NAMIC Wiki - User contributions [en]

2016 Winter Project Week/Projects/CryoPlanningSlicerModule

2016-01-08T13:38:22Z

Jayender:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]
Image:CryoModuleGUI.jpg|CryoPlanning Module GUI
Image:CryoModuleOutput1.jpg|Iceball and Tumor models
Image:CryoModuleOutput2.jpg|Distance model
Image:CryoModuleOutput3.jpg|Distance labelmap

</gallery>

==Key Investigators==

*Jayender Jagadeesan, BWH
*Steve Pieper, BWH
*Sandy Wells, BWH

==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;"
|

* The objective of this project is to refine the CryoPlanning module that has been developed to plan cryotherapy procedures
*Specifically, I will be working on the optimization algorithm to estimate the optimal pose of the ice ball to ensure complete overlap of the ice ball with the tumor while avoiding critical structures.
|

* The plan will be to implement the Broyden-Fletcher-Goldfarb-Shannon (BGFS) optimization algorithm. The pseudo Hessian will be generated to ensure fast and robust convergence for estimation of the optimal pose of the ice ball.
* If suboptimal performance is obtained using the BGFS algorithm (either slow or inaccurate estimation of the optimal pose), we will implement the simulated annealing optimization algorithm.
|

* We have developed a module in Slicer that helps plan the position and orientation of the ice ball for cryotherapy.
* The position, orientation and size of the ice ball can be manually adjusted.
*The user has the choice of three different ice probes - ice ball, ice rod and ice sphere.
* Given the ice ball and the tumor model, the amount of overlap and the distance between the two models can be computed and displayed to the interventionist.
* Automatic estimation of the optimal position and orientation of the ice ball based on BGFS optimization algorithm has been completed.
* The parameters of the algorithm have to be optimized since the output is dependent on the choice of initial parameters
|}

==Background and References==

File:CryoModuleOutput3.jpg

2016-01-08T13:36:15Z

Jayender:

2016 Winter Project Week/Projects/CryoPlanningSlicerModule

2016-01-08T13:35:35Z

Jayender:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]
Image:CryoModuleGUI.jpg|CryoPlanning Module GUI
Image:CryoModuleOutput1.jpg|Iceball and Tumor models
Image:CryoModuleOutput2.jpg|Distance model
Image:CryoModuleOutput3.jpg|Distance labelmap

</gallery>

==Key Investigators==

*Jayender Jagadeesan, BWH
*Steve Pieper, BWH
*Sandy Wells, BWH

==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;"
|

* The objective of this project is to refine the CryoPlanning module that has been developed to plan cryotherapy procedures
*Specifically, I will be working on the optimization algorithm to estimate the optimal pose of the ice ball to ensure complete overlap of the ice ball with the tumor while avoiding critical structures.
|

* The plan will be to implement the Broyden-Fletcher-Goldfarb-Shannon (BGFS) optimization algorithm. The pseudo Hessian will be generated to ensure fast and robust convergence for estimation of the optimal pose of the ice ball.
* If suboptimal performance is obtained using the BGFS algorithm (either slow or inaccurate estimation of the optimal pose), we will implement the simulated annealing optimization algorithm.
|

* We have developed a module in Slicer that helps plan the position and orientation of the ice ball for cryotherapy.
* The position, orientation and size of the ice ball can be manually adjusted.
*The user has the choice of three different ice probes - ice ball, ice rod and ice sphere.
* Given the ice ball and the tumor model, the amount of overlap and the distance between the two models can be computed and displayed to the interventionist.
* Automatic estimation of the optimal position and orientation of the ice ball has to be completed.
|}

==Background and References==

File:CryoModuleOutput2.jpg

2016-01-08T13:34:31Z

Jayender:

2016 Winter Project Week/Projects/CryoPlanningSlicerModule

2016-01-08T13:33:34Z

Jayender:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]
Image:CryoModuleGUI.jpg|CryoPlanning Module GUI
Image:CryoModuleOutput1.jpg|Iceball and Tumor models
Image:CryoModuleOutput2.jpg|Distance model

</gallery>

==Key Investigators==

*Jayender Jagadeesan, BWH
*Steve Pieper, BWH
*Sandy Wells, BWH

==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;"
|

* The objective of this project is to refine the CryoPlanning module that has been developed to plan cryotherapy procedures
*Specifically, I will be working on the optimization algorithm to estimate the optimal pose of the ice ball to ensure complete overlap of the ice ball with the tumor while avoiding critical structures.
|

* The plan will be to implement the Broyden-Fletcher-Goldfarb-Shannon (BGFS) optimization algorithm. The pseudo Hessian will be generated to ensure fast and robust convergence for estimation of the optimal pose of the ice ball.
* If suboptimal performance is obtained using the BGFS algorithm (either slow or inaccurate estimation of the optimal pose), we will implement the simulated annealing optimization algorithm.
|

* We have developed a module in Slicer that helps plan the position and orientation of the ice ball for cryotherapy.
* The position, orientation and size of the ice ball can be manually adjusted.
*The user has the choice of three different ice probes - ice ball, ice rod and ice sphere.
* Given the ice ball and the tumor model, the amount of overlap and the distance between the two models can be computed and displayed to the interventionist.
* Automatic estimation of the optimal position and orientation of the ice ball has to be completed.
|}

==Background and References==

File:CryoModuleOutput1.jpg

2016-01-08T13:32:48Z

Jayender:

2016 Winter Project Week/Projects/CryoPlanningSlicerModule

2016-01-08T13:31:40Z

Jayender:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]
Image:CryoModuleGUI.jpg|CryoPlanning Module GUI
Image:CryoModuleOutput1.jpg|Iceball and Tumor models

</gallery>

==Key Investigators==

*Jayender Jagadeesan, BWH
*Steve Pieper, BWH
*Sandy Wells, BWH

==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;"
|

* The objective of this project is to refine the CryoPlanning module that has been developed to plan cryotherapy procedures
*Specifically, I will be working on the optimization algorithm to estimate the optimal pose of the ice ball to ensure complete overlap of the ice ball with the tumor while avoiding critical structures.
|

* The plan will be to implement the Broyden-Fletcher-Goldfarb-Shannon (BGFS) optimization algorithm. The pseudo Hessian will be generated to ensure fast and robust convergence for estimation of the optimal pose of the ice ball.
* If suboptimal performance is obtained using the BGFS algorithm (either slow or inaccurate estimation of the optimal pose), we will implement the simulated annealing optimization algorithm.
|

* We have developed a module in Slicer that helps plan the position and orientation of the ice ball for cryotherapy.
* The position, orientation and size of the ice ball can be manually adjusted.
*The user has the choice of three different ice probes - ice ball, ice rod and ice sphere.
* Given the ice ball and the tumor model, the amount of overlap and the distance between the two models can be computed and displayed to the interventionist.
* Automatic estimation of the optimal position and orientation of the ice ball has to be completed.
|}

==Background and References==

File:CryoModuleGUI.jpg

2016-01-08T13:30:09Z

Jayender:

2016 Winter Project Week/Projects/CryoPlanningSlicerModule

2016-01-08T13:29:25Z

Jayender:

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

</gallery>

==Key Investigators==

*Jayender Jagadeesan, BWH
*Steve Pieper, BWH
*Sandy Wells, BWH

==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;"
|

* The objective of this project is to refine the CryoPlanning module that has been developed to plan cryotherapy procedures
*Specifically, I will be working on the optimization algorithm to estimate the optimal pose of the ice ball to ensure complete overlap of the ice ball with the tumor while avoiding critical structures.
|

* The plan will be to implement the Broyden-Fletcher-Goldfarb-Shannon (BGFS) optimization algorithm. The pseudo Hessian will be generated to ensure fast and robust convergence for estimation of the optimal pose of the ice ball.
* If suboptimal performance is obtained using the BGFS algorithm (either slow or inaccurate estimation of the optimal pose), we will implement the simulated annealing optimization algorithm.
|

* We have developed a module in Slicer that helps plan the position and orientation of the ice ball for cryotherapy.
* The position, orientation and size of the ice ball can be manually adjusted.
*The user has the choice of three different ice probes - ice ball, ice rod and ice sphere.
* Given the ice ball and the tumor model, the amount of overlap and the distance between the two models can be computed and displayed to the interventionist.
* Automatic estimation of the optimal position and orientation of the ice ball has to be completed.
|}

==Background and References==

2016 Winter Project Week/Projects/CryoPlanningSlicerModule

2016-01-08T13:28:25Z

Jayender:

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

</gallery>

==Key Investigators==

*Jayender Jagadeesan, BWH
*Steve Pieper, BWH
*Sandy Wells, BWH

==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;"
|

* The objective of this project is to refine the CryoPlanning module that has been developed to plan cryotherapy procedures
*Specifically, I will be working on the optimization algorithm to estimate the optimal pose of the ice ball to ensure complete overlap of the ice ball with the tumor while avoiding critical structures.
|

* The plan will be to implement the Broyden-Fletcher-Goldfarb-Shannon (BGFS) optimization algorithm. The pseudo Hessian will be generated to ensure fast and robust convergence for estimation of the optimal pose of the ice ball.
* If suboptimal performance is obtained using the BGFS algorithm (either slow or inaccurate estimation of the optimal pose), we will implement the simulated annealing optimization algorithm.
|

* We have developed a module in Slicer that helps plan the position and orientation of the ice ball for cryotherapy.
* The position, orientation and size of the ice ball can be manually adjusted.
*The user has the choice of three different ice probes - ice ball, ice rod and ice sphere.
* Given the ice ball and the tumor model, the amount of overlap and the distance between the two models can be computed and displayed to the interventionist.
* Automatic estimation of the optimal position and orientation of the ice ball has to be completed.
|}

==Background and References==

2016 Winter Project Week

2015-12-23T04:35:23Z

Jayender: /* IGT */

__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"|
|
|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/SlicerROSIntegration| Slicer for Medical Robotics Research]]
<br>
|'''8:30-9:30am''' TBD <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
|title=NAMIC Winter Project Week
|view=WEEK
}}

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

== 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)

== IGT ==
* [[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/SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard, Jayender Jagadeesan)
* [[2016_Winter_Project_Week/Projects/CryoPlanningSlicerModule | CryoPlanning Module in Slicer]] (Jayender Jagadeesan, Steve Pieper, Sandy Wells)
* [[2016_Winter_Project_Week/Projects/External_beam_planning | External beam radiotherapy planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week/Projects/EVD |Measuring Anatomic Factors for Extraventricular Drain Placement]] (Kirby Vosburgh, P. Jason White)

==Image Analysis==
*[[2016_Winter_Project_Week/Projects/ChestImagingPlatform|Chest Imaging Platform: COPD and other pulmonary diseases]] (Raúl San José, Jorge Onieva)
* [[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/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/DigitalPathologyNuclearSegmentation|Digital Pathology Nuclear Segmentation]] (Erich Bremer, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week/Projects/Interactive4DSegmentation | Interactive 4D Segmentation Module]] (Ethan Ulrich)
* [[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/SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[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]] (Csaba Pinter, Nicole Aucoin, 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, ??)

= '''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

2016 Winter Project Week/Projects/SlicerROSIntegration

2015-12-23T04:34:50Z

Jayender: /* Key Investigators */

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

==Key Investigators==
* Junichi Tokuda (Brigham and Women's Hospital)
* Axel Krieger (Children's National Medical Center)
* Simon Leonard (Johns Hopkins University)
* Tobias Frank (University Hannover, Germany)
* Jayender Jagadeesan (BWH)

==Project Description==
{| class="wikitable"
|- style="vertical-align:top;"
! style="text-align: left; width:27%" | Objective
* Define requirements and system architecture for medical robotics software system based on 3D Slicer and Robot Operating System (ROS)
! style="text-align: left; width:27%" | Approach, Plan
* Needs for 3D Slicer / ROS integration in ongoing research projects (presentations by participants)
** Axel (Autonomous Surgery using the KUKA LWR)
** Simon (dVRK?)
** Junichi (OpenIGTLink and medical robotics research)
** Tobias (OCT robot / Integration of KUKA robot and 3D Slicer
* Brainstorming 1: Requirements
** Applications (e.g. endoscopic surgery, percutaneous interventions, catheterization, etc.)
** Platforms -- Linux, Windows, MAC
** Roles for 3D Slicer -- visualization, image processing, etc.
** Roles for ROS -- vision, sensors, devices, etc.
* Brainstorming 2: Architecture for 3D Slicer-ROS integration
** Types of data exchanged between ROS and 3D Slicer
** Communication scheme between ROS and 3D Slicer
** Software package to provide
*** Independent middleware?
*** 3D Slicer plug-in modules
*** ROS modules
* Brainstorming 3: Collaborative tools / teams
** Platforms to support (ROS mainly support Linux)
** Repository
! style="text-align: left; width:27%" | Progress
*

2016 Winter Project Week/Projects/CryoPlanningSlicerModule

2015-12-23T04:33:26Z

Jayender: /* Project Description */

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

</gallery>

==Key Investigators==

*Jayender Jagadeesan, BWH
*Steve Pieper, BWH
*Sandy Wells, BWH

==Project Description==
{| class="wikitable"
|- style="vertical-align:top;"
! style="text-align: left; width:27%" | Objective

* The objective of this project is to refine the CryoPlanning module that has been developed to plan cryotherapy procedures
*Specifically, I will be working on the optimization algorithm to estimate the optimal pose of the ice ball to ensure complete overlap of the ice ball with the tumor while avoiding critical structures.

! style="text-align: left; width:27%" | Approach, Plan

* The plan will be to implement the Broyden-Fletcher-Goldfarb-Shannon (BGFS) optimization algorithm. The pseudo Hessian will be generated to ensure fast and robust convergence for estimation of the optimal pose of the ice ball.
* If suboptimal performance is obtained using the BGFS algorithm (either slow or inaccurate estimation of the optimal pose), we will implement the simulated annealing optimization algorithm.

! style="text-align: left; width:27%" | Progress

* We have developed a module in Slicer that helps plan the position and orientation of the ice ball for cryotherapy.
* The position, orientation and size of the ice ball can be manually adjusted.
*The user has the choice of three different ice probes - ice ball, ice rod and ice sphere.
* Given the ice ball and the tumor model, the amount of overlap and the distance between the two models can be computed and displayed to the interventionist.
* Automatic estimation of the optimal position and orientation of the ice ball has to be completed.
|}

==Background and References==

2016 Winter Project Week/Projects/CryoPlanningSlicerModule

2015-12-23T03:52:34Z

Jayender: /* Key Investigators */

2016 Winter Project Week

2015-12-14T23:45:22Z

Jayender: /* IGT */

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

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

'''Location:''' MIT, 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 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==

Tentative 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"|
|
|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'''
|'''10:30am-12pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 1 by Sarang Joshi)<br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''10-11:30am:''' <font color="#503020">Breakout Session: New Slicer Extensions'''</font><br>
|
'''10-11:30am:''' <font color="#503020">Breakout Session: [[2015_Winter_Project_Week:SlicerROSIntegration| Slicer for Medical Robotics Research]] </font>
<br>
|'''9:00-10:30am''' TBD <br>
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>TBD <br>
|'''10am-12pm:''' [[#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"|'''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">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>
'''2:45-4pm:''' [[2016_Winter_Project_Week/Breakout_Sessions/Ultrasound| Breakout Session Ultrasound]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
<br>----------------------------------------<br>

'''4:00pm-5:30pm:''' '''Diffeomorphic registration and the more recent geodesic shooting methods for diffeomorphic registration.''' (Tutorial Part 2 by Sarang Joshi) <br> Room: [http://www.csail.mit.edu/resources/maps/5D/D507.gif 32-D507].
|'''1-3pm:''' <font color="#503020"> [[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]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2016_Winter_Project_Week/Breakout_Sessions/Diffusion MRI| Diffusion MRI]]
[[MIT_Project_Week_Rooms#Kiva|Kiva]] <br> -------- <br>
'''3-4:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2016_Winter_Project_Week/Breakout_Sessions/QIICR Tools| QIICR Tools]]
|
|
|-
|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
|
|}
<googlecalendar>kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com</googlecalendar>

