapeAnalysis|Spherical Wavelet Shape Analysis]] (Yi Gao, Erich Bremer, Allen Tannenbaum, Ron Kikinis)
* [[2016_Winter_Project_Week/Projects/DigitalPathologyNuclearSegmentation|Digital Pathology Nuclear Segmentation]] (Erich Bremer, Yi Gao, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/SlicerCMFNextSteps | Moving beyond SlicerCMF and Future Projects]] (Beatriz Paniagua, Lucia Cevidanes, Steve Pieper, Juan Prieto)
*[[2016_Winter_Project_Week/Projects/ChestImagingPlatform|Chest Imaging Platform: COPD and Other Pulmonary Diseases]] (Raúl San José, Jorge Onieva, James Ross)
* [[2016_Winter_Project_Week/Projects/ChestImagingPlatformWorkflows|Nipype Workflows for the Chest Imaging Platform]] (James Ross, Raúl San José)
* [[2016 Winter Project Week/Projects/Cluster-Driven Lung Segmentation | Cluster-Driven Segmentation of Lung Nodules]] (Vivek Narayan, Raúl San José, Daniel Blezek, Steve Pieper, Chintan Parmar)
* [[2016_Winter_Project_Week/Projects/BatchImageAnalysis | Batch Clinical Image Analysis]] (Sandy Wells, Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Randy Gollub)
* [[2016_Winter_Project_Week/Projects/SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/Interactive4DSegmentation | Interactive 4D Segmentation Module]] (Ethan Ulrich, Andrey Fedorov, Andras Lasso)
* [[2016_Winter_Project_Week/Projects/DSCAnalysis | Dynamic Susceptibility Contrast (DSC) MRI Analysis]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)

* [[2016_Winter_Project_Week/Projects/ShapeAnalysis | Low-dimensional Principal Geodesic Analysis On the Manifold of Diffeomorphisms]] (Miaomiao Zhang, Polina Golland)

==Infrastructure==
*[[2016_Winter_Project_Week/Projects/UpgradeNAMICSlicerWiki|Upgrade the NAMIC + Slicer Web Infrastructure]] (Mike Halle, JC)
* [[2016_Winter_Project_Week/Projects/CommonDataStructure | Common Data Structure for CMF modules in Slicer]] (Jean-Baptiste Vimort, François Budin, Lucia Cevidanes, Beatriz Paniagua, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/StatisticalShapeModeling | Statistical Shape Modeling in Slicer: OA Index]] (Laura Pascal, Beatriz Paniagua, François Budin, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week/Projects/CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab Asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week/Projects/BRAINSFit_in_MeVisLab | Interoperability Tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week/Projects/CLI_Dashboard | Kibana Dashboard for Browsing All Available CLI Modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week/Projects/SegmentationEditorWidget | Editor Widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper)
* [[2016_Winter_Project_Week/Projects/SlicerTerminologyEditor | Terminology Editor]] (Nicole Aucoin, Csaba Pinter, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/DICOMSegObjIntegration | Integration of DICOM Segmentation Image Storage with Segmentations Module]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)

* [[2016_Winter_Project_Week/Projects/Data Persisting | Mechanism to Persist Clinical User Data from Different Modules Based on SQLite and/or other Database Engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/Workflows | Workflow Module that Enables the Navigation and Data Sharing between Different Modules in a Clinical Workflow ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/AIMInteroperability | AIM for Interoperability]] (Hans Meine, Andrey Fedorov, ??)
* [[2016_Winter_Project_Week/Projects/SlicerEnhancedMR | Developing support for Enhanced MR in Slicer]] (Michael Onken, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/CLIImprovement| Improve CLI robustness and testing]] (Johan Andruejol)
* [[2016_Winter_Project_Week/Projects/ExploringCollaborationVisualization| Exploring a collaboration in visualization]] (SK Semwal)

= '''Logistics''' =

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

= '''Registrants''' =

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

#Polina Golland, MIT
#Ron Kikinis, BWH
#Nicole Aucoin, BWH/SPL
#Peter Anderson
#Daniel Blezek, Isomics, Inc.
#Lucia Cevidanes, University of Michigan
#Adrian Dalca, MIT
#Simon Drouin, Montreal Neurological Institute
#Janek Groehl, German Cancer Research Center
#Tina Kapur, BWH/HMS
#Thomas Kirchner, German Cancer Research Center
#Hans Meine, University of Bremen/MEVIS
#Vivek Narayan, Dana Farber Cancer Institute
#Danielle Pace, MIT
#Laura Pascal, University of Michigan
#Steve Pieper, Isomics, Inc.
#Csaba Pinter, Queen's University
#Gregory Sharp, MGH
#James Miller, GE Research
#Kyle Sunderland, Queen's University
#Ethan Ulrich, University of Iowa
#Jean-Baptiste Vimort, University of Michigan
#Miaomiao Zhang, MIT
#Beatriz Paniagua, University of North Carolina at Chapel Hill
#Sonia Pujol, BWH
#Junichi Tokuda, BWH
#Katie Mastrogiacomo, BWH
#Niravkumar Patel, Worcester Polytechnic Institute
#Michael Onken, Open Connections (Germany)
#Erich Bremer, Stony Brook University
#Xiao Da, MGH
#Tobias Frank, Leibniz Universität Hannover
#Kirby Vosburgh, BWH
#P. Jason White, BWH
#Lauren O'Donnell, BWH
#Pegah Kahali, BWH
#Fan Zhang, BWH
#Adam Rankin, Robarts Research Institute
#Simon Leoard, Johns Hopkins University
#David Gering, HealthMyne
#Johan Andruejol, Kitware
#Jean-Christophe Fillion-Robin, Kitware
#Kelli Xu, MIT
#Christian Askeland, SINTEF
#Katharine Carter, BWH
#Nick Todd, BWH
#Ye Cheng, BWH
#Andriy Fedorov, BWH/HMS
#Sudhanshu Semwal, UCCS Professor
#Michael Halle, BWH
#Kallirroi Retzepi, MGH
#Jayender Jagadeesan, BWH
#Nathalie Agar, BWH
#Curtis Lisle, KnowledgeVis, LLC
#Andras Lasso, PerkLab, Queen's University
#Sarah Frisken, BWH
#Yi Gao, Stony Brook University
#Christian Herz, BWH
#Prashin Unadkat, SPL/BWH
#Jorge Onieva, BWH
#James Ross, BWH
#Raul SanJose, BWH
#Jayashree Kalpathy-Cramer, MGH/HMS
#Daniel Glazer, BWH
#Valentin Demeusy, SPL Intern
#Ameet Jain, Phillips Research
#Utsav Soni, BWH
#Matthew Toews, Ecole de Technologie Superieure
#Isaiah Norton, BWH
#Sean Doyle, MGH
#Stuart Pomerantz, MGH
#Randy Gollub, MGH
#Melissa Mallory, BWH
#Axel Krieger, Children's National Medical Center
#Nobuhiko Hata, BWH
#Carl-Fredrik Westin, BWH/HMS
#Terry Yoo, NLM-NIH/Harvard IACS

2016 Winter Project Week/Projects/CongenitalHeart

2016-01-08T15:01:27Z

Dpace:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]
Image:congenitalMICCAI15.png|Results after user manually segments 3, 8 or 14 slices
</gallery>

==Key Investigators==
*Danielle Pace (MIT)
*Adrian Dalca (MIT)
*Polina Golland (MIT)

==Project Description==

* We have developed an interactive segmentation algorithm for cardiac MR images from patients with severe congenital heart disease, in which the user manually segments a few short-axis slices and the remainder is segmented automatically using patch-based segmentation (Pace et al, MICCAI 2015)

{| 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;"
|

* Continue improving the method, especially focusing on correctly segmenting thin walls of the heart when few slices are manually segmented
|

* Continue investigating algorithm modifications to enhance / correctly segment the thin walls.
|

* Worked on integrating new "thin wall" features to improve thin wall detection
|}

==Background and References==
* [http://link.springer.com/chapter/10.1007/978-3-319-24574-4_10 Pace et al,, Interactive Whole-Heart Segmentation in Congenital Heart Disease, MICCAI 2015]

2016 Winter Project Week/Projects/CongenitalHeart

2016-01-04T18:06:32Z

Dpace:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]
Image:congenitalMICCAI15.png|Results after user manually segments 3, 8 or 14 slices
</gallery>

==Key Investigators==
*Danielle Pace (MIT)
*Adrian Dalca (MIT)
*Polina Golland (MIT)

==Project Description==

* We have developed an interactive segmentation algorithm for cardiac MR images from patients with severe congenital heart disease, in which the user manually segments a few short-axis slices and the remainder is segmented automatically using patch-based segmentation (Pace et al, MICCAI 2015)

{| 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;"
|

* Continue improving the method, especially focusing on correctly segmenting thin walls of the heart when few slices are manually segmented
|

* Continue investigating algorithm modifications to enhance / correctly segment the thin walls.
|

*
|}

==Background and References==
* [http://link.springer.com/chapter/10.1007/978-3-319-24574-4_10 Pace et al,, Interactive Whole-Heart Segmentation in Congenital Heart Disease, MICCAI 2015]

2016 Winter Project Week/Projects/CongenitalHeart

2016-01-04T17:25:30Z

Dpace:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]
Image:congenitalMICCAI15.png|Results after user manually segments 3, 8 or 14 slices
</gallery>

==Key Investigators==
*Danielle Pace (MIT)
*Adrian Dalca (MIT)
*Polina Golland (MIT)

==Project Description==

* We have developed an interactive segmentation algorithm for cardiac MR images from patients with severe congenital heart disease, in which the user manually segments a few short-axis slices and the remainder is segmented automatically using patch-based segmentation (Pace et al, MICCAI 2015)

{| 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;"
|

* Continue improving the method, especially focusing on correctly segmenting thin walls of the heart when few slices are manually segmented
|

*
|

*
|}

==Background and References==
* [http://link.springer.com/chapter/10.1007/978-3-319-24574-4_10 Pace et al,, Interactive Whole-Heart Segmentation in Congenital Heart Disease, MICCAI 2015]

2016 Winter Project Week/Projects/CongenitalHeart

2016-01-04T17:25:06Z

Dpace:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]
Image:congenitalMICCAI15.png|Results after user manually segments 3, 8 or 14 slices
</gallery>

==Key Investigators==
*Danielle Pace (MIT)
*Adrian Dalca (MIT)
*Polina Golland (MIT)

==Project Description==

* We have developed an interactive segmentation algorithm for cardiac MR images from patients with severe congenital heart disease, in which the user manually segments a few short-axis slices and the remainder is segmented automatically using patch-based segmentation (Pace et al, MICCAI 2015)

{| 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;"
|

* Continue improving the method, especially focusing on correctly segmenting thin walls of the heart when few slices are manually segmented
|

*
|

*
|}

==Background and References==
[http://link.springer.com/chapter/10.1007/978-3-319-24574-4_10 Pace et al,, Interactive Whole-Heart Segmentation in Congenital Heart Disease, MICCAI 2015]

2016 Winter Project Week/Projects/CongenitalHeart

2016-01-04T17:22:12Z

Dpace:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]
Image:congenitalMICCAI15.png|Results after user manually segments 3, 8 or 14 slices
</gallery>

==Key Investigators==
*Danielle Pace (MIT)
*Adrian Dalca (MIT)
*Polina Golland (MIT)

==Project Description==

* We have developed an interactive segmentation algorithm for cardiac MR images from patients with severe congenital heart disease, in which the user manually segments a few short-axis slices and the remainder is segmented automatically using patch-based segmentation (Pace et al, MICCAI 2015)

{| 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;"
|

* Continue improving the method, especially focusing on correctly segmenting thin walls of the heart when few slices are manually segmented
|

*
|

*
|}

==Background and References==

2016 Winter Project Week/Projects/CongenitalHeart

2016-01-04T17:20:34Z

Dpace:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]
Image:congenitalMICCAI15.png|Results after user manually segments 3, 8 or 14 slices
</gallery>

==Key Investigators==
*Danielle Pace (MIT)
*Adrian Dalca (MIT)
*Polina Golland (MIT)

==Project Description==

* We have developed an interactive segmentation algorithm for cardiac MR images from patients with severe congenital heart disease, in which the user manually segments a few short-axis slices and the remainder is segmented automatically (Pace et al, MICCAI 2015)

{| 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;"
|

*
|

*
|

*
|}

==Background and References==

File:CongenitalMICCAI15.png

2016-01-04T16:27:06Z

Dpace:

2016 Winter Project Week/Projects/CongenitalHeart

2016-01-04T16:26:53Z

Dpace:

2016 Winter Project Week/Projects/CongenitalHeart

2016-01-04T16:23:07Z

Dpace:

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

</gallery>

==Key Investigators==
*Danielle Pace (MIT)
*Adrian Dalca (MIT)
*Polina Golland (MIT)

==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;"
|

*
|

*
|

*
|}

==Background and References==

2016 Winter Project Week/Projects/CongenitalHeart

2016-01-04T16:22:18Z

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

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

</gallery>

==Key Investigators==


==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;"
|

*
|

*
|

*
|}

==Background and References==

2016 Winter Project Week

2016-01-04T16:21:51Z

Dpace:

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

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

'''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/namic16 here].
<br>

== 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 [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|here]].