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

== Non-categorized ==
*Digital Pathology Nuclear Segmentation (Erich Bremer, Nicole Aucoin, Andrey Fedorov)
*Chest Imaging Platform: COPD and other pulmonary diseases (Raúl San José, Jorge Onieva)
*Upgrade the namic (and Slicer?) wiki (JC, Mike Halle)
* [[2016_Winter_Project_Week:BatchImageAnalysis | Batch Clinical Image Analysis]] (Kalli Retzepi, Yangming Ou, Matt Toews, Steve Pieper, Sandy Wells, Randy Gollub)
* [[2016_Winter_Project_Week:ImageRestoration | Image Restoration via Patch GMMs]] (Adrian Dalca, Katie Bouman, Polina Golland)
* [[2016_Winter_Project_Week:PatchRegistration | Patch Based Discrete Registration for Difficult Images]] (Adrian Dalca, Andreea Bobu, Polina Golland)
* [[2016_Winter_Project_Week:External_beam_planning | External beam radiotherapy planning]] (Greg Sharp, others)
* [[2016_Winter_Project_Week:SlicerOpenCVExtension | Slicer OpenCV Extension]] (Nicole Aucoin, Erich Bremer, Andrey Fedorov)
* [[2016_Winter_Project_Week: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:StatisticalShapeModeling | Statistical Shape Modeling in Slicer: OA Index]] (Laura Pascal, Beatriz Paniagua, François Budin, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week:SlicerCMFNextSteps | Moving beyond SlicerCMF and future projects]] (Beatriz Paniagua, Lucia Cevidanes, Steve Pieper, Juan Prieto)
* [[2016_Winter_Project_Week:Tract_io_interop | Tractography format interoperability]] (Isaiah Norton, Michael Onken, Lauren O'Donnell, others)
* [[2016_Winter_Project_Week:SlicerDMRI_documentation | Slicer diffusion MR / tractography workflow documentation]] (Pegah Kahaliardabili, Fan Zhang, Isaiah Norton, Lauren O'Donnell, others)

== IGT ==
* [[2016_Winter_Project_Week:TrackedUltrasoundStandardization | Tracked ultrasound standardization]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Steve Pieper, Adam Rankin)
*Integration of CustusX with PLUS on BK System (Christian A, Adam Rankin)
* [[2016_Winter_Project_Week:MITK_Plus_Integration | Integration of Plus and MITK]] (Thomas Kirchner, Janek Groehl)
*Integration of ImFusion MR-US registration with BWH AMIGO neurosurgery setup (Christian A, Tina Kapur, Steve Pieper, Sandy Wells, Andras Lasso)
* [[2015_Winter_Project_Week:SlicerROSIntegration | 3D Slicer + ROS Integration]] (Junichi Tokuda, Axel Krieger, Simon Leonard)
* [[2015_Winter_Project_Week:CryoPlanningSlicerModule | CryoPlanning Module in Slicer]] (Jayender Jagadeesan, Steve Pieper, Sandy Wells)

==Infrastructure==
* [[2016_Winter_Project_Week:CommonGL | CommonGL]] (Steve Pieper, Jim Miller)
* [[2016_Winter_Project_Week:WebTechnologies | Web Technologies and Slicer]] (Steve Pieper, Hans Meine)
* [[2016_Winter_Project_Week:CLIModules Backgrounding in MeVisLab | Running CLI Modules in MeVisLab asynchronously]] (Hans Meine)
* [[2016_Winter_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit (or other interesting CLIs) in MeVisLab]] (Hans Meine, Steve Pieper)
* [[2016_Winter_Project_Week:CLI_Dashboard | Kibana dashboard for browsing all available CLI modules]] (Hans Meine, JC?)
* [[2016_Winter_Project_Week:SegmentationEditorWidget | Editor widget using Segmentations]] (Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:SlicerTerminologyEditor | Terminology Editor]] (Csaba Pinter, Nicole Aucoin, Andrey Fedorov)
* [[2016_Winter_Project_Week:DICOMSegObjIntegration | Integration of DICOM segmentation image storage with Segmentations module]] (Kyle Sunderland, Csaba Pinter, Andras Lasso, Andrey Fedorov, Steve Pieper?)
* [[2016_Winter_Project_Week:CondaSlicer | Integration of Anaconda Python in Slicer]] (JC, Raúl San José, Jorge Onieva, Slicer Community?)
* [[2016_Winter_Project_Week: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: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:AIMInteroperability | AIM for interoperability]] (Hans Meine, Andrey Fedorov, ??)

= '''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 [https://www.regonline.com/namic16 this registration url].

#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
#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

2015 Summer Project Week

2015-06-25T09:35:31Z

Jayender: /* Feature Based Image Analysis */

__NOTOC__

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

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

==Logistics==

*'''Dates:''' June 21-24, 2015.
*'''Location:''' [http://www.nh-collection.com/hotel/nh-collection-barcelona-constanza NH Collection Constanza Hotel, Barcelona, Spain]
*'''REGISTRATION:''' Please register by adding your name to the list at the end of this page
*'''Registration Fee:''' None. The organizers will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.
*'''Hotel:''' You are welcome to book a room using the CARS 2015 conference services ([http://www.cars-int.org/fileadmin/templates/download/2015/CARS_2015_accomondation.pdf Click here for form])
*To attend the CARS meeting, please visit [http://www.cars-int.org/ http://www.cars-int.org/]
*Premium Network at Berlin Room:
**username: EVENT/CARS2015
**Password=CARS

*Please get a badge for CARS, even if you did not register for the CARS conference. Otherwise you will not be able to come in tomorrow.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Sunday, June 21
!style="width:18%" |Monday, June 22 <br> Room Berlin
!style="width:18%" |Tuesday, June 23 <br> Room Berlin
!style="width:18%" |Wednesday, June 24 <br> Room Berlin
|-
|bgcolor="#ffffdd"|'''9:00am-3:00pm:'''
|rowspan=3 valign=bottom|<hr>'''6pm''' Meeting with All Participants in Hotel Constanza Lobby
|'''10:00-11am:''' <font color="#503020">Rapid Introduction of all Projects and Teams <br>
'''11am-3pm''' <font color="#503020">Work <br>

|
'''10:00am-11am:''' <font color="#503020">'''Breakout Session:'''</font> - <br>[[2014_Project_Week_Breakout_Session: Slicer for users| Ask expert physicians]] (Ron Kikinis, Clare Tempany) <br>
'''11am-3pm''' <font color="#503020">Work
| <font color="#503020">Work <br>
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffaa"|Lunch <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]]
|-
|bgcolor="#ffffdd"|'''4:00-7:00pm'''
|<font color="#503020"> Work
|'''5:00-7:00pm:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2015_Summer_Project_Week/SoftwareStack| Open Software Stack]] (Steve Pieper) <br>4pm-6pm: Registration Desk Open for CARS attendees. Please pick up badges. <br>
|'''4:00-5:00pm:''' <font color="#503020"> Work <br>
'''4:30-6pm:''' Report Progress
|-
|bgcolor="#ffffdd"|'''7:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|Adjourn for the day <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#f0e68b"|Adjourn for the day <br> [http://www.barcelona-tourist-guide.com/en/events/sant-joan/feast-sant-joan.html Sant Joan Festival]
|bgcolor="#f0e68b"|'''6:00pm''' Adjourn Project Week and relocate to CARS Opening<br> '''7:30pm''' CARS Welcome Reception
|}

*Please note that start, end, and mealtimes have been set to match local schedules in Barcelona.
*Here is a list of [[Barcelona Restaurants | locally recommended places to eat]] in the vicinity of the conference hotel. All participants are responsible for their own meals.

== '''Background''' ==

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

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

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

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

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

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

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

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

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

==Equipment==

*[[2015_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)

==Image-Guided Therapy==
*[[2015_Summer_Project_Week:SlicerIGT|SlicerIGT tutorials for use cases]] (Tamas, Andras, Jay, Steve, Alvaro, Javier, Adam, Caroline, Noby, Tina)
*[http://www.na-mic.org/Wiki/index.php/2015_Refinement_Registration_Module Refinement of RegistrationModule] (Peter Behringer, Andrey Fedorov)
*[[2015_Summer_Project_Week:IGTSliceletBase| Create base classes for IGT slicelet]] (Andras Lasso, Andrey Fedorov, Adam Rankin)
*[http://www.na-mic.org/Wiki/index.php/2015_BRAINSFit_registration_in_SimpleITK BRAINSFit registration in SimpleITK] (Peter Behringer, Andrey Fedorov, Dženan Zukić)
*[http://www.na-mic.org/Wiki/index.php/2015_Multi_atlas_based_prostate_segmentation Multi atlas based prostate segmentation] (Paolo Zaffino, Giampaolo Pileggi, Salvatore Scaramuzzino, Peter Behringer, Andrey Fedorov, Maria Francesca Spadea)
*[http://www.na-mic.org/Wiki/index.php/2015_Multimodal_Guidance_for_Breast_Cancer_Surgery Multimodal Guidance for Breast Cancer Surgery] (Mikael Brudfors, David García, Javier Pascau)
*[[2015_pilot trajectory planning | Pilot Trajectory Planning(Caroline Essert, Sonia Pujol)]]
*[[2015_Summer_Project_Week:LinearFeatureRegistration|Linear Feature Registration]] (Matthew Holden)
*[[2015_Summer_Project_Week:LightWeightRobotIGT | Integration of a KUKA robot using OpenIGTLink ]] (Sebastian Tauscher, Junichi Tokuda)
*[[2015_Summer_Project_Week:USReconstruction | Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer ]] (Frank Preiswerk, Laurent Chauvin)
*[[2015 Orthognathic Surgery|Orthognathic Surgery]] (Dženan Zukić, Kitware)
*[[2015_Summer_Project_Week:SlicerTAVI | SlicerTAVI ]] (Adam Rankin)
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]
*[[2015_Summer_Project_Week:OpenSource_MRTRUS_Fusion_for_Prostate_biopsy|Open-source MRI-TRUS Fusion for Prostate biopsy]] (Andrey Fedorov, Andras Lasso, Clare Tempany)
*[[2015_Summer_Project_Week:TrackerlessMRIUSFusion | Trackerless MRI - US Registration ]] (Utsav Pardasani)
*[[2015_Summer_Project_Week:SordinaLinacPath | Sordina LINAC Guidance ]] (Eugenio Marinetto)
*[[2015_Summer_Project_Week:USRecon | US Reconstruction ]] (Steve Pieper, Tamas Ungi,Mikael Brudfors)