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

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

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 4
!style="width:18%" |Tuesday, January 5
!style="width:18%" |Wednesday, January 6
!style="width:18%" |Thursday, January 7
!style="width:18%" |Friday, January 8
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-12:00pm'''
|'''10:30am-12pm:''' [Tutorial] Diffeomorphic registration and geodesic shooting methods (I). (Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10:00-11:30am:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/NewSlicerExtensions | Slicer Extensions Birds of a Feather]]
|
'''10:00-11:30am:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/SlicerForMedicalRoboticsResearch| Slicer for Medical Robotics Research]]
<br>
|'''8:30-9:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Image-guided Breast Surgery| MR, US, Mass Spect guided Breast Surgery]] (Melissa Mallory, Nathalie Agar, Gabrielle Gauvin, Andras Lasso) <br>
'''9:30-10:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Image-guided Neurosurgery| Clinical perspective on Image Guided Neurosurgery]] (Alexandra Golby) <br>
'''10:30-11:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Multiparametric MRI| Clinical perspective on Multiparametric MRI]] (Fiona Fennessy)<br>
'''11:30am-12:30pm''' TBD <br>
|'''10:00am-12:00pm:''' [[#Projects|Project Progress Updates]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''12pm:''' [[Events:TutorialContestJanuary2016|Tutorial Contest Winner Announcement]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|-
|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-1:05pm: <font color="#503020">Welcome</font>'''<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''2:45-4:00pm:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Ultrasound]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>

'''4:00-5:30pm:''' [Tutorial] Diffeomorphic registration geodesic shooting methods (II). (Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|
|'''1:00-2:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/DiffusionMRI| Diffusion MRI]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br>
'''3:00-4:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/QIICRTools| QIICR Tools]]
|'''1:00-3:00pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Session/What's_Planned_for_Slicer_Core|What's Planned for Slicer Core]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|
|-
|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
|
|}

==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20160103%2F20160110
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20160103/20160110
}}

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

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

== IGT ==
* [[2016_Winter_Project_Week/Projects/SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard, Jayender Jagadeesan)
* [[2016_Winter_Project_Week/Projects/External_beam_planning | External Beam Radiotherapy Planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week/Projects/CryoPlanningSlicerModule | CryoPlanning Module in Slicer]] (Jayender Jagadeesan, Steve Pieper, Sandy Wells)
* [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/IntegrationCustusX|Integration of CustusX with PLUS on BK System]] (Christian A, Andras Lasso, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
*[[2016_Winter_Project_Week/Projects/IntegrationImFusion| Integration of ImFusion MR-US Registration with BWH AMIGO Neurosurgery Setup]] (Sarah Frisken, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso, Christian Askelan)
* [[2016_Winter_Project_Week/Projects/PLUS | Improvement of PLUS communication with Slicer]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/SliceTracker | Prostate motion tracking and navigation in Slicer ]] (Christian Herz, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/EVD |Measuring Anatomic Factors for Extraventricular Drain Placement]] (Kirby Vosburgh, P. Jason White)
* [[2016_Winter_Project_Week/Projects/GABA_Delivery |Localized GABA delivery via BBB disruption]] (Nick Todd)

== Tractography ==
* [[2016_Winter_Project_Week/Projects/Tractography_format_interoperability | Tractography Format Interoperability]] (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/SlicerDMRI_documentation | Slicer Diffusion MR / tractography workflow documentation]] (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/TractographyModuleDevelop&Test | Tractography Analysis Module Development and Testing]] (Fan Zhang, Pegah Kahaliardabili, Isaiah Norton, Lauren O'Donnell, others)

==Image Analysis==
* [[2016_Winter_Project_Week/Projects/ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week/Projects/PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week/Projects/SphericalWaveletShapeAnalysis|Spherical Wavelet Shape Analysis]] (Yi Gao, Erich Bremer, Allen Tannenbaum, Ron Kikinis)
* [[2016_Winter_Project_Week/Projects/DigitalPathologyNuclearSegmentation|Digital Pathology Nuclear Segmentation]] (Erich Bremer, Yi Gao, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/SlicerCMFNextSteps | Moving beyond SlicerCMF and Future Projects]] (Beatriz Paniagua, Lucia Cevidanes, Steve Pieper, Juan Prieto)
*[[2016_Winter_Project_Week/Projects/ChestImagingPlatform|Chest Imaging Platform: COPD and Other Pulmonary Diseases]] (Raúl San José, Jorge Onieva, James Ross)
* [[2016_Winter_Project_Week/Projects/ChestImagingPlatformWorkflows|Nipype Workflows for the Chest Imaging Platform]] (James Ross, Raúl San José)
* [[2016 Winter Project Week/Projects/Cluster-Driven Lung Segmentation | Cluster-Driven Segmentation of Lung Nodules]] (Vivek Narayan, Raúl San José, Daniel Blezek, Steve Pieper, Chintan Parmar)
* [[2016_Winter_Project_Week/Projects/BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week/Projects/SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/Interactive4DSegmentation | Interactive 4D Segmentation Module]] (Ethan Ulrich, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/CongenitalHeart | Interactive patch-based segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)
* [[2016_Winter_Project_Week/Projects/DSCAnalysis | Dynamic Susceptibility Contrast (DSC) MRI Analysis]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)
* [[2016_Winter_Project_Week/Projects/ShapeAnalysis | Low-dimensional Principal Geodesic Analysis On the Manifold of Diffeomorphisms]] (Miaomiao Zhang, Polina Golland)

==Infrastructure==
*[[2016_Winter_Project_Week/Projects/UpgradeNAMICSlicerWiki|Upgrade the NAMIC (and Slicer?) Wiki]] (Mike Halle, JC)
* [[2016_Winter_Project_Week/Projects/CommonDataStructure | Common Data Structure for CMF modules in Slicer]] (Jean-Baptiste Vimort, François Budin, Lucia Cevidanes, Beatriz Paniagua, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/StatisticalShapeModeling | Statistical Shape Modeling in Slicer: OA Index]] (Laura Pascal, Beatriz Paniagua, François Budin, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week/Projects/CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab Asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week/Projects/BRAINSFit_in_MeVisLab | Interoperability Tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week/Projects/CLI_Dashboard | Kibana Dashboard for Browsing All Available CLI Modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week/Projects/SegmentationEditorWidget | Editor Widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper)
* [[2016_Winter_Project_Week/Projects/SlicerTerminologyEditor | Terminology Editor]] (Nicole Aucoin, Csaba Pinter, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/DICOMSegObjIntegration | Integration of DICOM Segmentation Image Storage with Segmentations Module]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week/Projects/CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week/Projects/Data Persisting | Mechanism to Persist Clinical User Data from Different Modules Based on SQLite and/or other Database Engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/Workflows | Workflow Module that Enables the Navigation and Data Sharing between Different Modules in a Clinical Workflow ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/AIMInteroperability | AIM for Interoperability]] (Hans Meine, Andrey Fedorov, ??)
* [[2016_Winter_Project_Week/Projects/PLUSOCR | Exploration of open-source OCR libraries for device meta-data capture without research interface ]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/3DNrrdSequences | Sequences extension support for 3D+t NRRD]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/SlicerEnhancedMR | Developing support for Enhanced MR in Slicer]] (Michael Onken, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/CLIImprovement| Improve CLI robustness and testing]] (Johan Andruejol)

= '''Logistics''' =

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

= '''Registrants''' =

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

#Polina Golland, MIT
#Ron Kikinis, BWH
#Nicole Aucoin, BWH/SPL
#Peter Anderson
#Daniel Blezek, Isomics, Inc.
#Lucia Cevidanes, University of Michigan
#Adrian Dalca, MIT
#Simon Drouin, Montreal Neurological Institute
#Janek Groehl, German Cancer Research Center
#Tina Kapur, BWH/HMS
#Thomas Kirchner, German Cancer Research Center
#Hans Meine, University of Bremen/MEVIS
#Vivek Narayan, Dana Farber Cancer Institute
#Danielle Pace, MIT
#Laura Pascal, University of Michigan
#Steve Pieper, Isomics, Inc.
#Csaba Pinter, Queen's University
#Gregory Sharp, MGH
#James Miller, GE Research
#Kyle Sunderland, Queen's University
#Ethan Ulrich, University of Iowa
#Jean-Baptiste Vimort, University of Michigan
#Miaomiao Zhang, MIT
#Beatrize Paniagua, University of North Carolina at Chapel Hill
#Sonia Pujol, BWH
#Junichi Tokuda, BWH
#Katie Mastrogiacomo, BWH
#Niravkumar Patel, Worcester Polytechnic Institute
#Michael Onken, Open Connections (Germany)
#Erich Bremer, Stony Brook University
#Xiao Da, MGH
#Tobias Frank, Leibniz Universität Hannover
#Kirby Vosburgh, BWH
#P. Jason White, BWH
#Lauren O'Donnell, BWH
#Pegah Kahali, BWH
#Fan Zhang, BWH
#Adam Rankin, Robarts Research Institute
#Simon Leoard, Johns Hopkins University
#David Gering, HealthMyne
#Johan Andruejol, Kitware
#Jean-Christophe Fillion-Robin, Kitware
#Kelly Xu, MIT
#Christian Askeland, SINTEF
#Katharine Carter, BWH
#Nick Todd, BWH
#Ye Cheng, BWH
#Andriy Fedorov, BWH/HMS
#Sudhanshu Semwal, UCCS Professor
#Michael Halle, BWH
#Kallirroi Retzepi, MGH
#Jayender Jagadeesan, BWH
#Nathalie Agar, BWH
#Curtis Lisle, KnowledgeVis, LLC
#Andras Lasso, PerkLab, Queen's University
#Sarah Frisken, BWH
#Yi Gao, Stony Brook University
#Christian Herz, BWH
#Prashin Unadkat, SPL/BWH

2016 Winter Project Week

2016-01-04T16:21:27Z

Dpace:

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

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

'''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/namic16 here].
<br>

== 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 [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|here]].

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

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

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, January 4
!style="width:18%" |Tuesday, January 5
!style="width:18%" |Wednesday, January 6
!style="width:18%" |Thursday, January 7
!style="width:18%" |Friday, January 8
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#6494ec"| '''Work on Projects'''
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9:00am-12:00pm'''
|'''10:30am-12pm:''' [Tutorial] Diffeomorphic registration and geodesic shooting methods (I). (Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10:00-11:30am:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/NewSlicerExtensions | Slicer Extensions Birds of a Feather]]
|
'''10:00-11:30am:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/SlicerForMedicalRoboticsResearch| Slicer for Medical Robotics Research]]
<br>
|'''8:30-9:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Image-guided Breast Surgery| MR, US, Mass Spect guided Breast Surgery]] (Melissa Mallory, Nathalie Agar, Gabrielle Gauvin, Andras Lasso) <br>
'''9:30-10:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Image-guided Neurosurgery| Clinical perspective on Image Guided Neurosurgery]] (Alexandra Golby) <br>
'''10:30-11:30am''' [[2016_Winter_Project_Week/Breakout_Sessions/IGT#Multiparametric MRI| Clinical perspective on Multiparametric MRI]] (Fiona Fennessy)<br>
'''11:30am-12:30pm''' TBD <br>
|'''10:00am-12:00pm:''' [[#Projects|Project Progress Updates]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''12pm:''' [[Events:TutorialContestJanuary2016|Tutorial Contest Winner Announcement]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|-
|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-1:05pm: <font color="#503020">Welcome</font>'''<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''1:05-2:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>
'''2:45-4:00pm:''' Breakout Session: [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Ultrasound]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>-----------------<br>

'''4:00-5:30pm:''' [Tutorial] Diffeomorphic registration geodesic shooting methods (II). (Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|
|'''1:00-2:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/DiffusionMRI| Diffusion MRI]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br>
'''3:00-4:30pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Sessions/QIICRTools| QIICR Tools]]
|'''1:00-3:00pm:''' Breakout Session:[[2016_Winter_Project_Week/Breakout_Session/What's_Planned_for_Slicer_Core|What's Planned for Slicer Core]]<br>
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|
|-
|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
|
|}

==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20160103%2F20160110
|title=NAMIC Winter Project Week
|view=WEEK
|dates=20160103/20160110
}}