==Feature Based Image Analysis==
*[[2015_Summer_Project_Week:LungCAD| LungCAD]] (Jayender Jagadeesan, Tobias Penzkofer, Sandy Wells, Clara Meinzer, Raúl San José Estepar, Jorge Onieva)
*[[2015_Summer_Project_Week:QuantitativeProstate | Texture Analysis for Prostate Imaging]] (Tobias Penzkofer, Jay Jagadeesan, Matthew Toews, Tina Kapur)
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells, Raul San Jose Estepar, Tina Kapur)
*[[2015_Summer_Project_Week:AutomaticCephalometric | Automatic Cephalometric Analysis ]] (J. Jesus Montufar, Marcelo Romero)

==Chest Imaging Platform==
*[[2015_Summer_Project_Week:Slicer_CIP | Slicer CIP: advanced features and deployment ]] (Raúl San José, Alex Yarmarkovich, Jorge Onieva)
*[[2015_Summer_Project_Week:PAA_Ratio | PAA Ratio Module ]] (Jorge Onieva,Raúl San José)
*[[2015_Summer_Project_Week:Tracheal_Stent_Planning | Planning for tracheal stents ]] (Raúl San José, Jorge Onieva, George Cheng)
*[[2015_Summer_Project_Week:Atelectasis_Quantification | Volumetric Quantification of Atelectasis ]] (Ángel Torrado-Carvajal, Carolina Romero, Norberto Malpica)

==QIICR==
*[[2015_Summer_Project_Week:DSC | Dynamic Susceptibility Contrast (DSC) MRI for brain ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)
*[[2015_Summer_Project_Week:T1 mapping | T1 mapping for Dynamic Contrast Enhanced (DCE) MRI ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Jayashree Kalpathy-Cramer)
*[[2015_Summer_Project_Week:DCMTK| Integration and testing of new DCMTK with Slicer]] (Michael Onken, Andrey Fedorov, Steve Pieper)

==Infrastructure==
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin,Hans Meine)
*[[2015_Summer_Project_Week:Integrated Virtual Reality Viewer | Integrated Virtual Reality Viewer]] (Franklin King, Utsav Pardasani)
*[[2015_Summer_Project_Week:SegmentationNode| Use new Segmentation node in Editor]] (Andras Lasso, Steve Pieper)
*[[2015_Summer_Project_Week:Slicer_Conda | Integrate Conda Python in Slicer]] (Jorge Onieva, Raúl San José, Utsav Pardasani, Steve Pieper)

==Web==
*[[2015_Summer_Project_Week:Dicom parsing with DCMJS | Dicom parsing with DCMJS]] (Nicolas Rannou, Yves Martelli, Michael Onken, Steve Pieper)
*[[2015_Summer_Project_Week:Volume rendering with DCMJS and THREEJS | Volume Rendering with DCMJS and THREEJS]] (Nicolas Rannou, Steve Pieper)
*[[2015_Summer_Project_Week:CTK for the web and touch devices| CTK for the web and touch devices]] (Nicolas Rannou, Yves Martelli, Steve Pieper)
*[[2015_Summer_Project_Week:SlicerCardboard| Slicer for mobile-based vr goggles]] (Utsav Pardasani, Adam Rankin)
*[[2015_Summer_Project_Week:PythonDevelopmentTutorial | Python developer tutorial]] (Adam Rankin)

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

== '''Registrants''' ==

Please add your name to the list. This is the registration mechanism for this project week.
#Tina Kapur, BWH
#Ron Kikinis, BWH & Fraunhofer
#Steve Pieper, Isomics
#Tamas Ungi, Queen's University, Canada
#Andras Lasso, Queen's University, Canada
#Paolo Zaffino, ImagEngLab, Magna Graecia University, Italy
#Salvatore Scaramuzzino, ImagEngLab, Magna Graecia University, Italy
#Giampaolo Pileggi, ImagEngLab, Magna Graecia University, Italy
#Nicole Aucoin, BWH
#Sonia Pujol, BWH
#Dženan Zukić, Kitware, Carrboro, NC
#Jayender Jagadeesan, BWH
#Guido Gerig, Utah
#Sandy Wells, BWH
#Matthew Toews, École de Technologie Supérieure, Montreal, Canada
#Frank Preiswerk, BWH
#Raul San Jose, BWH
#Jorge Onieva, BWH
#Yulong Zhao, Université de Rennes
#Laurent Chauvin, BWH
#Michael Onken, Open Connections
#Tobias Penzkofer, Department of Radiology, Charité Berlin, Germany
#Javier Pascau, Universidad Carlos III de Madrid, Spain
#Angel Torrado-Carvajal, Universidad Rey Juan Carlos, Madrid, Spain
#Nobuhiko Hata, BWH
#Robert H. Owen, BK Medical ApS, Denmark
#Clare Tempany, BWH
#Adam Rankin, Robarts
#Utsav Pardasani, Robarts
#Marcelo Romero, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#J. Jesus Montufar, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
#Andrey Fedorov, BWH
#Nicolas Rannou, BCH
#Mikael Brudfors, Universidad Carlos III de Madrid, Spain
#Laura Sanz, Universidad Carlos III de Madrid, Spain
#Eugenio Marinetto, Universidad Carlos III de Madrid, Spain
#David García, Universidad Carlos III de Madrid, Spain
#Franklin King, Queen's University / BWH
#Jorge García, Universidad Politécnica de Madrid, Spain
#Peter Behringer, BWH
#Caroline Essert, University of Strasbourg
#Sebastian Tauscher, Institute of Mechatronic Systems, Leibniz Universität Hannover, Germany
#Matthew Holden, Queen's University, Canada
#Sara Fernandez Vidal, ICM, France
#Laszlo Kanyasi, Perk Lab affiliate, Hungary
#Xiao Da, MGH
#Arnaud De Bruecker, École supérieure d'informatique, Brussels, Belgium
#Ali Gottschalk, École supérieure d'informatique, Brussels, Belgium
#Christophe Teixeira Pereira, École supérieure d'informatique, Brussels, Belgium
#Tsotne Shonia, École supérieure d'informatique, Brussels, Belgium
#Clara Meinzer, Semmelweis University, Hungary
#Yves Martelli, Galgo Medical, Barcelona, Spain
#Alvaro Gomez (Universidad de la Republica, Uruguay)
#Alfredo Higueras, Galgo Medical, Barcelona, Spain

2015 Summer Project Week:LungCAD

2015-06-24T15:26:33Z

Jayender: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:LungCAD-module.png
Image:Seg1n.png
Image:Seg1.png
Image:Seg2n.png
Image:Seg2.png
</gallery>

==Key Investigators==
* Jayender Jagadeesan (BWH)
* Tobias Penskofer (Charite, Berlin)
* Sandy Wells (BWH)
* Clara Meiner (previously BWH)
* Raul San Jose Estepar (BWH)
* Jorge Onieva (BWH)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a module in 3D Slicer to segment the ground glass opacity (GGO) tumor, apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] to obtain imaging metrics and classify the GGO.
* Provide the module as an extension part of [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/OpenCAD OpenCAD]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a simple region growing algorithm
* Apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] module
* Use predetermined SVM classifier to decide the lesion type
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Completed analysis for 248 GGOs and trained SVM with an accuracy of 89% to classify GGOs
* Developed the framework for the LungCAD module in Slicer
* Evaluated the Lesion segmentation algorithm as part of the Chest Imaging Platform
* Segmentation works well and is able to prevent the segmentation of vessels running through the lesion
* LungCAD calls Lesion Segmentation CLI for segmentation and HeterogeneityCAD to evaluate features
* Pre-processed SVM will be utilized to classify the GGOs
</div>
</div>