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

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

== IGT ==
* [[2016_Winter_Project_Week/Projects/SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard, Jayender Jagadeesan)
* [[2016_Winter_Project_Week/Projects/External_beam_planning | External Beam Radiotherapy Planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week/Projects/CryoPlanningSlicerModule | CryoPlanning Module in Slicer]] (Jayender Jagadeesan, Steve Pieper, Sandy Wells)
* [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | Tracked Ultrasound Standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/IntegrationCustusX|Integration of CustusX with PLUS on BK System]] (Christian A, Andras Lasso, Adam Rankin)
*[[2016_Winter_Project_Week/Projects/MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
*[[2016_Winter_Project_Week/Projects/IntegrationImFusion| Integration of ImFusion MR-US Registration with BWH AMIGO Neurosurgery Setup]] (Sarah Frisken, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso, Christian Askelan)
* [[2016_Winter_Project_Week/Projects/PLUS | Improvement of PLUS communication with Slicer]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/SliceTracker | Prostate motion tracking and navigation in Slicer ]] (Christian Herz, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/EVD |Measuring Anatomic Factors for Extraventricular Drain Placement]] (Kirby Vosburgh, P. Jason White)
* [[2016_Winter_Project_Week/Projects/GABA_Delivery |Localized GABA delivery via BBB disruption]] (Nick Todd)

== Tractography ==
* [[2016_Winter_Project_Week/Projects/Tractography_format_interoperability | Tractography Format Interoperability]] (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/SlicerDMRI_documentation | Slicer Diffusion MR / tractography workflow documentation]] (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week/Projects/TractographyModuleDevelop&Test | Tractography Analysis Module Development and Testing]] (Fan Zhang, Pegah Kahaliardabili, Isaiah Norton, Lauren O'Donnell, others)

==Image Analysis==
* [[2016_Winter_Project_Week/Projects/ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week/Projects/PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week/Projects/SphericalWaveletShapeAnalysis|Spherical Wavelet Shape Analysis]] (Yi Gao, Erich Bremer, Allen Tannenbaum, Ron Kikinis)
* [[2016_Winter_Project_Week/Projects/DigitalPathologyNuclearSegmentation|Digital Pathology Nuclear Segmentation]] (Erich Bremer, Yi Gao, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/SlicerCMFNextSteps | Moving beyond SlicerCMF and Future Projects]] (Beatriz Paniagua, Lucia Cevidanes, Steve Pieper, Juan Prieto)
*[[2016_Winter_Project_Week/Projects/ChestImagingPlatform|Chest Imaging Platform: COPD and Other Pulmonary Diseases]] (Raúl San José, Jorge Onieva, James Ross)
* [[2016_Winter_Project_Week/Projects/ChestImagingPlatformWorkflows|Nipype Workflows for the Chest Imaging Platform]] (James Ross, Raúl San José)
* [[2016 Winter Project Week/Projects/Cluster-Driven Lung Segmentation | Cluster-Driven Segmentation of Lung Nodules]] (Vivek Narayan, Raúl San José, Daniel Blezek, Steve Pieper, Chintan Parmar)
* [[2016_Winter_Project_Week/Projects/BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week/Projects/SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/Interactive4DSegmentation | Interactive 4D Segmentation Module]] (Ethan Ulrich, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/CongenitalHeart | Interactive patch-based segmentation for congenital heart disease}] (Danielle Pace, Adrian Dalca, Polina Golland)
* [[2016_Winter_Project_Week/Projects/DSCAnalysis | Dynamic Susceptibility Contrast (DSC) MRI Analysis]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)
* [[2016_Winter_Project_Week/Projects/ShapeAnalysis | Low-dimensional Principal Geodesic Analysis On the Manifold of Diffeomorphisms]] (Miaomiao Zhang, Polina Golland)

==Infrastructure==
*[[2016_Winter_Project_Week/Projects/UpgradeNAMICSlicerWiki|Upgrade the NAMIC (and Slicer?) Wiki]] (Mike Halle, JC)
* [[2016_Winter_Project_Week/Projects/CommonDataStructure | Common Data Structure for CMF modules in Slicer]] (Jean-Baptiste Vimort, François Budin, Lucia Cevidanes, Beatriz Paniagua, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/StatisticalShapeModeling | Statistical Shape Modeling in Slicer: OA Index]] (Laura Pascal, Beatriz Paniagua, François Budin, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week/Projects/CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week/Projects/CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab Asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week/Projects/BRAINSFit_in_MeVisLab | Interoperability Tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week/Projects/CLI_Dashboard | Kibana Dashboard for Browsing All Available CLI Modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week/Projects/SegmentationEditorWidget | Editor Widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper)
* [[2016_Winter_Project_Week/Projects/SlicerTerminologyEditor | Terminology Editor]] (Nicole Aucoin, Csaba Pinter, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/DICOMSegObjIntegration | Integration of DICOM Segmentation Image Storage with Segmentations Module]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week/Projects/CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week/Projects/Data Persisting | Mechanism to Persist Clinical User Data from Different Modules Based on SQLite and/or other Database Engines ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/Workflows | Workflow Module that Enables the Navigation and Data Sharing between Different Modules in a Clinical Workflow ]] (Raúl San José, Jorge Onieva)
* [[2016_Winter_Project_Week/Projects/AIMInteroperability | AIM for Interoperability]] (Hans Meine, Andrey Fedorov, ??)
* [[2016_Winter_Project_Week/Projects/PLUSOCR | Exploration of open-source OCR libraries for device meta-data capture without research interface ]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/3DNrrdSequences | Sequences extension support for 3D+t NRRD]] (Adam Rankin)
* [[2016_Winter_Project_Week/Projects/SlicerEnhancedMR | Developing support for Enhanced MR in Slicer]] (Michael Onken, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/CLIImprovement| Improve CLI robustness and testing]] (Johan Andruejol)

= '''Logistics''' =

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

= '''Registrants''' =

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

#Polina Golland, MIT
#Ron Kikinis, BWH
#Nicole Aucoin, BWH/SPL
#Peter Anderson
#Daniel Blezek, Isomics, Inc.
#Lucia Cevidanes, University of Michigan
#Adrian Dalca, MIT
#Simon Drouin, Montreal Neurological Institute
#Janek Groehl, German Cancer Research Center
#Tina Kapur, BWH/HMS
#Thomas Kirchner, German Cancer Research Center
#Hans Meine, University of Bremen/MEVIS
#Vivek Narayan, Dana Farber Cancer Institute
#Danielle Pace, MIT
#Laura Pascal, University of Michigan
#Steve Pieper, Isomics, Inc.
#Csaba Pinter, Queen's University
#Gregory Sharp, MGH
#James Miller, GE Research
#Kyle Sunderland, Queen's University
#Ethan Ulrich, University of Iowa
#Jean-Baptiste Vimort, University of Michigan
#Miaomiao Zhang, MIT
#Beatrize Paniagua, University of North Carolina at Chapel Hill
#Sonia Pujol, BWH
#Junichi Tokuda, BWH
#Katie Mastrogiacomo, BWH
#Niravkumar Patel, Worcester Polytechnic Institute
#Michael Onken, Open Connections (Germany)
#Erich Bremer, Stony Brook University
#Xiao Da, MGH
#Tobias Frank, Leibniz Universität Hannover
#Kirby Vosburgh, BWH
#P. Jason White, BWH
#Lauren O'Donnell, BWH
#Pegah Kahali, BWH
#Fan Zhang, BWH
#Adam Rankin, Robarts Research Institute
#Simon Leoard, Johns Hopkins University
#David Gering, HealthMyne
#Johan Andruejol, Kitware
#Jean-Christophe Fillion-Robin, Kitware
#Kelly Xu, MIT
#Christian Askeland, SINTEF
#Katharine Carter, BWH
#Nick Todd, BWH
#Ye Cheng, BWH
#Andriy Fedorov, BWH/HMS
#Sudhanshu Semwal, UCCS Professor
#Michael Halle, BWH
#Kallirroi Retzepi, MGH
#Jayender Jagadeesan, BWH
#Nathalie Agar, BWH
#Curtis Lisle, KnowledgeVis, LLC
#Andras Lasso, PerkLab, Queen's University
#Sarah Frisken, BWH
#Yi Gao, Stony Brook University
#Christian Herz, BWH
#Prashin Unadkat, SPL/BWH

2014 Summer Project Week:Cardiac-Congenital

2014-06-27T04:32:22Z

Dpace:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:CongenitalHeartModelsSlicer.png|Results of patch-based segmentation
Image:CongenitalHeartModels.png|Patient-specific heart model
Image:CongenitalHeartModels2.png|Printed model

</gallery>

==Key Investigators==
* Danielle Pace, MIT
* Adrian Dalca, MIT
* Polina Golland, MIT

==Project Description==

This project involves semi-automatic segmentation of gated 3D magnetic resonance images of hearts with congenital heart defects. Our aim is to create patient-specific heart models for surgical planning, which can be viewed either graphically on a computer, or with a 3D printer to create a physical model for surgeons.

We have had initial success in significantly reducing segmentation time with the following pipeline:
1) User manually segments ~10 axial slices
2) Segment the remaining slices using patch-based majority voting.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Continue testing the patch based methods on an additional five datasets.
* Address main remaining challenge: segmenting thin interior heart walls.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Manually segment ~10 axial slices for each of the five additional datasets.
* Explore remaining parameters for the patch-based segmentation: e.g. weighted voting, varying k in k-nearest neighbors patch lookup

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Did manual initial segmentations and and ran patch-based segmentation on additional datasets.
</div>
</div>

2014 Summer Project Week:Cardiac-Congenital

2014-06-23T16:11:35Z

Dpace:

File:CongenitalHeartModelsSlicer.png

2014-06-23T16:11:03Z

Dpace:

2014 Summer Project Week:Cardiac-Congenital

2014-06-23T16:06:56Z

Dpace:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:WMH_T1.png|Clinical Stroke Image
Image:CongenitalHeartModels.png|Patient-specific heart model
Image:CongenitalHeartModels2.png|Printed model

</gallery>

==Key Investigators==
* Danielle Pace, MIT
* Adrian Dalca, MIT
* Polina Golland, MIT

==Project Description==

This project involves semi-automatic segmentation of gated 3D magnetic resonance images of hearts with congenital heart defects. Our aim is to create patient-specific heart models for surgical planning, which can be viewed either graphically on a computer, or with a 3D printer to create a physical model for surgeons.

We have had initial success in significantly reducing segmentation time with the following pipeline:
1) User manually segments ~10 axial slices
2) Segment the remaining slices using patch-based majority voting.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Continue testing the patch based methods on an additional five datasets.
* Address main remaining challenge: segmenting thin interior heart walls.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Manually segment ~10 axial slices for each of the five additional datasets.
* Explore remaining parameters for the patch-based segmentation: e.g. weighted voting, varying k in k-nearest neighbors patch lookup

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

File:CongenitalHeartModels2.png

2014-06-23T16:06:11Z

Dpace:

File:CongenitalHeartModels.png

2014-06-23T16:05:57Z

Dpace:

2014 Summer Project Week:Cardiac-Congenital

2014-06-23T16:05:43Z

Dpace:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:WMH_T1.png|Clinical Stroke Image
Image:WMH_T1.png|Clinical Stroke Image
Image:WMH_T1.png|Clinical Stroke Image

</gallery>

==Key Investigators==
* Danielle Pace, MIT
* Adrian Dalca, MIT
* Polina Golland, MIT

==Project Description==

This project involves semi-automatic segmentation of gated 3D magnetic resonance images of hearts with congenital heart defects. Our aim is to create patient-specific heart models for surgical planning, which can be viewed either graphically on a computer, or with a 3D printer to create a physical model for surgeons.

We have had initial success in significantly reducing segmentation time with the following pipeline:
1) User manually segments ~10 axial slices
2) Segment the remaining slices using patch-based majority voting.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Continue testing the patch based methods on an additional five datasets.
* Address main remaining challenge: segmenting thin interior heart walls.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Manually segment ~10 axial slices for each of the five additional datasets.
* Explore remaining parameters for the patch-based segmentation: e.g. weighted voting, varying k in k-nearest neighbors patch lookup

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

2014 Summer Project Week:Cardiac-Congenital

2014-06-23T16:03:35Z

Dpace:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Danielle Pace, MIT
* Adrian Dalca, MIT
* Polina Golland, MIT

==Project Description==

This project involves semi-automatic segmentation of gated 3D magnetic resonance images of hearts with congenital heart defects. Our aim is to create patient-specific heart models for surgical planning, which can be viewed either graphically on a computer, or with a 3D printer to create a physical model for surgeons.