2015 Summer Project Week:LungCAD

2015-06-24T15:08:05Z

Jayender: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:LungCAD-module.png
Image:Seg1n.png
Image:Seg1.png
Image:Seg2n.png
Image:Seg2.png
</gallery>

==Key Investigators==
* Jayender Jagadeesan (BWH)
* Tobias Penskofer (Charite, Berlin)
* Sandy Wells (BWH)
* Clara Meiner (previously BWH)
* Raul San Jose Estepar (BWH)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a module in 3D Slicer to segment the ground glass opacity (GGO) tumor, apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] to obtain imaging metrics and classify the GGO.
* Provide the module as an extension part of [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/OpenCAD OpenCAD]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a simple region growing algorithm
* Apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] module
* Use predetermined SVM classifier to decide the lesion type
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Completed analysis for 248 GGOs and trained SVM with an accuracy of 89% to classify GGOs
* Developed the framework for the LungCAD module in Slicer
* Evaluated the Lesion segmentation algorithm as part of the Chest Imaging Platform
* Segmentation works well and is able to prevent the segmentation of vessels running through the lesion
* LungCAD calls Lesion Segmentation CLI for segmentation and HeterogeneityCAD to evaluate features
* Pre-processed SVM will be utilized to classify the GGOs
</div>
</div>

2015 Summer Project Week:LungCAD

2015-06-24T14:41:54Z

Jayender: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:LungCAD-module.png
Image:Seg1n.png
Image:Seg1.png
Image:Seg2n.png
Image:Seg2.png
</gallery>

==Key Investigators==
* Jayender Jagadeesan
* Tobias Penskofer
* Sandy Wells
* Clara Meiner
* Raul San Jose Estepar

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a module in 3D Slicer to segment the ground glass opacity (GGO) tumor, apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] to obtain imaging metrics and classify the GGO.
* Provide the module as an extension part of [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/OpenCAD OpenCAD]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a simple region growing algorithm
* Apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] module
* Use predetermined SVM classifier to decide the lesion type
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Completed analysis for 248 GGOs and trained SVM with an accuracy of 89% to classify GGOs
* Developed the framework for the LungCAD module in Slicer
* Evaluated the Lesion segmentation algorithm as part of the Chest Imaging Platform
* Segmentation works well and is able to prevent the segmentation of vessels running through the lesion
* LungCAD calls Lesion Segmentation CLI for segmentation and HeterogeneityCAD to evaluate features
* Pre-processed SVM will be utilized to classify the GGOs
</div>
</div>

2015 Summer Project Week:LungCAD

2015-06-24T14:41:36Z

Jayender: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:LungCAD-module.png
Image:Seg1n.png
Image:Seg1.png
Image:Seg2n.png
Image:Seg2.png
</gallery>

==Key Investigators==
* Jayender Jagadeesan
* Tobias Penskofer
* Sandy Wells
* Clara Meiner
* Raul San Jose Estepar

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a module in 3D Slicer to segment the ground glass opacity (GGO) tumor, apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] to obtain imaging metrics and classify the GGO.
* Provide the module as an extension part of [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/OpenCAD OpenCAD]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a simple region growing algorithm
* Apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] module
* Use predetermined SVM classifier to decide the lesion type
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Completed analysis for 248 GGOs and trained SVM with an accuracy of 89% to classify GGOs
* Developed the framework for the LungCAD module in Slicer
* Evaluated the Lesion segmentation algorithm as part of the Chest Imaging Platform
* Segmentation works well and is able to prevent the segmentation of vessels running through the lesion
* LungCAD will call Lesion Segmentation CLI for segmentation and HeterogeneityCAD to evaluate features
* Pre-processed SVM will be utilized to classify the GGOs
</div>
</div>

File:LungCAD-module.png

2015-06-24T14:40:16Z

Jayender: uploaded a new version of "File:LungCAD-module.png"

2015 Summer Project Week:LungCAD

2015-06-24T14:20:58Z

Jayender: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:LungCAD-module.png
Image:Seg1n.png
Image:Seg1.png
Image:Seg2n.png
Image:Seg2.png
</gallery>

==Key Investigators==
* Jayender Jagadeesan
* Tobias Penskofer
* Sandy Wells
* Clara Meiner
* Raul San Jose Estepar

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a module in 3D Slicer to segment the ground glass opacity (GGO) tumor, apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] to obtain imaging metrics and classify the GGO.
* Provide the module as an extension part of [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/OpenCAD OpenCAD]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a simple region growing algorithm
* Apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] module
* Use predetermined SVM classifier to decide the lesion type
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Completed analysis for 248 GGOs and trained SVM with an accuracy of 89% to classify GGOs
* Developed the framework for the LungCAD module in Slicer
* Evaluate the Lesion segmentation algorithm as part of the Chest Imaging Platform
* Segmentation works well and is able to prevent the segmentation of vessels running through the lesion
* LungCAD will call Lesion Segmentation CLI for segmentation and HeterogeneityCAD to evaluate features
* Pre-processed SVM will be utilized to classify the GGOs
</div>
</div>

2015 Summer Project Week:LungCAD

2015-06-24T14:20:08Z

Jayender: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:LungCAD-module.png
Image:Seg1n.png
Image:Seg1.png
Image:Seg2n.png
Image:Seg2.png
</gallery>

==Key Investigators==
* Jayender Jagadeesan
* Tobias Penskofer
* Sandy Wells
* Clara Meinzer

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a module in 3D Slicer to segment the ground glass opacity (GGO) tumor, apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] to obtain imaging metrics and classify the GGO.
* Provide the module as an extension part of [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/OpenCAD OpenCAD]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a simple region growing algorithm
* Apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] module
* Use predetermined SVM classifier to decide the lesion type
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Completed analysis for 248 GGOs and trained SVM with an accuracy of 89% to classify GGOs
* Developed the framework for the LungCAD module in Slicer
* Evaluate the Lesion segmentation algorithm as part of the Chest Imaging Platform
* Segmentation works well and is able to prevent the segmentation of vessels running through the lesion
* LungCAD will call Lesion Segmentation CLI for segmentation and HeterogeneityCAD to evaluate features
* Pre-processed SVM will be utilized to classify the GGOs
</div>
</div>

File:Seg2n.png

2015-06-24T14:11:36Z

Jayender:

File:Seg2.png

2015-06-24T14:11:09Z

Jayender:

File:Seg1n.png

2015-06-24T14:10:14Z

Jayender:

File:Seg1.png

2015-06-24T14:09:53Z

Jayender:

File:LungCAD-module.png

2015-06-24T14:08:57Z

Jayender:

2015 Summer Project Week:LungCAD

2015-06-24T14:04:35Z

Jayender:

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:LungCAD-module.png
Image:Seg1n.png
Image:Seg1.png
Image:Seg2n.png
Image:Seg2.png
</gallery>

==Key Investigators==
* Jayender Jagadeesan
* Tobias Penskofer
* Sandy Wells
* Clara Meinzer

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a module in 3D Slicer to segment the ground glass opacity (GGO) tumor, apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] to obtain imaging metrics and classify the GGO.
* Provide the module as an extension part of [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/OpenCAD OpenCAD]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a simple region growing algorithm
* Apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] module
* Use predetermined SVM classifier to decide the lesion type
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Completed analysis for 248 GGOs and trained SVM with an accuracy of 89% to classify GGOs
</div>
</div>

2015 Summer Project Week:QuantitativeProstate

2015-06-22T09:38:21Z

Jayender: /* Key Investigators */

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

==Key Investigators==
* Tobias Penzkofer
* Jayender Jagadeesan
* Tina Kapur
* Clare Tempany
* Everybody else interested (please add yourself)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* To establish the methods found in Heterogeneity CAD for prostate MRI purposes
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Establish Slicer pipeline for prostate MRI texture analyis
* Subgoal: define best way to organize data
* Scripting support for automated analysis after data preparation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Project initiated
</div>
</div>

2015 Summer Project Week:LightWeightRobotIGT

2015-06-22T09:13:55Z

Jayender: /* Key Investigators */

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:FiniteStateMachine_colored.png|Finite state machine which can be operated using Slicer Module
Image:ScreenshotLWRIGT.jpg|Screenshot of the Slicer module and the current robot position in CT data of the Femur phantom
Image:StatemachineColoring.jpg|Color coding for the robot state
</gallery>

==Key Investigators==
* Sebastian Tauscher
* Junichi Tokuda
* Jayender Jagadeesan

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* The LightWeightRobotIGT [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/LightWeightRobotIGT] module allows to communicate with a light weight robot (LWR iiwa, KUKA Laboratories GmbH, Germany, Augsburg) using an open interface concept based on the OpenIGTLink protocol (LWROpenIGTIF). Therefore, a state machine example is available at Git Hub containing the necessary interface classes for the communication on the robot control.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
During the project week the definition of virtaul fixtures and the definition of the target point via fiducials is planned.
* Definition of virtual fixtures via 2 points
* Definition of target point and target orientation
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2015 Summer Project Week:LungCAD

2015-06-22T09:02:36Z

Jayender: /* Project Description */

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

==Key Investigators==
* Jayender Jagadeesan
* Tobias Penskofer
* Sandy Wells
* Clara Meinzer

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a module in 3D Slicer to segment the ground glass opacity (GGO) tumor, apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] to obtain imaging metrics and classify the GGO.
* Provide the module as an extension part of [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/OpenCAD OpenCAD]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a simple region growing algorithm
* Apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] module
* Use predetermined SVM classifier to decide the lesion type
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Completed analysis for 248 GGOs and trained SVM with an accuracy of 89% to classify GGOs
</div>
</div>

2015 Summer Project Week:LungCAD

2015-06-22T08:56:12Z

Jayender: /* Key Investigators */

2015 Summer Project Week

2015-06-22T08:55:32Z

Jayender: /* Feature Based Image Analysis */

__NOTOC__

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

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

==Logistics==

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

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Sunday, June 21
!style="width:18%" |Monday, June 22 <br> Room Berlin
!style="width:18%" |Tuesday, June 23 <br> Room Berlin
!style="width:18%" |Wednesday, June 24 <br> Room Berlin
|-
|bgcolor="#ffffdd"|'''9:00am-3:00pm:'''
|rowspan=3 valign=bottom|<hr>'''6pm''' Meeting with All Participants in Hotel Constanza Lobby
|'''10:00-11am:''' <font color="#503020">Rapid Introduction of all Projects and Teams <br>
'''11am-3pm''' <font color="#503020">Work <br>

|
'''10:00am-11am:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis) <br>
'''11am-3pm''' <font color="#503020">Work
| <font color="#503020">Work <br>
|-
|bgcolor="#ffffdd"|'''2:00pm-4:00pm'''
|bgcolor="#ffffaa"|Lunch <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]]
|-
|bgcolor="#ffffdd"|'''4:00-7:00pm'''
|<font color="#503020"> Work
|'''5:00-7:00pm:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2015_Summer_Project_Week/SoftwareStack| Open Software Stack]] (Steve Pieper) <br>4pm-6pm: Registration Desk Open for CARS attendees. Please pick up badges. <br>
|'''4:00-5:00pm:''' <font color="#503020"> Work <br>
'''5:00-6pm:''' Report Progress
|-
|bgcolor="#ffffdd"|'''7:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|Adjourn for the day <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#f0e68b"|Adjourn for the day <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#f0e68b"|'''6:00pm''' Adjourn Project Week and relocate to CARS Opening<br> '''7:30pm''' CARS Welcome Reception
|}

*Please note that start, end, and mealtimes have been set to match local schedules in Barcelona.
*Here is a list of [[Barcelona Restaurants | locally recommended places to eat]] in the vicinity of the conference hotel. All participants are responsible for their own meals.

== '''Background''' ==

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

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

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

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

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

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

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

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

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

==Equipment==

*[[2015_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)

==Image-Guided Therapy==
*[[2015_Summer_Project_Week:SlicerIGT|SlicerIGT tutorials for use cases]] (Tamas Ungi, Andras Lasso, Jayender Jagadeesan, Alvaro Gomez, Noby Hata)
*[http://www.na-mic.org/Wiki/index.php/2015_Refinement_Registration_Module Refinement of RegistrationModule] (Peter Behringer, Andrey Fedorov)
*[[2015_Summer_Project_Week:IGTSliceletBase| Create base classes for IGT slicelet]] (Andras Lasso, Andrey Fedorov, Adam Rankin)
*[http://www.na-mic.org/Wiki/index.php/2015_BRAINSFit_registration_in_SimpleITK BRAINSFit registration in SimpleITK] (Peter Behringer, Andrey Fedorov, Dženan Zukić)
*[http://www.na-mic.org/Wiki/index.php/2015_Multi_atlas_based_prostate_segmentation Multi atlas based prostate segmentation] (Paolo Zaffino, Giampaolo Pileggi, Salvatore Scaramuzzino, Peter Behringer, Andrey Fedorov, Maria Francesca Spadea)
*[http://www.na-mic.org/Wiki/index.php/2015_Multimodal_Guidance_for_Breast_Cancer_Surgery Multimodal Guidance for Breast Cancer Surgery] (Mikael Brudfors, Javier Pascau)
*[[2015_pilot trajectory planning | Pilot Trajectory Planning(Caroline Essert, Sonia Pujol)]]
*[[2015_Summer_Project_Week:LinearFeatureRegistration|Linear Feature Registration]] (Matthew Holden)
*[[2015_Summer_Project_Week:LightWeightRobotIGT | Integration of a KUKA robot using OpenIGTLink ]] (Sebastian Tauscher, Junichi Tokuda)
*[[2015_Summer_Project_Week:USReconstruction | Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer ]] (Frank Preiswerk, Laurent Chauvin)
*[[2015 Orthognathic Surgery|Orthognathic Surgery]] (Dženan Zukić, Kitware)
*[[2015_Summer_Project_Week:SlicerTAVI | SlicerTAVI ]] (Adam Rankin)
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]
*[[2015_Summer_Project_Week:OpenSource_MRTRUS_Fusion_for_Prostate_biopsy|Open-source MRI-TRUS Fusion for Prostate biopsy]] (Andrey Fedorov, Andras Lasso, Clare Tempany)
*[[2015_Summer_Project_Week:TrackerlessMRIUSFusion | Trackerless MRI - US Registration ]] (Utsav Pardasani)

==Feature Based Image Analysis==
*[[2015_Summer_Project_Week:LungCAD| LungCAD]] (Jayender Jagadeesan, Tobias Penzkofer, Sandy Wells, Clara Meinzer)
*[[2015_Summer_Project_Week:QuantitativeProstate | Texture Analysis for Prostate Imaging]] (Tobias Penzkofer, Jay Jagadeesan, Tina Kapur)
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells, Raul San Jose Estepar, Tina Kapur)
*[[2015_Summer_Project_Week:AutomaticCephalometric | Automatic Cephalometric Analysis ]] (J. Jesus Montufar, Marcelo Romero)

==Chest Imaging Platform==
*[[2015_Summer_Project_Week:Slicer_CIP | Slicer CIP: advanced features and deployment ]] (Raúl San José, Alex Yarmarkovich, Jorge Onieva)
*[[2015_Summer_Project_Week:PAA_Ratio | PAA Ratio Module ]] (Jorge Onieva,Raúl San José)
*[[2015_Summer_Project_Week:Tracheal_Stent_Planning | Planning for tracheal stents ]] (Raúl San José, Jorge Onieva, George Cheng)

==QIICR==
*[[2015_Summer_Project_Week:DSC | Dynamic Susceptibility Contrast (DSC) MRI for brain ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)
*[[2015_Summer_Project_Week:T1 mapping | T1 mapping for Dynamic Contrast Enhanced (DCE) MRI ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Jayashree Kalpathy-Cramer)
*[[2015_Summer_Project_Week:DCMTK| Integration and testing of new DCMTK with Slicer]] (Michael Onken, Andrey Fedorov, Steve Pieper)

==Infrastructure==
*[[2015_Summer_Project_Week:Python_scripts_from_command_line|Simplify use of python scripts from the command line]] (Andrey Fedorov, Steve Pieper, Robin Weiss, Artem Mamonov)
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin,Hans Meine)
*[[2015_Summer_Project_Week:Update Checker | Update Checker]] (Franklin King, BWH)
*[[2015_Summer_Project_Week:Integrated Virtual Reality Viewer | Integrated Virtual Reality Viewer]] (Franklin King, BWH, Utsav Pardasani)
*[[2015_Summer_Project_Week:SegmentationNode| Use new Segmentation node in Editor]] (Andras Lasso, Steve Pieper)
*[[2015_Summer_Project_Week:Slicer_Conda | Integrate Conda Python in Slicer]] (Raúl San José, Jorge Onieva, Utsav Pardasani)
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC, Steve Pieper)
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, Steve Pieper, Nicolas Rannou)
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with "interesting" CLI modules (BRAINSFit, CIP, UKFTractography?) in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)