We have had initial success in significantly reducing segmentation time with the following pipeline:
1) User manually segments ~10 axial slices
2) Segment the remaining slices using patch-based majority voting.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Continue testing the patch based methods on an additional five datasets.
* Address main remaining challenge: segmenting thin interior heart walls.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Manually segment ~10 axial slices for each of the five additional datasets.
* Explore remaining parameters for the patch-based segmentation: e.g. weighted voting, varying k in k-nearest neighbors patch lookup

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

2014 Summer Project Week

2014-06-23T15:55:58Z

Dpace:

__NOTOC__

[[image:PW-MIT2014.png|300px]]

Dates: June 23-27, 2014.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 23
!style="width:18%" |Tuesday, June 24
!style="width:18%" |Wednesday, June 25
!style="width:18%" |Thursday, June 26
!style="width:18%" |Friday, June 27
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)
<br>
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Neuro|Image-Guided Therapy - Neurosurgery]] (Alexandra Golby, Tina Kapur) <br>
[[MIT_Project_Week_Rooms#Star|Star]]

<br>----------------------------------------<br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Prostate|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Noby Hata)
[[MIT_Project_Week_Rooms#Star|Star]]
<br>----------------------------------------<br>
|
|-
|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
|
|}

== '''Background''' ==

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient NA-MIC coverage for all. Subsequent teleconferences allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

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=
* [[2014_Project_Week_Template | Template for project pages]]

==Image-Guided Therapy==

* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata)
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras Lasso)
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer WPI, Nirav Patel WPI, Nobuhiko Hata BWH)
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias)
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)
* [[2014_Summer_Project_Week:Image To Mesh Conversion for Brain MRI | Image To Mesh Conversion for Brain MRI]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift | An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
*[[2014_Summer_Project_Week:Intraoperative_Registration_of_preoperative_CT_and_C-arm_CT_of_the_lung | Intraoperative Registration of preoperative CT and C-arm CT of the lung]] (Katharina Breininger, Jay Jagadeesan)
*[[2014_Summer_Project_Week:Image guided neuroendoscope | Making realistic clinical story board for image guided skull base endoscopic surgery]] (Keryn Palmer, Nobuhiko Hata)
*[[2014_Summer_Project_Week:PathExplorer_Extension | PathExplorer Extension (code refactoring, documentation, tutorial)]] (Laurent Chauvin, Tamas Ungi, Nobuhiko Hata)
*[[2014_Summer_Project_Week:Cortical_Dysplasia_Identification | Tools for Dysplasia Identification in Epilepsy]] (Luiz Murta; Emylin Souza; Tina Kapur; Ron Kikinis)
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)

==Huntington's Disease==
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)

==TBI==
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Stroke==
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)

==Cardiac==
*[[2014_Summer_Project_Week:Cardiac-Congenital | MRI segmentation for congenital heart disease]] (Danielle Pace, Adrian Dalca, Polina Golland)

==Chronic Obstructive Pulmonary Disease, Lung, Chest ==

*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:Multiscale_Non_Local_Means_filter_(NLM)_for_chest_CT_images | Multiscale Non Local Means filter (NLM) for chest CT images]] (Pietro Nardelli, Raul San Jose)

==Head and Neck Cancer / Radiotherapy ==
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques)
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp, Steve Pieper)
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)

==[http://qiicr.org QIICR]==
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim)
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})
* [[2014_Summer_Project_Week: DICOM SEG conversion to support archival of QIN Grand challenges results|DICOM SEG conversion to support archival of QIN Grand challenges results]] (Jayashree, Andrey, Steve, {David remotely})
* [[2014_Summer_Project_Week: ColorBar support|Color Bar Support for Slice Views]] (Alireza, Andrey, Steve, Kevin)
* [[2014_Summer_Project_Week: Slicer DICOM|Slicer DICOM Improvements]] (Alireza, Andrey, Steve, Ron)

==Feature Extraction==
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)

==Additional Brain Image Analysis==
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).
*[[2014_Summer_Project_Week:Slicer_LDDMM_Shape_Analysis | Slicer Interface to LDDMM shape anlaysis]] (Saurabh Jain, JHU; Steve Pieper, Isomics; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders | CAD Toolbox for Neurological Disorders]] (Sidong Liu, Siqi Liu, Fan Zhang, Yang Song, Weidong Cai, Sonia Pujol, Ron Kikinis)
*[[2014_Summer_Project_Week:Longitudinal_patient_specific_DTI_analysis | Longitudinal patient-specific DTI analysis using Slicer for neonatal asphyxia]] (Anuja Sharma, SCI, Utah; Francois Budin, UNC; Martin Styner, UNC; Guido Gerig, SCI, Utah)
*[[2014_Summer_Project_Week:Pipeline_Visualization | Pipeline Visualization]] (Ramesh, Adrian, Polina)

==Slicer4 Extensions==

*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Andras Lasso, Kevin Wang)
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)
*[[2014_Summer_Project_Week:DRAMMS_Slicer| Integrating DRAMMS deformable registration into Slicer]] (Yangming Ou, Steve Pieper, Andriy Fedorov, Tina Kapur, Christos Davatzikos, Ron Kikinis, Randy Gollub, Jayashree Kalpathy-Cramer)

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim)
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras)
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc)
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba)
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)
*[[2014_Summer_Project_Week:Slicer Tutorial Updates | Slicer Tutorial Updates]] (Parth Amin, Farukh Kohistani)

== '''Logistics''' ==

*'''Dates:''' June 23-27, 2014.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' https://www.regonline.com/namic2014summerprojectweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([https://www.regonline.com/namic2014summerprojectweek Please click here to register.])

#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com
#Parth Amin, Brigham & Women's Hospital, aminp@wit.edu
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Saskia Camps, SPL, saskiacamps@gmail.com
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
#Adrian Dalca, MIT CSAIL, adalca@mit.edu
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu
#Polina Golland, MIT CSAIL, polina@csail.mit.edu
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu
#Jayender Jagadeesan, BWH/SPL, jayender@bwh.harvard.edu
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu
#Franklin King, Queen's University, franklin.king@queensu.ca
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu
#Ivan Kolesov, Stony Brook University, ivan.kolesov1@gmail.com
#Robin Kouver, BWH/SPL, r.kouver@gmail.com
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca
#Yangming Li, University of Washington, ymli81@uw.edu
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu
#Jim Miller, GE Research, millerjv@ge.com
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu
#Isaiah Norton, Brigham & Women's Hospital, isaiah.norton@gmail.com
#Jorge Onieva, Brigham & Women's Hospital, jorgeonieva@gmail.com
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu
#Danielle Pace, MIT CSAIL, dfpace@mit.edu
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org
#Nirav Patel, WPI, napatel@wpi.edu
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu
#Adam Rankin, Queen's University, rankin@queensu.ca
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu
#Clare Tempany, Brigham & Women's Hospital, ctempany@bwh.harvard.edu
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu
#Tamas Ungi, Queen's University, ungi@queensu.ca
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca
#David Welch, University of Iowa, david-welch@uiowa.edu
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

2014 Summer Project Week:Cardiac-Congenital

2014-06-23T15:55:41Z

Dpace: Created page with '__NOTOC__ <gallery> Image:PW-MIT2014.png|Projects List </gallery> ==Key Investigators== * Danielle Pace, MIT * Adrian Dalca, MIT * Polina G…'

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Danielle Pace, MIT
* Adrian Dalca, MIT
* Polina Golland, MIT

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</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>

2014 Summer Project Week

2014-06-23T15:54:52Z

Dpace:

__NOTOC__

[[image:PW-MIT2014.png|300px]]

Dates: June 23-27, 2014.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 23
!style="width:18%" |Tuesday, June 24
!style="width:18%" |Wednesday, June 25
!style="width:18%" |Thursday, June 26
!style="width:18%" |Friday, June 27
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11:30am''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''11am-12noon''' Breakout Session: [[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis)
<br>
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Neuro|Image-Guided Therapy - Neurosurgery]] (Alexandra Golby, Tina Kapur) <br>
[[MIT_Project_Week_Rooms#Star|Star]]

<br>----------------------------------------<br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2014 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Prostate|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Noby Hata)
[[MIT_Project_Week_Rooms#Star|Star]]
<br>----------------------------------------<br>
|
|-
|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
|
|}

== '''Background''' ==

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient NA-MIC coverage for all. Subsequent teleconferences allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

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=
* [[2014_Project_Week_Template | Template for project pages]]

==Image-Guided Therapy==

* [[2014_Summer_Project_Week:SlicerIGT|SlicerIGT extension: testing, tutorials, website]] (Tamas Ungi, Nobuhiko Hata)
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras Lasso)
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* [[2014_Summer_Project_Week:Robot_Control_With_OpenIGTLink | Robot Control With OpenIGTLink]] ( Gregory Fischer WPI, Nirav Patel WPI, Nobuhiko Hata BWH)
* [[Gestural Point of Care Interface for IGT]] (Saskia, Franklin, Steve, Tobias)
* [[2014_Summer_Project_Week:Intelligent_Steering | Steered image registration using intelligent interfaces for minimal user interaction]] (Marcel Prastawa, Jim Miller, Steve Pieper)
* [[2014_Summer_Project_Week:Image To Mesh Conversion for Brain MRI | Image To Mesh Conversion for Brain MRI]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift | An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz, Ron Kikinis, Nikos Chrisochoides)
* [[2014_Summer_Project_Week:Open_source_electromagnetic_trackers_usingOpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
*[[2014_Summer_Project_Week:Intraoperative_Registration_of_preoperative_CT_and_C-arm_CT_of_the_lung | Intraoperative Registration of preoperative CT and C-arm CT of the lung]] (Katharina Breininger, Jay Jagadeesan)
*[[2014_Summer_Project_Week:Image guided neuroendoscope | Making realistic clinical story board for image guided skull base endoscopic surgery]] (Keryn Palmer, Nobuhiko Hata)
*[[2014_Summer_Project_Week:PathExplorer_Extension | PathExplorer Extension (code refactoring, documentation, tutorial)]] (Laurent Chauvin, Tamas Ungi, Nobuhiko Hata)
*[[2014_Summer_Project_Week:Cortical_Dysplasia_Identification | Tools for Dysplasia Identification in Epilepsy]] (Luiz Murta; Emylin Souza; Tina Kapur; Ron Kikinis)
*[[2014_Summer_Project_Week:mipiX | Rapid Visualization of Large Image Collections]] (Adrian, Ramesh, Polina)

==Huntington's Disease==
*[[2014_Summer_Project_Week:FiberTractDispersion| Fiber Tract Dispersion and UKF Tractography]] (Peter Savadjiev, Yogesh Rathi, Hans Johnson, C-F Westin)

==TBI==
*[[2014_Summer_Project_Week:TBI_Segmentation| Interactive segmentation for traumatic brain injury ]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Stroke==
*[[2014_Summer_Project_Week:Stroke-ImagingGenetics | Stroke Imaging Genetics]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)
*[[2014_Summer_Project_Week:Stroke-SuperResolution | Stroke Super Resolution]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)

==Cardiac==
*[[2014_Summer_Project_Week:Cardiac-Congenital | MRI segmentation for congenital heart disease]] (Danielle Pace, Polina Golland)

==Chronic Obstructive Pulmonary Disease, Lung, Chest ==

*[[2014_Summer_Project_Week: Pectoralis muscle segmentation| Pectoralis muscle segmentation]] (Rola Harmouche, James Ross, Raul San Jose)
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:Multiscale_Non_Local_Means_filter_(NLM)_for_chest_CT_images | Multiscale Non Local Means filter (NLM) for chest CT images]] (Pietro Nardelli, Raul San Jose)

==Head and Neck Cancer / Radiotherapy ==
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg Sharp, Maxime Desplanques)
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg Sharp, Ivan Kolesov, Allen Tannenbaum)
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg Sharp, Paolo Zaffino)
*[[2014_Summer_Project_Week:DIR_stop_and_restart| DIR stop and restart]] (Paolo Zaffino, Greg Sharp, Steve Pieper)
*[[2014_Summer_Project_Week:InteractiveRegistration| Interactive Registration]] (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)
*[[2014_Summer_Project_Week:Proton_pencil_beam| Proton pencil beam dose calculation]] (Maxime Desplanques, Kevin Wang, Greg Sharp)

==[http://qiicr.org QIICR]==
* [[2014_Summer_Project_Week: RWV mapping support|Real world value mapping support]] (Andrey, Ethan, Andras, Steve, Jim)
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})
* [[2014_Summer_Project_Week: DICOM SEG conversion to support archival of QIN Grand challenges results|DICOM SEG conversion to support archival of QIN Grand challenges results]] (Jayashree, Andrey, Steve, {David remotely})
* [[2014_Summer_Project_Week: ColorBar support|Color Bar Support for Slice Views]] (Alireza, Andrey, Steve, Kevin)
* [[2014_Summer_Project_Week: Slicer DICOM|Slicer DICOM Improvements]] (Alireza, Andrey, Steve, Ron)

==Feature Extraction==
*[[2014_Summer_Project_Week:Tumor_DCE-MRI_Segmentation | Breast Tumor Segmentation]] (Vivek Narayan, Jay Jagadeesan)
*[[2014_Summer_Project_Week:Tumor_Heterogeneity_Analysis | Breast Tumor Heterogeneity Analysis]] (Vivek Narayan, Jay Jagadeesan)
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)
*[[2014_Summer_Project_Week:Invariant_Feature_Extraction_Slicer | Invariant Feature Methods in Slicer]] (Matthew Toews, Nicole Aucoin, Sandy Wells)

==Additional Brain Image Analysis==
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).
*[[2014_Summer_Project_Week:Slicer_LDDMM_Shape_Analysis | Slicer Interface to LDDMM shape anlaysis]] (Saurabh Jain, JHU; Steve Pieper, Isomics; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders | CAD Toolbox for Neurological Disorders]] (Sidong Liu, Siqi Liu, Fan Zhang, Yang Song, Weidong Cai, Sonia Pujol, Ron Kikinis)
*[[2014_Summer_Project_Week:Longitudinal_patient_specific_DTI_analysis | Longitudinal patient-specific DTI analysis using Slicer for neonatal asphyxia]] (Anuja Sharma, SCI, Utah; Francois Budin, UNC; Martin Styner, UNC; Guido Gerig, SCI, Utah)
*[[2014_Summer_Project_Week:Pipeline_Visualization | Pipeline Visualization]] (Ramesh, Adrian, Polina)

==Slicer4 Extensions==

*[[2014_Summer_Project_Week:Multidim Data| Multidimensional Data]] (Andras Lasso, Kevin Wang)
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp, Paolo Zaffino, Andras, Csaba, Kevin)
*[[2014_Summer_Project_Week:DRAMMS_Slicer| Integrating DRAMMS deformable registration into Slicer]] (Yangming Ou, Steve Pieper, Andriy Fedorov, Tina Kapur, Christos Davatzikos, Ron Kikinis, Randy Gollub, Jayashree Kalpathy-Cramer)

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)
* [[2014_Summer_Project_Week: Factory and Testing Process Post NA-MIC| Post NA-MIC Factory and Testing]] (Steve, Jc, Ron)
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)
*[[2014_Summer_Project_Week:Pluggable Label Statistics |Pluggable Label Statistics]] (Andrey , Ethan, Steve, Brad, Jim)
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras)
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc)
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba)
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)
*[[2014_Summer_Project_Week:Slicer Tutorial Updates | Slicer Tutorial Updates]] (Parth Amin, Farukh Kohistani)

== '''Logistics''' ==

*'''Dates:''' June 23-27, 2014.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' https://www.regonline.com/namic2014summerprojectweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list: [[2014_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([https://www.regonline.com/namic2014summerprojectweek Please click here to register.])

#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu
#Nassim Alikacem, Brigham & Women's Hospital, Nassim.Alikacem@gmail.com
#Parth Amin, Brigham & Women's Hospital, aminp@wit.edu
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu
#Eva Breininger, Brigham & Women's Hospital, ebreininger@partners.org
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Saskia Camps, SPL, saskiacamps@gmail.com
#Lucia Cevidanes, University of Michigan, luciacev@umich.edu
#Laurent Chauvin, SPL, lchauvin@bwh.harvard.edu
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
#Adrian Dalca, MIT CSAIL, adalca@mit.edu
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
#Maxime Desplanques, MGH/Politecnico di Milano, maxime.desplanques@cnao.it
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Sneha Durgapal, Brigham & Women's Hospital, durgapalsneha@gmail.com
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#James Fishbaugh, SCI Institute/University of Utah, jfishbaugh@gmail.com
#Jessica Forbes, University of Iowa, jessica-forbes@uiowa.edu
#Polina Golland, MIT CSAIL, polina@csail.mit.edu
#Jeffrey Grethe, University of CA San Diego, jgrethe@ncmir.ucsd.edu
#Rola Harmouche, Brigham & Women's Hospital, rolaharmouche@gmail.com
#Nobuhiko Hata, Brigham & Women's Hospital, hata@bwh.harvard.edu
#Jayender Jagadeesan, BWH/SPL, jayender@bwh.harvard.edu
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu
#Jayashree Kalpathy-Cramer, MGH, kalpathy@nmr.mgh.harvard.edu
#Tina Kapur, BWH/Harvard Medical School, tkapur@bwh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Regina Kim, University of Iowa, eunyoung-kim@uiowa.edu
#Franklin King, Queen's University, franklin.king@queensu.ca
#Tassilo Klein, SPL/BWH, TJKlein@bwh.harvard.edu
#Farukh Kohistani, BWH Radiology, kohistan@bc.edu
#Ivan Kolesov, Stony Brook University, ivan.kolesov1@gmail.com
#Robin Kouver, BWH/SPL, r.kouver@gmail.com
#Andreas Lasso, PerkLab - Queen's University, lasso@queensu.ca
#Yangming Li, University of Washington, ymli81@uw.edu
#Sidong Liu, SPL/BWH, sliu@bwh.harvard.edu
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu
#Dominik Meier, Brigham & Women's Hospital, meier@bwh.harvard.edu
#Jim Miller, GE Research, millerjv@ge.com
#Luiz Otavio Murta Junor, SPL/BWH, lmurta@partners.org
#Vivek Narayan, NCIGT, narayan.vivek9@gmail.com
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu
#Isaiah Norton, Brigham & Women's Hospital, isaiah.norton@gmail.com
#Jorge Onieva, Brigham & Women's Hospital, jorgeonieva@gmail.com
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu
#Danielle Pace, MIT CSAIL, dfpace@mit.edu
#Keryn Palmer, Brigham & Women's Hospital, kpalmer5@partners.org
#Nirav Patel, WPI, napatel@wpi.edu
#Tobias Penzkofer, SPL, pt@bwh.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu
#Adam Rankin, Queen's University, rankin@queensu.ca
#Aymeric Reshef, Brigham & Women's Hospital, areshef@bwh.harvard.edu
#Rahul Sastry, BWH/SPL, rahul_sastry@hms.harvard.edu
#Peter Savadjiev, Brigham & Women's Hospital, petersv@bwh.harvard.edu
#Gregory Sharp, MGH, gcsharp@mgh.harvard.edu
#Emylin Sousa, BWH/SPL, emylin.sousa@gmail.com
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu
#Clare Tempany, Brigham & Women's Hospital, ctempany@bwh.harvard.edu
#Matthew Toews, BWH/Harvard Medical School, mt@bwh.harvard.edu
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu
#Tamas Ungi, Queen's University, ungi@queensu.ca
#Kevin Wang, Princess Margaret Cancer Centre, kevin.wang@rmp.uhn.ca
#David Welch, University of Iowa, david-welch@uiowa.edu
#William Wells, Brigham & Women's Hospital, sw@bwh.harvard.edu
#Phillip White, BWH/Harvard Medical School, white@bwh.harvard.edu
#Alex Yarmarkovich, ISOMICS Inc., alexy@bwh.harvard.edu
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

2014 Project Week:CardiacCongenitalSegmentation

2014-01-10T15:15:47Z

Dpace:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:Normal_vs_DORV_lrg.gif|Double outlet right ventricle
Image:carreraScribbles.png|Example input to Carrera on axial slice
Image:carreraOutput.png|Carrera output after manual interaction
</gallery>

==Key Investigators==

Danielle Pace, MIT

Polina Golland, MIT

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a semi-automatic segmentation algorithm for cardiac MR images of patients with congenital heart defects.
* Goal is to build a surface model showing the endocardial and epicardial boundaries, for surgical planning.
* Challenges:
** Very large inter-subject variability due to heart defects
** Intensity inhomogeneities within myocardium and blood pool
** Similar intensity distributions within adjacent tissues (e.g. liver, chest muscle)
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Try existing open-source tools for segmentation and registration on the five datasets that we have so far.
* See where these methods fail, to focus our efforts for developing algorithms for segmenting hearts with congenital defects.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Focused on blood pool segmentation in one test case. Tried:
** CARMA tools: isolated connected / connected threshold operators
** Editor level tracing effect
** Editor Fast Marching effect
** Editor Grow Cuts effect
** Carrera interactive segmentation
** Robust statistic active contour segmentation
* Best tool = Carrera interactive segmentation
** Main difficulty = small chamber/vessel walls assigned as blood pool, but these can be fixed within Carrera somewhat easily
* Also tried affine registrations across my 5 subjects, using BRAINSFIT
** Works very roughly, as expected
* Next steps:
** Try Carrera on additional datasets for blood pool segmentation
** Myocardium segmentation is still a challenge
* Thanks to: Josh Cates, Salma Bengali, Yi Gao, Ivan Kolesov for your help and suggestions!
</div>
</div>

2014 Project Week:CardiacCongenitalSegmentation

2014-01-10T15:14:44Z

Dpace:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:Normal_vs_DORV_lrg.gif|Double outlet right ventricle
Image:carreraScribbles.png|Example input to Carrera on axial slice
Image:carreraOutput.png|Carrera output after manual interaction
</gallery>

==Key Investigators==

Danielle Pace, MIT

Polina Golland, MIT

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a semi-automatic segmentation algorithm for cardiac MR images of patients with congenital heart defects.
* Goal is to build a surface model showing the endocardial and epicardial boundaries, for surgical planning.
* Challenges:
** Very large inter-subject variability due to heart defects
** Intensity inhomogeneities within myocardium and blood pool
** Similar intensity distributions within adjacent tissues (e.g. liver, chest muscle)
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Try existing open-source tools for segmentation and registration on the five datasets that we have so far.
* See where these methods fail, to focus our efforts for developing algorithms for segmenting hearts with congenital defects.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Focused on blood pool segmentation in one test case. Tried:
** CARMA tools: isolated connected / connected threshold operators
** Editor level tracing effect
** Editor Fast Marching effect
** Editor Grow Cuts effect
** Carrera interactive segmentation
** Robust statistic active contour segmentation
* Best tool = Carrera interactive segmentation
** Main difficulty = small chamber/vessel walls assigned as blood pool, but these can be fixed within Carrera somewhat easily
* Also tried affine registrations across my 5 subjects, using BRAINSFIT
** Works very roughly, as expected
* Thanks to: Josh Cates, Salma Bengali, Yi Gao, Ivan Kolesov for your help and suggestions!
</div>
</div>

File:CarreraScribbles.png

2014-01-10T15:13:41Z

Dpace:

File:CarreraOutput.png

2014-01-10T15:13:31Z

Dpace:

2014 Project Week:CardiacCongenitalSegmentation

2014-01-10T15:10:04Z

Dpace:

__NOTOC__
<gallery>
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:Normal_vs_DORV_lrg.gif|Double outlet right ventricle
</gallery>

==Key Investigators==

Danielle Pace, MIT

Polina Golland, MIT

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a semi-automatic segmentation algorithm for cardiac MR images of patients with congenital heart defects.
* Goal is to build a surface model showing the endocardial and epicardial boundaries, for surgical planning.
* Challenges:
** Very large inter-subject variability due to heart defects
** Intensity inhomogeneities within myocardium and blood pool
** Similar intensity distributions within adjacent tissues (e.g. liver, chest muscle)
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Try existing open-source tools for segmentation and registration on the five datasets that we have so far.
* See where these methods fail, to focus our efforts for developing algorithms for segmenting hearts with congenital defects.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Focused on blood pool segmentation in one test case. Tried:
** CARMA tools: isolated connected / connected threshold operators
** Editor level tracing effect
** Editor Fast Marching effect
** Editor Grow Cuts effect
** Carrera interactive segmentation
** Robust statistic active contour segmentation
* Best tool = Carrera interactive segmentation
** Main difficulty = small chamber/vessel walls assigned as blood pool, but these can be fixed within Carrera somewhat easily
* Also tried affine registrations across my 5 subjects, using BRAINSFIT
** Works very roughly, as expected
* Thanks to: Josh Cates, Salma Bengali, Yi Gao, Ivan Kolesov for your help and suggestions!
</div>
</div>

2014 Project Week:CardiacCongenitalSegmentation

2014-01-05T02:13:13Z

Dpace:

File:Normal vs DORV lrg.gif

2014-01-05T02:12:05Z

Dpace:

2014 Project Week:CardiacCongenitalSegmentation

2014-01-05T02:05:54Z

Dpace:

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

==Key Investigators==

Danielle Pace, MIT

Polina Golland, MIT

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a semi-automatic segmentation algorithm for cardiac MR images of patients with congenital heart defects.
* Goal is to build a surface model showing the endocardial and epicardial boundaries, for surgical planning.
* Challenges:
** Very large inter-subject variability due to heart defects
** Intensity inhomogeneities within myocardium and blood pool
** Similar intensity distributions within adjacent tissues (e.g. liver, chest muscle)
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Try existing open-source tools for segmentation and registration on the five datasets that we have so far.
* See where these methods fail, to focus our efforts for developing algorithms for segmenting hearts with congenital defects.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2014 Project Week:CardiacCongenitalSegmentation

2014-01-05T02:02:13Z

Dpace:

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

==Key Investigators==

Danielle Pace, MIT

Polina Golland, MIT

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a semi-automatic segmentation algorithm for cardiac MR images of patients with congenital heart defects.
* Goal is to build a surface model showing the endocardial and epicardial boundaries, for surgical planning.
* Challenges:
** Very large inter-subject variability due to heart defects
** Intensity inhomogeneities within myocardium and blood pool
** Similar intensity distributions within adjacent tissues (e.g. liver, chest muscle)
</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>

2014 Project Week:CardiacCongenitalSegmentation

2014-01-05T01:52:47Z

Dpace:

2014 Project Week:CardiacCongenitalSegmentation

2014-01-05T01:51:46Z

Dpace: Created page with '__NOTOC__ <gallery> Image:PW-SLC2014.png|Projects List </gallery> ==Key Investigators== ==Project Description== <div style="margin: 20px;…'

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

==Key Investigators==

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</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>

2014 Winter Project Week

2014-01-05T01:51:18Z

Dpace:

Back to [[Project Events]], [[AHM_2014]], [[Events]]

__NOTOC__
[[image:PW-SLC2014.png|300px]]

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient NA-MIC coverage for all. Subsequent teleconferences allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].
= Dates.Venue.Registration =

Please [[AHM_2014#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

= [[AHM_2014#Agenda|'''AGENDA''']] and Project List=

Please:
* [[AHM_2014#Agenda|'''Click here for the agenda for AHM 2014 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

=Background and Preparation=

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

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

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==TBI==
*[[2014_Project_Week:TBIatrophy|Multimodal neuroimaging for the quantification of brain atrophy at six months following severe traumatic brain injury]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:TBIdemyelination|Systematic evaluation of axonal demyelination subsequent to traumatic brain injury using structural T1- and T2-weighted magnetic resonance imaging]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:BrainAging|Mapping the effect of traumatic brain injury upon white matter connections in the human brain using 3D Slicer]] (Andrei Irimia, John D. Van Horn)
*[[2014_Project_Week:LongitudinalDTI|Patient-specific longitudinal DTI analysis in traumatic brain injury]] (Anuja Sharma, Andrei Irimia, Bo Wang, John D. Van Horn, Martin Styner, Guido gerig)
*[[2014_Project_Week:TBISegmentation|Testing the interactive segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Atrial Fibrillation==
*[[2014_Project_Week:MRAFusionRegistration|DEMRI LA Segmentation via Image Fusion (MRA)]] (Josh, Salma, Alan)
*[[2014_Project_Week:LAFibrosisVisualizationModule|LA Fibrosis / Scar Visualization]] (Josh, Salma, Alan)
*[[2014_Project_Week:CARMADocumentation|CARMA Extension Documentation Project]] (Josh, Salma)
*[[2014_Project_Week:GraphCutsLASegmentationModule|LA Segmentation module using multi-column Graph Cuts]] (Gopal, Salma, Josh, Rob, Ross)
*[[2014_Project_Week:JointImageAndShapeAnalysisForFibrosisDistribution|Joint Image and Shape Analysis for Fibrosis Distribution]](Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
*[[2014_Project_Week:GrowCutLevelSetLA|Grow cut, level set integration for interactive LA segmentation]] ( Liangjia Zhu, Ivan Kolesov, Yi Gao, Allen Tannenbaum)

==Cardiac==
*[[2014_Project_Week:CardiacStemCellMonitoring|Monitoring engrafted stem cells in cardiac tissue with time series manganese enhanced MRI]] (Karl Diedrich)
*[[2014_Project_Week:CardiacCongenitalSegmentation|Whole-heart segmentation of cardiac MR images in congenital heart defect cases]] (Danielle Pace, Polina Golland)

==Slicer4 Extensions==
*[[2014_Project_Week:ShapePopulationViewer|Surface Visualization - ShapePopulationViewer]] (Alexis Girault, Francois Budin, Beatriz Panaigua, Martin Styner)

==Huntington's Disease==
*[[2014_Project_Week:DWIDispersion|DWI Dispersion]] (Hans, CF, Peter Savadjiev)
*[[2014_Project_Week:DTIAnalysis|DTI Compressed Sensing?]] (Hans, CF)
*[[2014_Project_Week:Modules scripting|Slicer module scripting?]] (Dave)
*[[2014_Project_Week:DWIConverter|DWIConverter?]] (Hans, Kent)
*[[2014_Project_Week:Slicer_Based_Surface_Template_Estimation|Slicer Based Surface Template Estimation]] (Saurabh JHU, Steve Pieper, Hans Johnson, Josh Cates)
*[[2014_Project_Week:HD_4DShapes|4D shape analysis: application to HD ]] (James Fishbaugh,Hans Johnson, Guido Gerig)
*[[2014_Project_Week:Shape_Registration_and_Regression|Shape registration and regression in Slicer4 ]] (James Fishbaugh,Hans Johnson, Guido Gerig)

==Head and Neck Cancer==
*[[2014_Project_Week:DIR_validation|DIR Validation]] (Nadya and Greg)
*[[2014_Project_Week:Hybrid_bspline|Hybrid B Spline]] (Nadya, Greg, Steve)
*[[2014_Project_Week:CarreraSlice|Interactive Segmentation]] (Ivan, LiangJia, Nadya, Yi, Greg, Allen)

==Stroke==

*[[2014_Project_Week:Multi-Tissue_Stroke_Segmentation|Multi-Tissue Stroke Segmentation]] (Ramesh, Polina B., Polina G.)

==Brain Segmentation==
*[[2014_Project_Week:MultiAtlas_MultiImage_Segmentation|Multi-Atlas based Multi-Image Segmentation]] (Minjeong Kim, Xiaofeng Liu, Jim Miller, Dinggang Shen)

==Image-Guided Interventions==
*[[2014_Project_Week:Ultrasound Visualization and Navigation in Neurosurgery|Ultrasound Visualization and Navigation in Neurosurgery]] (Matthew Toews, Alireza Mehrtash, Csaba Pinter, Andras Lasso, Steve Pieper, William M. Wells III)
*[[2014_Project_Week:OpenIGTLink| OpenIGTLink Interface: New data types and structures]] (Junichi Tokuda, Andras Lasso, Steve Piper, ???)
*[[2014_Project_Week:Statistical Shape Model for robotic spine surgery| Statistical Shape Model for robotic spine surgery]] (Marine Clogenson, ???)
*[[2014_Project_Week:PercutaneousApproachAnalysis| Percutaneous Approach Analysis]] (Atsushi Yamada, Junichi Tokuda, Koichiro Murakami, ??)

==Radiation Therapy==
*[[2014_Project_Week:DICOM_RT|DICOM RT Export]] (Greg Sharp, Kevin Wang, others??)
*[[2014_Project_Week:DICOM_SRO|DICOM Spatial Registration Export]] (Greg Sharp, Kevin Wang, others??)
*[[2014_Project_Week:Registration_Evaluation|Interactive Registration and Evaluation]] (Kevin Wang, Greg Sharp, others??)
*[[2014_Project_Week:External_Beam_Planning|External Beam Planning Visualization]] (Kevin Wang, Greg Sharp, Csaba Pinter)

==Medical Robotics==
==[http://qiicr.org QIICR]==

*[[2014_Project_Week:4D_NIfTI_Multivolume|4D NIfTI Multivolume Support]] (Jayashree, Andrey, Jim, John)
*[[2014_Project_Week:RT_FormatConversions|RT and ITK Format Conversions]] (Jayashree, Andras, Csaba. John)
*[[2014_Project_Week:BatchConvertDICOM|Python Scripting Slicer DICOM read/write to convert segmentation objects]] (Jayashree, Andrey, Alireza, Steve, Jc, Hans, John)
*[[2014_Project_Week:PkModeling_user_tool|User module for DCE modeling]] (Andrey, Jayashree, Jim, Alireza, Steve, Ron)
*[[2014_Project_Week:DICOM_enhanced_multiframe|DICOM enhanced multiframe object support]] (Andrey, Alireza, David Clunie, Jayashree, Steve, Reinhard, Jim)
*[[2014_Project_Week:Quantitative_Index_Computation|Quantitative Index Computation]] (Ethan Ulrich, Reinhard Beichel, Nicole, Andrey, Jim)
*[[2014_Project_Week:TCIA Browser Extension in Slicer|TCIA Browser Extension in Slicer]] (Alireza, Andrey, Steve, Ron)

==TMJ-OA==
* [[2014_Winter_Project_Week:Constrain Fiducial along Suface|Constrain Fiducial along Suface]] (Vinicius Boen, Nicole Aucoin, Beatriz Paniagua)
* [[2014_Winter_Project_Week:Cropping Multiple Surfaces|Cropping multiple surfaces simultaneously]] (Alexander, Jc, Steve, Vinicius, Beatriz Paniagua)
* [[2014_Winter_Project_Week:Color Code Tables|Color Coded Tables]] (Beatriz Paniagua, Vinicius Boen, Nicole Aucoin, Steve Pieper, Francois Budin)
* [[2014_Winter_Project_Week:4DShape Analysis of mandibular changes|4DShape Analysis of mandibular changes]] (James Fishbaugh, Guido Gerig, Vinicius Boen)

==Chronic Obstructive Pulmonary Disease ==
* [[2014_Winter_Project_Week:CIP Core|Chest Imaging Platform (CIP) - Core Infrastructure]] (Raul San Jose, Rola Harmouche, Pietro Nardelli, James Ross)
* [[2014_Winter_Project_Week:CIP Infrastructure Testing and SuperBuild|CIP Testing and SuperBuild]] (James Ross, Raul San Jose)
* [[2014_Winter_Project_Week:Slicer CIP Slicer MRML| Slicer CIP- MRML consolidation]] (Pietro Nardelli, Rola Harmouche, James Ross, Raul San Jose)
* [[2014_Winter_Project_Week:Slicer CIP Modules| Slicer CIP- Modules]] (Rola Harmouche, Pietro Nardelli, James Ross, Raul San Jose)

==Infrastructure==
*[[2014_Project_Week:MRMLSceneSpeedUp|MRML Scene speed up]] (Jc, Andras Lasso)
*[[2014_Project_Week:MultidimensionalDataSupport|Multidimensional data support]] (Andras Lasso, Andriy Fedorov, Steve Pieper, JC, Kevin Wang)
*CLI - Resources? Conditionals? Autonaming? Provenance? CTK unification? (Jim Miller)
*[[2014_Project_Week:MarkupsModule|Markups Module]] (Nicole Aucoin)
* [[2014_Winter_Project_Week:Steered Registration|Steered Registration]] (Steve, Greg, Kevin, Vinicius, Marcel)
* [[2014_Winter_Project_Week:MRB Extension Dependencies|MRB Extension Dependencies]] (Steve, Jc, Jim, Nicole, Alex)
* [[2014_Winter_Project_Week:SubjectHierarchy|Subject hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper, Jc, Jayashree, John, Alireza, Andrey)
* [[2014_Winter_Project_Week:IntegrationOfContourObject|Integration of Contour object]] (Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:NonlinearTransforms|Integration nonlinear transforms]] (Alex Yarmarkovich, Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:Logging|Logging (standardization, logging to file)]] (Nicole Aucoin, Steve Pieper, Jc, Andras Lasso, Csaba Pinter, ???)
* [[2014_Winter_Project_Week:XNATSlicerLink| 3DSlicer annotations in XNAT]] (Erwin Vast, Nicole Aucoin, Andrey Fedorov)
* [[2014_Winter_Project_Week:ParameterSerialization | JSON Parameter Serialization]] (Matt McCormick, ???)

2014 Winter Project Week

2014-01-05T01:50:49Z

Dpace:

Back to [[Project Events]], [[AHM_2014]], [[Events]]

__NOTOC__
[[image:PW-SLC2014.png|300px]]

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient NA-MIC coverage for all. Subsequent teleconferences allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].
= Dates.Venue.Registration =

Please [[AHM_2014#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

= [[AHM_2014#Agenda|'''AGENDA''']] and Project List=

Please:
* [[AHM_2014#Agenda|'''Click here for the agenda for AHM 2014 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

=Background and Preparation=

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

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

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==TBI==
*[[2014_Project_Week:TBIatrophy|Multimodal neuroimaging for the quantification of brain atrophy at six months following severe traumatic brain injury]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:TBIdemyelination|Systematic evaluation of axonal demyelination subsequent to traumatic brain injury using structural T1- and T2-weighted magnetic resonance imaging]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:BrainAging|Mapping the effect of traumatic brain injury upon white matter connections in the human brain using 3D Slicer]] (Andrei Irimia, John D. Van Horn)
*[[2014_Project_Week:LongitudinalDTI|Patient-specific longitudinal DTI analysis in traumatic brain injury]] (Anuja Sharma, Andrei Irimia, Bo Wang, John D. Van Horn, Martin Styner, Guido gerig)
*[[2014_Project_Week:TBISegmentation|Testing the interactive segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Atrial Fibrillation==
*[[2014_Project_Week:MRAFusionRegistration|DEMRI LA Segmentation via Image Fusion (MRA)]] (Josh, Salma, Alan)
*[[2014_Project_Week:LAFibrosisVisualizationModule|LA Fibrosis / Scar Visualization]] (Josh, Salma, Alan)
*[[2014_Project_Week:CARMADocumentation|CARMA Extension Documentation Project]] (Josh, Salma)
*[[2014_Project_Week:GraphCutsLASegmentationModule|LA Segmentation module using multi-column Graph Cuts]] (Gopal, Salma, Josh, Rob, Ross)
*[[2014_Project_Week:JointImageAndShapeAnalysisForFibrosisDistribution|Joint Image and Shape Analysis for Fibrosis Distribution]](Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
*[[2014_Project_Week:GrowCutLevelSetLA|Grow cut, level set integration for interactive LA segmentation]] ( Liangjia Zhu, Ivan Kolesov, Yi Gao, Allen Tannenbaum)