==Web==
*[[2015_Summer_Project_Week:Dicom parsing with DCMJS | Dicom parsing with DCMJS]] (Nicolas Rannou, Michael Onken, Steve Pieper)
*[[2015_Summer_Project_Week:Volume rendering with DCMJS and THREEJS | Volume Rendering with DCMJS and THREEJS]] (Nicolas Rannou, Steve Pieper)
*[[2015_Summer_Project_Week:CTK for the web and touch devices| CTK for the web and touch devices]] (Nicolas Rannou, Yves Martelli, Steve Pieper)
*[[2015_Summer_Project_Week:SlicerCardboard| Slicer for mobile-based vr goggles]] (Utsav Pardasani, Adam Rankin)

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

== '''Registrants''' ==

Please add your name to the list. This is the registration mechanism for this project week.
#Tina Kapur, BWH
#Ron Kikinis, BWH & Fraunhofer
#Steve Pieper, Isomics
#Tamas Ungi, Queen's University, Canada
#Andras Lasso, Queen's University, Canada
#Paolo Zaffino, ImagEngLab, Magna Graecia University, Italy
#Salvatore Scaramuzzino, ImagEngLab, Magna Graecia University, Italy
#Giampaolo Pileggi, ImagEngLab, Magna Graecia University, Italy
#Nicole Aucoin, BWH
#Sonia Pujol, BWH
#Dženan Zukić, Kitware, Carrboro, NC
#Jayender Jagadeesan, BWH
#Guido Gerig, Utah
#Sandy Wells, BWH
#Matthew Toews, École de Technologie Supérieure, Montreal, Canada
#Frank Preiswerk, BWH
#Raul San Jose, BWH
#Jorge Onieva, BWH
#Yulong Zhao, Université de Rennes
#Laurent Chauvin, BWH
#Michael Onken, Open Connections
#Tobias Penzkofer, Department of Radiology, Charité Berlin, Germany
#Javier Pascau, Universidad Carlos III de Madrid, Spain
#Angel Torrado-Carvajal, Universidad Rey Juan Carlos, Madrid, Spain
#Nobuhiko Hata, BWH
#Robert H. Owen, BK Medical ApS, Denmark
#Clare Tempany, BWH
#Adam Rankin, Robarts
#Utsav Pardasani, Robarts
#Marcelo Romero, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#J. Jesus Montufar, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
#Andrey Fedorov, BWH
#Nicolas Rannou, BCH
#Mikael Brudfors, Universidad Carlos III de Madrid, Spain
#Laura Sanz, Universidad Carlos III de Madrid, Spain
#Eugenio Marinetto, Universidad Carlos III de Madrid, Spain
#David García, Universidad Carlos III de Madrid, Spain
#Franklin King, Queen's University / BWH
#Jorge García, Universidad Politécnica de Madrid, Spain
#Peter Behringer, BWH
#Caroline Essert, University of Strasbourg
#Sebastian Tauscher, Institute of Mechatronic Systems, Leibniz Universität Hannover, Germany
#Matthew Holden, Queen's University, Canada
#Sara Fernandez Vidal, ICM, France
#Laszlo Kanyasi, Perk Lab affiliate, Hungary
#Xiao Da, MGH
#Arnaud De Bruecker, École supérieure d'informatique, Brussels, Belgium
#Ali Gottschalk, École supérieure d'informatique, Brussels, Belgium
#Christophe Teixeira Pereira, École supérieure d'informatique, Brussels, Belgium
#Tsotne Shonia, École supérieure d'informatique, Brussels, Belgium
#Clara Meinzer, Semmelweis University, Hungary
#Yves Martelli, Galgo Medical, Barcelona, Spain

2015 Summer Project Week:LungCAD

2015-06-09T22:19:04Z

Jayender: /* Project Description */

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

==Key Investigators==
* Jayender Jagadeesan
* Tobias Penskofer
* Sandy Wells

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a module in 3D Slicer to segment the ground glass opacity (GGO) tumor, apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] to obtain imaging metrics and classify the GGO.
* Provide the module as an extension part of [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/OpenCAD OpenCAD]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a simple region growing algorithm
* Apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] module
* Use predetermined SVM classifier to decide the lesion type
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

</div>
</div>

2015 Summer Project Week

2015-06-09T22:16:22Z

Jayender: /* Feature Based Image Analysis */

__NOTOC__

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

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

==Logistics==

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

==Agenda==

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

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

== '''Background''' ==

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

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

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

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

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

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

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

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

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

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

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

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

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

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

==QIICR==
*[[2015_Summer_Project_Week:DSC | Dynamic Susceptibility Contrast MRI (DSC) for brain ]] (Xiao Da)
*[[2015_Summer_Project_Week:T1 mapping | T1 mapping for DCE ]] (Xiao Da)

== '''Registrants''' ==

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

2015 Summer Project Week:LungCAD

2015-06-09T22:15:54Z

Jayender: /* Key Investigators */

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

==Key Investigators==
* Jayender Jagadeesan
* Tobias Penskofer
* Sandy Wells

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a module in 3D Slicer to segment the ground glass opacity (GGO) tumor, apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] to obtain imaging metrics and classify the GGO.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a simple region growing algorithm
* Apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] module
* Use predetermined SVM classifier to decide the lesion type
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

</div>
</div>

2015 Summer Project Week:LungCAD

2015-06-09T22:11:55Z

Jayender: Created page with '__NOTOC__ <gallery> Image:PW-Summer2015.png|Projects List </gallery> ==Key Investigators== * Jayender Jagadeesan ==Project Description== <…'

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

==Key Investigators==
* Jayender Jagadeesan

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a module in 3D Slicer to segment the ground glass opacity (GGO) tumor, apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] to obtain imaging metrics and classify the GGO.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a simple region growing algorithm
* Apply [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD HeterogeneityCAD] module
* Use predetermined SVM classifier to decide the lesion type
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>

</div>
</div>

2015 Summer Project Week

2015-04-02T16:31:57Z

Jayender: /* Chronic Obstructive Pulmonary Disease, Lung, Chest */

__NOTOC__

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

==Logistics==

Location: NH COLLECTION CONSTANZA Hotel, Barcelona

Dates:

*Start: Sunday, June 21st (early evening start with project presentations)
**3 days of work: Monday June 22, Tuesday June 23, Wednesday June 24
*Adjourn: Wednesday June 24th at 5pm

Registration Fee: zero. We will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.

== '''Background''' ==

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

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

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next event in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Summer_Project_Week Barcelona, Spain] in June 2015.

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

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

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

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

==Image-Guided Therapy==
*[[2015 Orthognatic Surgery|Orthognatic Surgery]]

==Huntington's Disease==
==TBI==

==Stroke==

==Cardiac==

==Chronic Obstructive Pulmonary Disease, Lung, Chest ==
*[[2015_Summer_Project_Week:LungCAD| LungCAD]] (Jayender Jagadeesan)

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

==Feature Extraction==
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells)

==Additional Brain Image Analysis==
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]

==Slicer4 Extensions==

==TMJOA RO1 - Collaboration with NAMIC==

==Infrastructure==
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC)
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, ??)
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin, Jim Miller)

== '''Logistics''' ==

*'''Dates:''' June 21-24, 2015.
*'''Location:''' Barcelona, Spain
*'''REGISTRATION:''' 0
*'''Registration Fee:''' TBD
*'''Hotel:''' TBD
*'''Room sharing''': If interested, add your name to the list: [[2015_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Please add your name to the list. This is the registration mechanism for this project week.