==Cardiac==
*[[2014_Project_Week:CardiacStemCellMonitoring|Monitoring engrafted stem cells in cardiac tissue with time series manganese enhanced MRI]] (Karl Diedrich)
*[[2014_Project_Week:CardiacCongenitalSegmentation|Whole-heart segmentation of cardiac MR images in congenital heart defect cases] (Danielle Pace, Polina Golland)

==Slicer4 Extensions==
*[[2014_Project_Week:ShapePopulationViewer|Surface Visualization - ShapePopulationViewer]] (Alexis Girault, Francois Budin, Beatriz Panaigua, Martin Styner)

==Huntington's Disease==
*[[2014_Project_Week:DWIDispersion|DWI Dispersion]] (Hans, CF, Peter Savadjiev)
*[[2014_Project_Week:DTIAnalysis|DTI Compressed Sensing?]] (Hans, CF)
*[[2014_Project_Week:Modules scripting|Slicer module scripting?]] (Dave)
*[[2014_Project_Week:DWIConverter|DWIConverter?]] (Hans, Kent)
*[[2014_Project_Week:Slicer_Based_Surface_Template_Estimation|Slicer Based Surface Template Estimation]] (Saurabh JHU, Steve Pieper, Hans Johnson, Josh Cates)
*[[2014_Project_Week:HD_4DShapes|4D shape analysis: application to HD ]] (James Fishbaugh,Hans Johnson, Guido Gerig)
*[[2014_Project_Week:Shape_Registration_and_Regression|Shape registration and regression in Slicer4 ]] (James Fishbaugh,Hans Johnson, Guido Gerig)

==Head and Neck Cancer==
*[[2014_Project_Week:DIR_validation|DIR Validation]] (Nadya and Greg)
*[[2014_Project_Week:Hybrid_bspline|Hybrid B Spline]] (Nadya, Greg, Steve)
*[[2014_Project_Week:CarreraSlice|Interactive Segmentation]] (Ivan, LiangJia, Nadya, Yi, Greg, Allen)

==Stroke==

*[[2014_Project_Week:Multi-Tissue_Stroke_Segmentation|Multi-Tissue Stroke Segmentation]] (Ramesh, Polina B., Polina G.)

==Brain Segmentation==
*[[2014_Project_Week:MultiAtlas_MultiImage_Segmentation|Multi-Atlas based Multi-Image Segmentation]] (Minjeong Kim, Xiaofeng Liu, Jim Miller, Dinggang Shen)

==Image-Guided Interventions==
*[[2014_Project_Week:Ultrasound Visualization and Navigation in Neurosurgery|Ultrasound Visualization and Navigation in Neurosurgery]] (Matthew Toews, Alireza Mehrtash, Csaba Pinter, Andras Lasso, Steve Pieper, William M. Wells III)
*[[2014_Project_Week:OpenIGTLink| OpenIGTLink Interface: New data types and structures]] (Junichi Tokuda, Andras Lasso, Steve Piper, ???)
*[[2014_Project_Week:Statistical Shape Model for robotic spine surgery| Statistical Shape Model for robotic spine surgery]] (Marine Clogenson, ???)
*[[2014_Project_Week:PercutaneousApproachAnalysis| Percutaneous Approach Analysis]] (Atsushi Yamada, Junichi Tokuda, Koichiro Murakami, ??)

==Radiation Therapy==
*[[2014_Project_Week:DICOM_RT|DICOM RT Export]] (Greg Sharp, Kevin Wang, others??)
*[[2014_Project_Week:DICOM_SRO|DICOM Spatial Registration Export]] (Greg Sharp, Kevin Wang, others??)
*[[2014_Project_Week:Registration_Evaluation|Interactive Registration and Evaluation]] (Kevin Wang, Greg Sharp, others??)
*[[2014_Project_Week:External_Beam_Planning|External Beam Planning Visualization]] (Kevin Wang, Greg Sharp, Csaba Pinter)

==Medical Robotics==
==[http://qiicr.org QIICR]==

*[[2014_Project_Week:4D_NIfTI_Multivolume|4D NIfTI Multivolume Support]] (Jayashree, Andrey, Jim, John)
*[[2014_Project_Week:RT_FormatConversions|RT and ITK Format Conversions]] (Jayashree, Andras, Csaba. John)
*[[2014_Project_Week:BatchConvertDICOM|Python Scripting Slicer DICOM read/write to convert segmentation objects]] (Jayashree, Andrey, Alireza, Steve, Jc, Hans, John)
*[[2014_Project_Week:PkModeling_user_tool|User module for DCE modeling]] (Andrey, Jayashree, Jim, Alireza, Steve, Ron)
*[[2014_Project_Week:DICOM_enhanced_multiframe|DICOM enhanced multiframe object support]] (Andrey, Alireza, David Clunie, Jayashree, Steve, Reinhard, Jim)
*[[2014_Project_Week:Quantitative_Index_Computation|Quantitative Index Computation]] (Ethan Ulrich, Reinhard Beichel, Nicole, Andrey, Jim)
*[[2014_Project_Week:TCIA Browser Extension in Slicer|TCIA Browser Extension in Slicer]] (Alireza, Andrey, Steve, Ron)

==TMJ-OA==
* [[2014_Winter_Project_Week:Constrain Fiducial along Suface|Constrain Fiducial along Suface]] (Vinicius Boen, Nicole Aucoin, Beatriz Paniagua)
* [[2014_Winter_Project_Week:Cropping Multiple Surfaces|Cropping multiple surfaces simultaneously]] (Alexander, Jc, Steve, Vinicius, Beatriz Paniagua)
* [[2014_Winter_Project_Week:Color Code Tables|Color Coded Tables]] (Beatriz Paniagua, Vinicius Boen, Nicole Aucoin, Steve Pieper, Francois Budin)
* [[2014_Winter_Project_Week:4DShape Analysis of mandibular changes|4DShape Analysis of mandibular changes]] (James Fishbaugh, Guido Gerig, Vinicius Boen)

==Chronic Obstructive Pulmonary Disease ==
* [[2014_Winter_Project_Week:CIP Core|Chest Imaging Platform (CIP) - Core Infrastructure]] (Raul San Jose, Rola Harmouche, Pietro Nardelli, James Ross)
* [[2014_Winter_Project_Week:CIP Infrastructure Testing and SuperBuild|CIP Testing and SuperBuild]] (James Ross, Raul San Jose)
* [[2014_Winter_Project_Week:Slicer CIP Slicer MRML| Slicer CIP- MRML consolidation]] (Pietro Nardelli, Rola Harmouche, James Ross, Raul San Jose)
* [[2014_Winter_Project_Week:Slicer CIP Modules| Slicer CIP- Modules]] (Rola Harmouche, Pietro Nardelli, James Ross, Raul San Jose)

==Infrastructure==
*[[2014_Project_Week:MRMLSceneSpeedUp|MRML Scene speed up]] (Jc, Andras Lasso)
*[[2014_Project_Week:MultidimensionalDataSupport|Multidimensional data support]] (Andras Lasso, Andriy Fedorov, Steve Pieper, JC, Kevin Wang)
*CLI - Resources? Conditionals? Autonaming? Provenance? CTK unification? (Jim Miller)
*[[2014_Project_Week:MarkupsModule|Markups Module]] (Nicole Aucoin)
* [[2014_Winter_Project_Week:Steered Registration|Steered Registration]] (Steve, Greg, Kevin, Vinicius, Marcel)
* [[2014_Winter_Project_Week:MRB Extension Dependencies|MRB Extension Dependencies]] (Steve, Jc, Jim, Nicole, Alex)
* [[2014_Winter_Project_Week:SubjectHierarchy|Subject hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper, Jc, Jayashree, John, Alireza, Andrey)
* [[2014_Winter_Project_Week:IntegrationOfContourObject|Integration of Contour object]] (Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:NonlinearTransforms|Integration nonlinear transforms]] (Alex Yarmarkovich, Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:Logging|Logging (standardization, logging to file)]] (Nicole Aucoin, Steve Pieper, Jc, Andras Lasso, Csaba Pinter, ???)
* [[2014_Winter_Project_Week:XNATSlicerLink| 3DSlicer annotations in XNAT]] (Erwin Vast, Nicole Aucoin, Andrey Fedorov)
* [[2014_Winter_Project_Week:ParameterSerialization | JSON Parameter Serialization]] (Matt McCormick, ???)

LEGO IGT and Medical Robotics Tutorial

2013-08-15T02:52:53Z

Dpace:

[[Image:Slicer3-IGT-LEGOTutorial-biopsy.jpg|300px|thumb|The LEGO robot and phantom]]
[[Image:Slicer3-IGT-LEGOTutoral-screenshot.png|300px|thumb|Example tutorial screenshot]]

Back to [[IGT:ToolKit|IGT:ToolKit]]

=LEGO Image Guided Therapy and Medical Robotics Tutorial=

==Overview:==

This tutorial provides a thorough understanding of the main concepts in image-guided therapy and medical robotics, namely imaging, pre-operative planning, targeting by tracking, navigation and registration. The tutorial is open-source and completely free for anyone to use or modify (see http://www.slicer.org for details and for the BSD style open source license).

The tutorial is:
* Hands-on: Using a LEGO robot, a LEGO phantom (anatomical model) and a tutorial module in 3D Slicer v. 3 means that tutorial participants can use real physical equipment and software to learn about IGT and medical robotics.

* Accessible: The tutorial software is open-source, and the cost of the materials is approximately $300 USD + shipping and taxes.

==Tutorial Materials:==

Provided by NA-MIC and the Surgical Planning Lab:
* 3D Slicer v. 3 tutorial module
* CT volume of the phantom
* Tutorial slides
* Assembly instructions for the robot and the phantom
* Phantom placement guide

Provided by tutorial participants:
* 1 LEGO Mindstorms NXT kit
* 1 LEGO Deluxe Brick box
* 2 pom-poms
* Linux computer with root access or Windows with administrator privileges
For purchasing information for user-supplied materials, see the "Tutorial Slides Part 1 - Background and Materials" slides.

'''Getting the Tutorial Materials:'''

Click on the following links to get the tutorial materials:

* Robot assembly instructions: [http://wiki.na-mic.org/Wiki/images/8/81/LEGOIGTAndMedicalRoboticsTutorial_RobotAssemblyInstructions.pdf LEGOIGTAndMedicalRoboticsTutorial_RobotAssemblyInstructions.pdf]

* Phantom assembly instructions: [http://wiki.na-mic.org/Wiki/images/0/0d/LEGOIGTAndMedicalRoboticsTutorial_PhantomAssemblyInstructions.pdf LEGOIGTAndMedicalRoboticsTutorial_PhantomAssemblyInstructions.pdf]

* Phantom placement guide: [http://wiki.na-mic.org/Wiki/images/6/64/LEGOIGTAndMedicalRoboticsTutorial_PhantomPlacementGuide.pdf LEGOIGTAndMedicalRoboticsTutorial_PhantomPlacementGuide.pdf]

* Tutorial Slides Part 1 - Background and Materials: [http://wiki.na-mic.org/Wiki/images/d/d1/LEGOIGTAndMedicalRoboticsTutorial_1_BackgroundAndMaterials.pdf LEGOIGTAndMedicalRoboticsTutorial_1_BackgroundAndMaterials.pdf]

* Tutorial Slides Part 2 - Basic Tutorial: [http://wiki.na-mic.org/Wiki/images/a/ab/LEGOIGTAndMedicalRoboticsTutorial_2_BasicTutorial.pdf LEGOIGTAndMedicalRoboticsTutorial_2_BasicTutorial.pdf]

* Tutorial Slides Part 3 - Advanced Tutorial: [http://wiki.na-mic.org/Wiki/images/f/f4/LEGOIGTAndMedicalRoboticsTutorial_3_AdvancedTutorial.pdf LEGOIGTAndMedicalRoboticsTutorial_3_AdvancedTutorial.pdf]

* CT volume of the LEGO phantom: [http://wiki.na-mic.org/Wiki/images/6/69/000003.SER.zip 000003.SER.zip]

* 3D Slicer LEGO tutorial module (including code to interface between a LEGO robot and a C++ program): Available on the NA-MIC Sandbox - access [http://viewvc.na-mic.org/viewvc.cgi/NAMICSandBox/trunk/LegoTutorial/ online] or through the [http://wiki.na-mic.org/Wiki/index.php/Engineering:SandBox NA-MIC subversion system]

* MICCAI 2007 "Open Source and Open Data for MICCAI" workshop paper: [[Image:AnAccessibleHandsOnTutorialSystemForIGTAndMedicalRobotics.pdf|Image:AnAccessibleHandsOnTutorialSystemForIGTAndMedicalRobotics.pdf]]

==Software Installation Instructions==
* Installing Slicer: go to the [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Install-Slicer3 Slicer3 Install] site.
* [http://wiki.na-mic.org/Wiki/index.php/LEGO_IGT_Compilation Compiling the LegoTutorial]

==Notes==
* Note that the code supplied above was modified from NXT++ (http://nxtpp.sourceforge.net) and Device::USB (http://search.cpan.org/~gwadej/Device-USB-0.21) and uses libusb (http://libusb.sourceforge.net). See the README file included with the source code for instructions on installation and use.

==People:==

[http://spl.harvard.edu/~dpace Danielle Pace], Surgical Planning Lab and Robarts Research Institute

[http://spl.harvard.edu/~kikinis Ron Kikinis], Surgical Planning Lab

[http://spl.harvard.edu/~noby Nobuhiko Hata], Surgical Planning Lab

'''Questions? Feedback?'''

Contact [http://spl.harvard.edu/~dpace Danielle Pace]

2012 Winter Project Week:GeometricMetamorphosisTBI

2012-01-13T15:15:20Z

Dpace:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Geometric Metamorphosis for TBI ==

==Key Investigators==
* Kitware: Danielle Pace, Stephen Aylward
* UNC: Marc Niethammer
* Utah: Marcel Prastawa
* UCLA: Andrei Irimia, Jack van Horn

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

<h3>Objective</h3>
* Image registration of longitudinal neuroimaging data of traumatic brain injury (TBI), with the aim of predicting long term outcome and designing treatment plans.
* The geometric metamorphosis registration algorithm jointly estimates global background deformations and local pathology changes. This allows injury changes to be analysed without the impact of background motion.
</div>

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

<h3>Approach, Plan</h3>
* Continue validation studies in simulated and actual image data.
* Meet together to discuss next steps.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Project discussions between Danielle, Stephen and Jack.
* Data discussions between Danielle and Marcel.
* Group discussion on TBI project identified requests from algorithm developers to DBP and clarified clinical realities.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer extension.

</div>

==References==

Marc Niethammer, Gabriel L. Hart, Danielle F. Pace, Paul M. Vespa, Andrei Irimia, John D. Van Horn, and Stephen R. Aylward, Geometric Metamorphosis, MICCAI 2011.

2012 Winter Project Week:GeometricMetamorphosis

2012-01-13T15:12:42Z

Dpace:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Estimating the infiltration / recession of pathologies independent of background deformations ==

==Key Investigators==
* Kitware: Danielle Pace, Stephen Aylward
* UNC: Marc Niethammer

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

<h3>Objective</h3>
* Image registration of longitudinal neuroimaging data of traumatic brain injury (TBI), with the aim of predicting long term outcome and designing treatment plans.
* The geometric metamorphosis registration algorithm jointly estimates global background deformations and local pathology changes. This allows injury changes to be analysed without the impact of background motion.
* Quantification of "infiltrative" versus "displacing" pathology changes may be a clinically-significant biomarker, and is enabled by geometric metamorphosis's separation of total deformation into background and pathology deformations.
</div>

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

<h3>Approach, Plan</h3>
* Develop and implement voxel-wise estimates of infiltrating versus displacing pathology growth/contraction.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Built CALA-TK: Cross-sectional And Longitudinal Atlas toolkit
* Fixed some small bugs to get geometric metamorphosis CLI into Slicer
* Got Slicer change tracker running on my data, with help of Andriy
* Future work is integrating geometric metamorphosis into change tracker

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer extension.

==References==

Marc Niethammer, Gabriel L. Hart, Danielle F. Pace, Paul M. Vespa, Andrei Irimia, John D. Van Horn, and Stephen R. Aylward, Geometric Metamorphosis, MICCAI 2011.

</div>

2012 Winter Project Week:SlidingOrgans

2012-01-13T15:10:05Z

Dpace:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Registration in the presence of sliding between organs ==

==Key Investigators==
* Kitware: Danielle Pace, Stephen Aylward
* UNC: Marc Niethammer

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

<h3>Objective</h3>
* Conventional deformable image registration enforces smooth motion, causing inaccurate displacement measurements near sliding motion.
* Sliding motion is common in intra-subject 4D image registration problems, for example respiration-induced sliding of the lungs and abdominal organs against the chest wall.
* We have developed an image registration algorithm based on anisotropic diffusion that handles sliding motion.
</div>

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

<h3>Approach, Plan</h3>
* Continue algorithm validation experiments in 4D chest CT.
* Improve CLI documentation and user interface.
* Fix user experience issues of integration of TubeTK CLIs into Slicer 4.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Improved Slicer's handling of external module paths that contain non-parseable executables
* Cleaned up TubeTK build output destinations
* Cleaned up CLI documentation and command-line options - rename parameters, improve descriptions, remove confusing options (inspired by BRAINSFit registration documentation)

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer extension as a CLI distributed in TubeTK (http://public.kitware.com/Wiki/TubeTK)

</div>

2012 Winter Project Week:SlidingOrgans

2012-01-13T15:09:43Z

Dpace:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Registration in the presence of sliding between organs ==

==Key Investigators==
* Kitware: Danielle Pace, Stephen Aylward
* UNC: Marc Niethammer

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

<h3>Objective</h3>
* Conventional deformable image registration enforces smooth motion, causing inaccurate displacement measurements near sliding motion.
* Sliding motion is common in intra-subject 4D image registration problems, for example respiration-induced sliding of the lungs and abdominal organs against the chest wall.
* We have developed an image registration algorithm based on anisotropic diffusion that handles sliding motion.
</div>

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

<h3>Approach, Plan</h3>
* Continue algorithm validation experiments in 4D chest CT.
* Improve CLI documentation and user interface.
* Fix user experience issues of integration of TubeTK CLIs into Slicer 4.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Improved Slicer's handling of external module paths that contain non-parseable executables
* Cleaned up destinations of TubeTK's build outputs
* Cleaned up CLI documentation and command-line options - rename parameters, improve descriptions, remove confusing options (inspired by BRAINSFit registration documentation)

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer extension as a CLI distributed in TubeTK (http://public.kitware.com/Wiki/TubeTK)

</div>

2012 Winter Project Week:GeometricMetamorphosisTBI

2012-01-13T15:07:42Z

Dpace:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Geometric Metamorphosis for TBI ==

==Key Investigators==
* Kitware: Danielle Pace, Stephen Aylward
* UNC: Marc Niethammer
* Utah: Marcel Prastawa
* UCLA: Andrei Irimia, Jack van Horn

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

<h3>Objective</h3>
* Image registration of longitudinal neuroimaging data of traumatic brain injury (TBI), with the aim of predicting long term outcome and designing treatment plans.
* The geometric metamorphosis registration algorithm jointly estimates global background deformations and local pathology changes. This allows injury changes to be analysed without the impact of background motion.
</div>

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

<h3>Approach, Plan</h3>
* Continue validation studies in simulated and actual image data.
* Meet together to discuss next steps.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Discussions between Danielle, Stephen and Jack.
* Group discussion on TBI project identified requests from algorithm developers to DBP and clarified clinical realities.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer extension.

</div>

==References==

Marc Niethammer, Gabriel L. Hart, Danielle F. Pace, Paul M. Vespa, Andrei Irimia, John D. Van Horn, and Stephen R. Aylward, Geometric Metamorphosis, MICCAI 2011.

2012 Winter Project Week:SlidingOrgans

2012-01-09T07:21:52Z

Dpace:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Registration in the presence of sliding between organs ==

==Key Investigators==
* Kitware: Danielle Pace, Stephen Aylward
* UNC: Marc Niethammer

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

<h3>Objective</h3>
* Conventional deformable image registration enforces smooth motion, causing inaccurate displacement measurements near sliding motion.
* Sliding motion is common in intra-subject 4D image registration problems, for example respiration-induced sliding of the lungs and abdominal organs against the chest wall.
* We have developed an image registration algorithm based on anisotropic diffusion that handles sliding motion.
</div>

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

<h3>Approach, Plan</h3>
* Continue algorithm validation experiments in 4D chest CT.
* Improve CLI documentation and user interface.
* Fix user experience issues of integration of TubeTK CLIs into Slicer 4.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer extension as a CLI distributed in TubeTK (http://public.kitware.com/Wiki/TubeTK)

</div>

2012 Winter Project Week:GeometricMetamorphosis

2012-01-09T07:17:24Z

Dpace:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Estimating the infiltration / recession of pathologies independent of background deformations ==

==Key Investigators==
* Kitware: Danielle Pace, Stephen Aylward
* UNC: Marc Niethammer

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

<h3>Objective</h3>
* Image registration of longitudinal neuroimaging data of traumatic brain injury (TBI), with the aim of predicting long term outcome and designing treatment plans.
* The geometric metamorphosis registration algorithm jointly estimates global background deformations and local pathology changes. This allows injury changes to be analysed without the impact of background motion.
* Quantification of "infiltrative" versus "displacing" pathology changes may be a clinically-significant biomarker, and is enabled by geometric metamorphosis's separation of total deformation into background and pathology deformations.
</div>

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

<h3>Approach, Plan</h3>
* Develop and implement voxel-wise estimates of infiltrating versus displacing pathology growth/contraction.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer extension.

==References==

Marc Niethammer, Gabriel L. Hart, Danielle F. Pace, Paul M. Vespa, Andrei Irimia, John D. Van Horn, and Stephen R. Aylward, Geometric Metamorphosis, MICCAI 2011.

</div>

2012 Winter Project Week:GeometricMetamorphosis

2012-01-09T07:17:04Z

Dpace:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Estimating the infiltration / recession of pathologies independent of background deformations ==

==Key Investigators==
* Kitware: Danielle Pace, Stephen Aylward
* UNC: Marc Niethammer

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

<h3>Objective</h3>
* Image registration of longitudinal neuroimaging data of traumatic brain injury (TBI), with the aim of predicting long term outcome and designing treatment plans.
* The geometric metamorphosis registration algorithm jointly estimates global background deformations and local pathology changes. This allows injury changes to be analysed without the impact of background motion.
* Quantification of "infiltrative" versus "displacing" pathology changes may be a clinically-significant biomarker, and is enabled by geometric metamorphosis's separation of total deformation into background and pathology deformations.
</div>

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

<h3>Approach, Plan</h3>
* Develop and implement voxel-wise estimates of infiltrating versus displacing pathology growth/contraction.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer extension.

</div>

2012 Winter Project Week:GeometricMetamorphosisTBI

2012-01-09T07:12:49Z

Dpace:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Geometric Metamorphosis for TBI ==

==Key Investigators==
* Kitware: Danielle Pace, Stephen Aylward
* UNC: Marc Niethammer
* Utah: Marcel Prastawa
* UCLA: Andrei Irimia, Jack van Horn

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

<h3>Objective</h3>
* Image registration of longitudinal neuroimaging data of traumatic brain injury (TBI), with the aim of predicting long term outcome and designing treatment plans.
* The geometric metamorphosis registration algorithm jointly estimates global background deformations and local pathology changes. This allows injury changes to be analysed without the impact of background motion.
</div>

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

<h3>Approach, Plan</h3>
* Continue validation studies in simulated and actual image data.
* Meet together to discuss next steps.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer extension.

</div>

==References==

Marc Niethammer, Gabriel L. Hart, Danielle F. Pace, Paul M. Vespa, Andrei Irimia, John D. Van Horn, and Stephen R. Aylward, Geometric Metamorphosis, MICCAI 2011.

2012 Winter Project Week:SlidingOrgans

2012-01-08T16:33:39Z

Dpace: Created page with '__NOTOC__ <gallery> Image:PW-SLC2012.png|Projects List Image:MP_RAGE_PRECONTRAST.png‎|An example T1 weighted image from a patient with TBI…'

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:MP_RAGE_PRECONTRAST.png‎|An example T1 weighted image from a patient with TBI
</gallery>

==Registration in the presence of sliding between organs ==

==Key Investigators==
* Kitware: Danielle Pace, Stephen Aylward
* UNC: Marc Niethammer

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

<h3>Objective</h3>
TODO
</div>

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

<h3>Approach, Plan</h3>
*TODO

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer extension as a CLI distributed in TubeTK (http://public.kitware.com/Wiki/TubeTK)

</div>

2012 Winter Project Week:GeometricMetamorphosis

2012-01-08T16:31:42Z

Dpace: Created page with '__NOTOC__ <gallery> Image:PW-SLC2012.png|Projects List Image:MP_RAGE_PRECONTRAST.png‎|An example T1 weighted image from a patient with TBI…'

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:MP_RAGE_PRECONTRAST.png‎|An example T1 weighted image from a patient with TBI
</gallery>

==Estimating the infiltration / recession of pathologies independent of background deformations ==

==Key Investigators==
* Kitware: Danielle Pace, Stephen Aylward
* UNC: Marc Niethammer

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

<h3>Objective</h3>
TODO
</div>

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

<h3>Approach, Plan</h3>
*TODO

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer extension.

</div>