#Tina Kapur, BWH
#Ron Kikinis, BWH & Fraunhofer
#Steve Pieper, Isomics
#Tamas Ungi (Queen's University, Canada)
#Andras Lasso, Queen's University, Canada
#Paolo Zaffino (ImagEngLab, Magna Graecia University, Italy)
#Salvatore Scaramuzzino (ImagEngLab, Magna Graecia University, Italy)
#Giampaolo Pileggi (ImagEngLab, Magna Graecia University, Italy)
#Hans Meine (Fraunhofer MEVIS, Bremen, Germany)
#Nicole Aucoin (BWH)
#Sonia Pujol (BWH)
#Dženan Zukić (Kitware, Carrboro, NC, USA)
#Jayender Jagadeesan (BWH)
#Guido Gerig
#Sandy Wells, BWH
#Matthew Toews (École de Technologie Supérieure, Montreal, Canada)
#Frank Preiswerk, BWH
#Junichi Tokuda, BWH
#Jonathan Scalera, BWH
#Raul San Jose, BWH
#Jorge Onieva, BWH
#James Ross, BWH
#Yulong Zhao, Université de Rennes
#Laurent Chauvin, BWH
#Michael Onken, Open Connections

2015 Summer Project Week

2015-03-27T20:08:54Z

Jayender: /* Registrants */

__NOTOC__

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

==Logistics==

Location: NH COLLECTION CONSTANZA Hotel, Barcelona

Dates:

*Start: Sunday, June 21st (early evening start with project presentations)
**3 days of work: Monday June 22, Tuesday June 23, Wednesday June 24
*Adjourn: Wednesday June 24th at 5pm

Registration Fee: zero. We will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.

== '''Background''' ==

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

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

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next event in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Summer_Project_Week Barcelona, Spain] in June 2015.

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

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

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

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

==Image-Guided Therapy==
*[[2015 Orthognatic Surgery|Orthognatic Surgery]]

==Huntington's Disease==
==TBI==

==Stroke==

==Cardiac==

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

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

==Feature Extraction==

==Additional Brain Image Analysis==
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]

==Slicer4 Extensions==

==TMJOA RO1 - Collaboration with NAMIC==

==Infrastructure==
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC)
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, ??)
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin, Jim Miller)

== '''Logistics''' ==

*'''Dates:''' June 21-24, 2015.
*'''Location:''' Barcelona, Spain
*'''REGISTRATION:''' 0
*'''Registration Fee:''' TBD
*'''Hotel:''' TBD
*'''Room sharing''': If interested, add your name to the list: [[2015_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Please add your name to the list. This is the registration mechanism for this project week.

#Tina Kapur
#Ron Kikinis
#Steve Pieper
#Tamas Ungi (Queen's University, Canada)
#Paolo Zaffino (ImagEngLab, Magna Graecia University, Italy)
#Salvatore Scaramuzzino (ImagEngLab, Magna Graecia University, Italy)
#Giampaolo Pileggi (ImagEngLab, Magna Graecia University, Italy)
#Hans Meine (Fraunhofer MEVIS, Bremen, Germany)
#Nicole Aucoin (BWH)
#Sonia Pujol (BWH)
#Dženan Zukić (Kitware, Carrboro, NC, USA)
#Jayender Jagadeesan (BWH)

2013 Summer Project Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer

2013-06-21T11:10:33Z

Jayender: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:OpenCAD.png|OpenCAD
Image:SlicerGUI3.png|OpenCAD GUI
Image:Breastopencad1.png|Example 1
Image:Breastopencad2.png|Example 2
Image:Breastopencad3.png|Example 3
</gallery>

==Key Investigators==
* Boston College: Sneha Dugapal
* RPI: Vivek Narayan
* BWH: Jayender Jagadeesan, Tobias Penskofer, Eva Gombos

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

<h3>Objective</h3>
We will develop a module in 3D Slicer to segment breast tumors and quantify their heterogeneity. Based off the heterogeneity of the breast tumors, we will categorize them as invasive ductal carcinoma, ductal carcinoma in situ, or fibroadenoma.
</div>

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

<h3>Approach, Plan</h3>
Our approach is to segment breast tumors using curve-analysis.
Our plan for the project week is to develop a module to segment tumors and determine their heterogeneity.
</div>

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

<h3>Progress</h3>
* We have developed a module called "OpenCAD" in 3D Slicer to automatically segment breast tumors.
* The module computes the regions of enhanced perfusion using the curve analysis method and overlays a mask on the DCE-MRI.
* The threshhold for initial increase and washout of contrast can be adjusted.
* Label statistics has also been included in the module to compute volume of tumor exhibiting Type I, II and III curves.
* Heterogeneity metric is also being implemented. We are working on evaluating the clinical relevance of this metric.
</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as an extension called OpenCAD.

==References==

2013 Summer Project Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer

2013-06-21T11:08:25Z

Jayender:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:OpenCAD.png|OpenCAD
Image:SlicerGUI3.png|OpenCAD GUI
Image:Breastopencad1.png|Example 1
Image:Breastopencad2.png|Example 2
Image:Breastopencad3.png|Example 3
</gallery>

==Key Investigators==
* Boston College: Sneha Dugapal
* RPI: Vivek Narayan
* BWH: Jayender Jagadeesan, Tobias Penskofer, Eva Gombos

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

<h3>Objective</h3>
We will develop a module in 3D Slicer to segment breast tumors and quantify their heterogeneity. Based off the heterogeneity of the breast tumors, we will categorize them as invasive ductal carcinoma, ductal carcinoma in situ, or fibroadenoma.
</div>

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

<h3>Approach, Plan</h3>
Our approach for is to segment breast tumors using curve-analysis.
Our plan for the project week is to develop the module to segment tumors and determine their heterogeneity.
</div>

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

<h3>Progress</h3>
* We have developed a module called "OpenCAD" in 3D Slicer to automatically segment breast tumors.
* The module computes the regions of enhanced perfusion using the curve analysis method and overlays a mask on the DCE-MRI.
* The threshhold for initial increase and washout of contrast can be adjusted.
* Label statistics has also been included in the module to compute volume of tumor exhibiting Type I, II and III curves.
* Heterogeneity metric is also being implemented. We are working on evaluating the clinical relevance of this metric.
</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as an extension called OpenCAD.

==References==

File:Breastopencad3.png

2013-06-21T11:07:58Z

Jayender:

File:Breastopencad2.png

2013-06-21T11:06:41Z

Jayender:

File:Breastopencad1.png

2013-06-21T11:03:46Z

Jayender:

2013 Summer Project Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer

2013-06-21T11:02:02Z

Jayender:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:OpenCAD.png|OpenCAD
Image:SlicerGUI3.png|OpenCAD GUI
</gallery>

==Key Investigators==
* Boston College: Sneha Dugapal
* RPI: Vivek Narayan
* BWH: Jayender Jagadeesan, Tobias Penskofer, Eva Gombos

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

<h3>Objective</h3>
We will develop a module in 3D Slicer to segment breast tumors and quantify their heterogeneity. Based off the heterogeneity of the breast tumors, we will categorize them as invasive ductal carcinoma, ductal carcinoma in situ, or fibroadenoma.
</div>

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

<h3>Approach, Plan</h3>
Our approach for is to segment breast tumors using curve-analysis.
Our plan for the project week is to develop the module to segment tumors and determine their heterogeneity.
</div>

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

<h3>Progress</h3>
* We have developed a module called "OpenCAD" in 3D Slicer to automatically segment breast tumors.
* The module computes the regions of enhanced perfusion using the curve analysis method and overlays a mask on the DCE-MRI.
* The threshhold for initial increase and washout of contrast can be adjusted.
* Label statistics has also been included in the module to compute volume of tumor exhibiting Type I, II and III curves.
* Heterogeneity metric is also being implemented. We are working on evaluating the clinical relevance of this metric.
</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as an extension called OpenCAD.

==References==

File:SlicerGUI3.png

2013-06-21T10:59:51Z

Jayender:

File:OpenCAD.png

2013-06-21T10:56:47Z

Jayender:

2013 Summer Project Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer

2013-06-21T10:48:58Z

Jayender: /* Delivery Mechanism */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Boston College: Sneha Dugapal
* RPI: Vivek Narayan
* BWH: Jayender Jagadeesan, Tobias Penskofer, Eva Gombos

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

<h3>Objective</h3>
We will develop a module in 3D Slicer to segment breast tumors and quantify their heterogeneity. Based off the heterogeneity of the breast tumors, we will categorize them as invasive ductal carcinoma, ductal carcinoma in situ, or fibroadenoma.
</div>

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

<h3>Approach, Plan</h3>
Our approach for is to segment breast tumors using curve-analysis.
Our plan for the project week is to develop the module to segment tumors and determine their heterogeneity.
</div>

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

<h3>Progress</h3>
* We have developed a module called "OpenCAD" in 3D Slicer to automatically segment breast tumors.
* The module computes the regions of enhanced perfusion using the curve analysis method and overlays a mask on the DCE-MRI.
* The threshhold for initial increase and washout of contrast can be adjusted.
* Label statistics has also been included in the module to compute volume of tumor exhibiting Type I, II and III curves.
* Heterogeneity metric is also being implemented. We are working on evaluating the clinical relevance of this metric.
</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as an extension called OpenCAD.

==References==

2013 Summer Project Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer

2013-06-21T10:47:38Z

Jayender: