NAMIC Wiki - User contributions [en]

2015 Winter Project Week COPD Breakout

2015-07-20T16:07:38Z

Raul: /* Brief intro to COPD */

== Introduction==
Chest Imaging Platform (CIP) and SlicerCIP is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD).
The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA]
=== Project Goals ===
* AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.

* AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.

* AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.

=== History ===
* 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
* Lung Imaging Platform (Jan 2009 - March 2012): Initial consolidation of our developments for high-throughput image analysis in [https://www.copdgene.org COPDGene].
* April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
* April 2013 - January 2014: Port to github and further consolidation under a private repository.
* Today: Release 0.0.0 of the [https://github.com/acil-bwh/ChestImagingPlatform Chest Imaging Platform]

=== Brief intro to COPD ===
[http://www.na-mic.org/Wiki/images/2/26/BreakoutSession-CIP-COPDIntro.pptx slides]

=== Team ===
* Raul San Jose
* James Ross
* Rola Harmouche
* Jorge Onieva
* German Gonzalez
* Alex Yarmakovich

Collaborators
* George Washko
* Alejandro Diaz

== Architecture ==
[[File:CIPArchitecture.png]]

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components [http://www.na-mic.org/Wiki/images/0/0b/CipTools.pptx slides]
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

2015 Winter Project Week COPD Breakout

2015-07-20T16:06:49Z

Raul: /* Brief intro to COPD */

== Introduction==
Chest Imaging Platform (CIP) and SlicerCIP is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD).
The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA]
=== Project Goals ===
* AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.

* AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.

* AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.

=== History ===
* 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
* Lung Imaging Platform (Jan 2009 - March 2012): Initial consolidation of our developments for high-throughput image analysis in [https://www.copdgene.org COPDGene].
* April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
* April 2013 - January 2014: Port to github and further consolidation under a private repository.
* Today: Release 0.0.0 of the [https://github.com/acil-bwh/ChestImagingPlatform Chest Imaging Platform]

=== Brief intro to COPD ===
[slides | http://www.na-mic.org/Wiki/images/2/26/BreakoutSession-CIP-COPDIntro.pptx]

=== Team ===
* Raul San Jose
* James Ross
* Rola Harmouche
* Jorge Onieva
* German Gonzalez
* Alex Yarmakovich

Collaborators
* George Washko
* Alejandro Diaz

== Architecture ==
[[File:CIPArchitecture.png]]

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components [http://www.na-mic.org/Wiki/images/0/0b/CipTools.pptx slides]
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

File:BreakoutSession-CIP-COPDIntro.pptx

2015-07-20T16:06:24Z

Raul: Intro to CIP

Intro to CIP

2015 Summer Project Week:Slicer CIP

2015-06-24T14:57:31Z

Raul: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:SlicerCIPLogo.png| SlicerCIP Logo
</gallery>

==Key Investigators==
Alex Yarmakovich, Jorge Onieva, Raul San Jose (Brigham and Women's Hospital)

==Project Description==
The Chest Imaging Platform (CIP) is a general purpose library for analysis of chest images for the characterization of chronic lung diseases.
SlicerCIP is the Slicer Extension that interface with CIP and provide access to the CLI toolkit and integrated clinical workflows.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improve the packaging of CIP into the Extension

* Advance in the integration of Anaconda as the python distribution

* Create module layout for the extension
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create new release of CIP (v.0.3.0)
* Update the extension to build against the latest CIP

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* CIP is in release 0.2.0.
* SilicerCIP superbuilds CIP
* Library dependencies update to keep CIP in sync with Slicer dependencies
* Community building:
** Opportunities to integrate CIP as a mutual dependency with OpenCAD
</div>
</div>

2015 Summer Project Week:Tracheal Stent Planning

2015-06-24T14:55:52Z

Raul: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:SlicerCIPLogo.png| SlicerCIP Logo
Image:TracheaStent.png| Trachea Stent Planning
</gallery>

==Key Investigators==
*Raul San Jose, Jorge Onieva (Brigham and Women's Hospital)
*George Cheng (Beth Israel Deaconess Medical Center)

==Project Description==
Different tracheal malformation (tracheobronchial malacia) and neck cancers with tumors invading the airway require the implantation of tracheal stent (T-tubes or Y-stents) to keep the airway opened.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a tracheal stent planning tool to fit T-tubes and Y-stent
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a minimization problem to fit a parameterized model of the stent to the patient tracheal model using constrained points provided by the user
* Build a module to interact with the user and show the stent fitting results and the model parameters.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial conversation with George Cheng
* Develop the algorithm for automatic fitting of an Y-stent using a cylindrical articulated model
[[Image:TracheaStent.png| Trachea Stent Planning]]
</div>
</div>

2015 Summer Project Week:Tracheal Stent Planning

2015-06-24T14:55:33Z

Raul:

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:SlicerCIPLogo.png| SlicerCIP Logo
Image:TracheaStent.png| Trachea Stent Planning
</gallery>

==Key Investigators==
*Raul San Jose, Jorge Onieva (Brigham and Women's Hospital)
*George Cheng (Beth Israel Deaconess Medical Center)

==Project Description==
Different tracheal malformation (tracheobronchial malacia) and neck cancers with tumors invading the airway require the implantation of tracheal stent (T-tubes or Y-stents) to keep the airway opened.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a tracheal stent planning tool to fit T-tubes and Y-stent
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a minimization problem to fit a parameterized model of the stent to the patient tracheal model using constrained points provided by the user
* Build a module to interact with the user and show the stent fitting results and the model parameters.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial conversation with George Cheng
* Develop the algorithm for automatic fitting of an Y-stent using a cylindrical articulated model
Image:TracheaStent.png| Trachea Stent Planning
</div>
</div>

File:TracheaStent.png

2015-06-24T14:53:09Z

Raul: Trachea Stent Planning

Trachea Stent Planning

2015 Summer Project Week:Tracheal Stent Planning

2015-06-24T14:52:16Z

Raul:

2015 Summer Project Week:Tracheal Stent Planning

2015-06-22T08:04:23Z

Raul: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:SlicerCIPLogo.png| SlicerCIP Logo
</gallery>

==Key Investigators==
*Raul San Jose, Jorge Onieva (Brigham and Women's Hospital)
*George Cheng (Beth Israel Deaconess Medical Center)

==Project Description==
Different tracheal malformation (tracheobronchial malacia) and neck cancers with tumors invading the airway require the implantation of tracheal stent (T-tubes or Y-stents) to keep the airway opened.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a tracheal stent planning tool to fit T-tubes and Y-stent
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a minimization problem to fit a parameterized model of the stent to the patient tracheal model using constrained points provided by the user
* Build a module to interact with the user and show the stent fitting results and the model parameters.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial conversation with George Cheng
</div>
</div>

2015 Summer Project Week:Tracheal Stent Planning

2015-06-22T07:58:16Z

Raul: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:SlicerCIPLogo.png| SlicerCIP Logo
</gallery>

==Key Investigators==
*Raul San Jose, Jorge Onieva (Brigham and Women's Hospital)
*George Cheng (Beth Israel Deaconess Medical Center)

==Project Description==
Different tracheal malformation and neck tumors require the implantation of tracheal stent (T-tubes or Y-stents) to keep the airway opened.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a tracheal stent planning tool to fit T-tubes and Y-stent
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a minimization problem to fit a parameterized model of the stent to the patient tracheal model using constrained points provided by the user
* Build a module to interact with the user and show the stent fitting results and the model parameters.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial conversation with George Cheng
</div>
</div>

2015 Summer Project Week:Tracheal Stent Planning

2015-06-22T07:57:18Z

Raul: Created page with '__NOTOC__ <gallery> Image:PW-2015SLC.png|Projects List Image:SlicerCIPLogo.png| SlicerCIP Logo </gallery> ==Key Investigators== Raul San Jo…'

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:SlicerCIPLogo.png| SlicerCIP Logo
</gallery>

==Key Investigators==
Raul San Jose, Jorge Onieva (Brigham and Women's Hospital)
George Cheng (Beth Israel)

==Project Description==
Different tracheal malformation and neck tumors require the implantation of tracheal stent (T-tubes or Y-stents) to keep the airway opened.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a tracheal stent planning tool to fit T-tubes and Y-stent
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a minimization problem to fit a parameterized model of the stent to the patient tracheal model using constrained points provided by the user
* Build a module to interact with the user and show the stent fitting results and the model parameters.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial conversation with George Cheng
</div>
</div>

2015 Summer Project Week

2015-06-22T07:50:55Z

Raul: /* Chest Imaging Platform */

__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, Junichi Tokuda)
*[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)]

==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, 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)
*[[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)
*[[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:Slicer CIP

2015-06-22T07:48:30Z

Raul:

2015 Summer Project Week:Slicer CIP

2015-06-22T07:47:25Z

Raul: /* Project Description */

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

==Key Investigators==
Alex Yarmakovich, Jorge Onieva, Raul San Jose (Brigham and Women's Hospital)

==Project Description==
The Chest Imaging Platform (CIP) is a general purpose library for analysis of chest images for the characterization of chronic lung diseases.
SlicerCIP is the Slicer Extension that interface with CIP and provide access to the CLI toolkit and integrated clinical workflows.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Improve the packaging of CIP into the Extension

* Advance in the integration of Anaconda as the python distribution

* Create module layout for the extension
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create new release of CIP (v.0.3.0)
* Update the extension to build against the latest CIP

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* CIP is in release 0.2.0.
* SilicerCIP superbuilds CIP

</div>
</div>

2015 Summer Project Week:Slicer CIP

2015-06-22T07:42:40Z

Raul: Created page with '__NOTOC__ <gallery> Image:PW-2015SLC.png|Projects List Image:SlicerCIPLogo.png| SlicerCIP Logo </gallery> ==Key Investigators== Alex Yarmak…'

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

==Key Investigators==
Alex Yarmakovich, Jorge Onieva, Raul San Jose (Brigham and Women's Hospital)

==Project Description==
The Chest Imaging Platform (CIP) is a general purpose library for analysis of chest images for the characterization of chronic lung diseases.
SlicerCIP is the Slicer Extension that interface with CIP and provide access to the CLI toolkit and integrated clinical workflows.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Integrate SlicerCIP as an Extension
** Full distribution of CIP and SlicerCIP as an extension
* Discuss with the Slicer community different requirements of SlicerCIP
** Update of Teem to the new release.
** Enhancing Slicer python with new modules.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Explore SlicerRT distribution model
* Follow Extension tutorial
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* SlicerCIP builds against CIP and Slicer nightly.
* Create an Extension SuperBuild.
</div>
</div>

2015 Summer Project Week

2015-06-22T02:36:03Z

Raul: /* Chest Imaging Platform */

__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)
*[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 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)]

==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, Raul San Jose Estepar, Tina Kapur)
*[[2015_Summer_Project_Week:USReconstruction | Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer ]] (Frank Preiswerk, Laurent Chauvin)
*[[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 ]] (Jorge Onieva,Raúl San José)

==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)
*[[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)
*[[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

2015-06-22T02:35:50Z

Raul:

__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)
*[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 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)]

==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, Raul San Jose Estepar, Tina Kapur)
*[[2015_Summer_Project_Week:USReconstruction | Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer ]] (Frank Preiswerk, Laurent Chauvin)
*[[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 ]] (Jorge Onieva,Raúl San José)

==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)
*[[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)
*[[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

2015-06-05T03:55:41Z

Raul: /* Registrants */

__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
|'''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)]
*[http://www.na-mic.org/Wiki/index.php/2015_Multi_atlas_based_prostate_segmentation Multi atlas based prostate segmentation] (Paolo Zaffino, Giampaolo Pileggi, Salvatore Scaramuzzino, Peter Behringer, Andrey Fedorov, Maria Francesca Spadea)
*[[2015_Summer_Project_Week:SlicerIGT|SlicerIGT tutorials for use cases]] (Tamas Ungi)
*[http://www.na-mic.org/Wiki/index.php/2015_Refinement_Registration_Module Refinement of RegistrationModule] (Peter Behringer, Andrey Fedorov)
*[http://www.na-mic.org/Wiki/index.php/2015_BRAINSFit_registration_in_SimpleITK BRAINSFit registration in SimpleITK] (Peter Behringer, Andrey Fedorov)

==Feature Based Image Analysis==
*[[2015_Summer_Project_Week:LungCAD| LungCAD]] (Jayender Jagadeesan)
*[[2015_Summer_Project_Week:QuantitativeProstate | Texture Analysis for Prostate Imaging]] (Tobias Penzkofer, Jay Jagadeesan, Tina Kapur)
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells, Tina Kapur)

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

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

==Web / DCMTKJS==
*[[2015_Summer_Project_Week:Porting Slicer to the web | Porting Slicer to the web]] (Nicolas Rannou)

== '''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

2015 Summer Project Week

2015-03-31T19:54:28Z

Raul: /* 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==
*[[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

Density Inspector

2015-01-09T16:31:52Z

Raul: /* Project Description */

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

==Key Investigators==
Alex Yarmakovich, Raul San Jose, Jorge Onieva (Brigham and Women's Hospital)

==Project Description==
Clinical investigators require tools to probe data that can help them to frame hypothesis about how pathophysiology affects changes in imaging. Densitometry is one of the primary assessment tools used to evaluate emphysema from CT scans.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a general-purpose probing tool to compute on-the-fly histogram related measurements over a active ROI.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create module to compute histogram and histogram measurements on ROIs
* Explore how to extend the current ROI available shapes
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Discuss specs for the module to be general enough that can be used to the core slicer distribution
* Future work: Adding spherical ROIs.
</div>
</div>

Slicer CIP

2015-01-09T16:28:57Z

Raul: /* Project Description */

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

==Key Investigators==
Alex Yarmakovich, Jorge Onieva, Raul San Jose (Brigham and Women's Hospital)

==Project Description==
The Chest Imaging Platform (CIP) is a general purpose library for analysis of chest images for the characterization of chronic lung diseases.
SlicerCIP is the Slicer Extension that interface with CIP and provide access to the CLI toolkit and integrated clinical workflows.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Integrate SlicerCIP as an Extension
** Full distribution of CIP and SlicerCIP as an extension
* Discuss with the Slicer community different requirements of SlicerCIP
** Update of Teem to the new release.
** Enhancing Slicer python with new modules.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Explore SlicerRT distribution model
* Follow Extension tutorial
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* SlicerCIP builds against CIP and Slicer nightly.
* Create an Extension SuperBuild.
</div>
</div>

2015 Winter Project Week

2015-01-09T08:21:40Z

Raul:

__NOTOC__

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

Welcome to the 20th Project week page!

== Note of Remembrance ==

[[file:ferenc.jpg|right]]
This project week is dedicated to Ferenc Jolesz, leader and mentor to many in the image guided therapy community. There is a [http://ferenc.jolesz.muchloved.com/ tribute page to Ferenc] for people who want to share their thoughts.

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

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

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

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

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

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

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

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

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

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

==Image-Guided Therapy==
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
* [[User:Yli|Quantitative Evaluation of Digitally Registered Pre and Post op DTI by 3D ROI Segmentation]] (Li Ye, Sonia Pujol, Steve Pieper, Alireza Mehrtash)
* [[New Distance|A new modified Frechet distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)
* [[ProstateNavigation workflow | Workflow for prostate navigation and its components]] (Peter Behringer, Andriy Fedorov)
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[Needle Finder Tutorial | Needle Finder Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*[[VR Radiology | Application of consumer virtual reality devices in creating environments for diagnostic radiology]] (Franklin King, Steve Pieper)
*[[Distribution modeling | Summary statistics versus distributions: evaluating improved ability to detect clinical differences using DTI]] (Anuja Sharma, Guido Gerig)
*[[Valve Replacement | Aortic valve replacement using tracked 3D ultrasound]] (Adam Rankin)
*[[2015_Winter_Project_Week:CommunicationProtocolForOpticalTrackingWithSurfaceScan| Communication Protocol for Optical Tracking with Surface Scan]] (Junichi Tokuda, Sangyong Kim, ByungHyun Cho, Brian Nini, Nobuhiko Hata)

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

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

==CTE==
* [[Slicer_Tract_Analysis | Measurement and visualization using white matter hierarchies in Slicer]] (Alexander Yarmarkovich, Lauren O'Donnell)

== Lung ==
*[[ Small lung nodule differential diagnosis using 3D Slicer | Small lung nodule differential diagnosis using 3D Slicer]] (Li Ming, Jay Jagadeesan)

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

==Feature Extraction==
* [[3D_SIFT_VIEW| 3D SIFT Feature Visualization in Slicer]] (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)
* [[Cortex_Clustering| Experimental tract-based cortical clustering ]] (Lauren O'Donnell, William Wells)

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

==TMJOA RO1 - Collaboration with NAMIC==
* [[2015_Winter_Project_Week:SlicerModelGlyphs | Display of point data vectors on Slicer models]] (Francois Budin, Steve Pieper)

==Infrastructure==

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

== '''Registrants''' ==

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

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

Feature Extraction with Particles

2015-01-09T08:19:39Z

Raul: /* Project Description */

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

==Key Investigators==
Raul San Jose, James Ross (Brigham and Women's Hospital)

==Project Description==
[http://www.ncbi.nlm.nih.gov/pubmed/19834216 Scale-space particles] are a feature extraction tool that samples an image domain looking for second-order features based on Hessian information in both scale and space. Scale-space particles are implemented in Teem as part of the pull library.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create a user-friendly interface to allow feature extraction based on space-scale particles in ROIs.
* The primary goal is to develop a module that
** can enable visual parameter exploration for whole image-domain feature extraction
** can provide interactive features extraction in ROIs
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Integrate the functionality of the pull library as a VTK class
* Create a python module that relies on a vtkSlicerLogic class to orchestrate the VTK functionality.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Integration of latest Teem into [https://github.com/Slicer/teem Slicer] (Special thanks to Hans Johnson and JC for their help).
* VTK class is almost complete. The main standing issue it the creation of a stack of blur volumes in memory.
</div>
</div>

Feature Extraction with Particles

2015-01-09T08:18:36Z

Raul: /* Project Description */

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

==Key Investigators==
Raul San Jose, James Ross (Brigham and Women's Hospital)

==Project Description==
[http://www.ncbi.nlm.nih.gov/pubmed/19834216 Scale-space particles] are a feature extraction tool that samples an image domain looking for second-order features based on Hessian information in both scale and space. Scale-space particles are implemented in Teem as part of the pull library.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create a user-friendly interface to allow feature extraction based on space-scale particles in ROIs.
* The primary goal is to develop a module that
** can enable visual parameter exploration for whole image-domain feature extraction
** can provide interactive features extraction in ROIs
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Integrate the functionality of the pull library as a VTK class
* Create a python module that relies on a vtkSlicerLogic class to orchestrate the VTK functionality.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Integration of latest Teem into Slicer (Special thanks to Hans Johnson and JC for their help).
* VTK class is almost complete. The main standing issue it the creation of a stack of blur volumes in memory.
</div>
</div>

Nodule Sizing

2015-01-09T08:13:50Z

Raul: /* Project Description */

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

==Key Investigators==
Raul San Jose

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create a Slicer module for lung nodule sizing
* Integrate the [https://public.kitware.com/LesionSizingKit/index.php/Main_Page Lesion Sizing Toolkit] nodule segmentation as part of CIP
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create CLI to integrate LST functionality
* Create a python module that computes lesion measurements based on nodule segmentation results
** Use ROI tools to select nodule region
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* The LST nodule segmentation tool has been integrated as a CLI into [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/CommandLineTools/GenerateLesionSegmentation CIP]
[[File:LesionSegmentation.png|300px|thumb|left|Lesion Segmentation]]
</div>
</div>

Nodule Sizing

2015-01-09T08:10:28Z

Raul:

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

==Key Investigators==
Raul San Jose

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create a Slicer module for lung nodule sizing
* Integrate the [https://public.kitware.com/LesionSizingKit/index.php/Main_Page Lesion Sizing Toolkit] nodule segmentation as part of CIP
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create CLI to integrate LST functionality
* Create a python module that computes lesion measurements based on nodule segmentation results
** Use ROI tools to select nodule region
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* The LST nodule segmentation tool has been integrated as a CLI into CIP
[[File:LesionSegmentation.png|200px|thumb|left|Lesion Segmentation]]
</div>
</div>

File:LesionSegmentation.png

2015-01-09T08:07:20Z

Raul: uploaded a new version of "File:LesionSegmentation.png": LesiongSegmentationCIP

Nodule Sizing

2015-01-09T08:05:55Z

Raul: /* Key Investigators */

2015 Winter Project Week Infrastructure Breakout

2015-01-08T00:54:10Z

Raul: /* Python Modules and Python Slicer */

== Updating Teem release ==
* Hans has merged the changes in Teem1.11.1 branch with his change and resolved a bunch of CMake issues [https://github.com/BRAINSia/teem/tree/20150107_Slicer git]
* Results are in this [http://cdash.airwayinspector.org/index.php?project=Teem Dashboard]
* Talk to Gordon to bring those changes into Teem trunk and make a new branch (Teem 1.11.2?)

== Python Modules and Python Slicer ==
* Can Slicer use a python distribution like [https://store.continuum.io/cshop/anaconda/ Anaconda] instead of building its own python?
** [http://docs.continuum.io/anaconda/pkg-docs.html Packages supported by Anaconda]

* Discussion
** We agree that Anaconda is a viable long term solution . Need to test this and package slicer

* Roadmap
** Build Slicer with miniAnaconda
*** Set variables in [https://github.com/Slicer/Slicer/blob/f877587c83a7648a442fea17b8f282932bf6b907/SuperBuild/External_python.cmake#L127-L145 External_python] to point to your Anaconda install.
*** Install numpy, scipy, pygithub… (get from build)
*** Build with VS13, OSX clang
** Create packages
*** make package
*** Look at install portion of Slicer python to bring anaconda (ExternalPython.cmake)
*** Test if conda works on the package version of python

== Extension and third party libraries ==
* Policy to use third party libraries like OpenCV with Extensions. Should they be part of Slicer main dependencies?

2015 Winter Project Week Infrastructure Breakout

2015-01-07T23:42:17Z

Raul: /* Python Modules and Python Slicer */

2015 Winter Project Week Infrastructure Breakout

2015-01-07T23:40:47Z

Raul: /* Updating Teem release */

2015 Winter Project Week Infrastructure Breakout

2015-01-07T22:46:32Z

Raul: Created page with '== Updating Teem release == * Hans has merged changes in Teem1.11.1 branch with his change and resolve a bunch of CMake issues * Results are in this [http://cdash.airwayinspector…'

== Updating Teem release ==
* Hans has merged changes in Teem1.11.1 branch with his change and resolve a bunch of CMake issues
* Results are in this [http://cdash.airwayinspector.org/index.php?project=Teem Dashboard]
* Talk to Gordon to bring those changes into Teem trunk and make a new branch (Teem 1.11.2?)

== Python Modules and Python Slicer ==
* Can Slicer move to a python distribution like Anaconda?

== Extension and third party libraries ==
* Policy to use third party libraries like OpenCV with Extensions. Should they be part of Slicer main dependencies?

2015 Winter Project Week

2015-01-07T00:00:34Z

Raul: /* Agenda */

__NOTOC__

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

Welcome to the 20th Project week page!

== Note of Remembrance ==

[[file:ferenc.jpg|right]]
This project week is dedicated to Ferenc Jolesz, leader and mentor to many in the image guided therapy community. There is a [http://ferenc.jolesz.muchloved.com/ tribute page to Ferenc] for people who want to share their thoughts.

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

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

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

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

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

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

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

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

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

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

==Image-Guided Therapy==
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
* [[User:Yli|Quantitative Evaluation of Digitally Registered Pre and Post op DTI by 3D ROI Segmentation]] (Li Ye, Sonia Pujol, Steve Pieper, Alireza Mehrtash)
* [[New Distance|A new modified Frechet distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)
* [[ProstateNavigation workflow | Workflow for prostate navigation and its components]] (Peter Behringer, Andriy Fedorov)
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[Needle Finder Tutorial | Needle Finder Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*[[VR Radiology | Application of consumer virtual reality devices in creating environments for diagnostic radiology]] (Franklin King, Steve Pieper)
*[[Distribution modeling | Summary statistics versus distributions: evaluating improved ability to detect clinical differences using DTI]] (Anuja Sharma, Guido Gerig)
*[[Valve Replacement | Aortic valve replacement using tracked 3D ultrasound]] (Adam Rankin)
*[[2015_Winter_Project_Week:CommunicationProtocolForOpticalTrackingWithSurfaceScan| Communication Protocol for Optical Tracking with Surface Scan]] (Junichi Tokuda, Sangyong Kim, ByungHyun Cho, Brian Nini, Nobuhiko Hata)

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

==CTE==
* [[Slicer_Tract_Analysis | Measurement and visualization using white matter hierarchies in Slicer]] (Alexander Yarmarkovich, Lauren O'Donnell)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Fissure Enhancement | Supervised fissure enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)
== Lung ==
*[[ Small lung nodule differential diagnosis using 3D Slicer | Small lung nodule differential diagnosis using 3D Slicer]] (Li Ming, Jay Jagadeesan)

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

==Feature Extraction==
* [[3D_SIFT_VIEW| 3D SIFT Feature Visualization in Slicer]] (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)
* [[Cortex_Clustering| Experimental tract-based cortical clustering ]] (Lauren O'Donnell, William Wells)

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

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

==Infrastructure==

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

== '''Registrants''' ==

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

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

2015 Winter Project Week

2015-01-06T23:59:24Z

Raul: /* Agenda */

__NOTOC__

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

Welcome to the 20th Project week page!

== Note of Remembrance ==

[[file:ferenc.jpg|right]]
This project week is dedicated to Ferenc Jolesz, leader and mentor to many in the image guided therapy community. There is a [http://ferenc.jolesz.muchloved.com/ tribute page to Ferenc] for people who want to share their thoughts.

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

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

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

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

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

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

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

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

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

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

==Image-Guided Therapy==
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
* [[User:Yli|Quantitative Evaluation of Digitally Registered Pre and Post op DTI by 3D ROI Segmentation]] (Li Ye, Sonia Pujol, Steve Pieper, Alireza Mehrtash)
* [[New Distance|A new modified Frechet distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)
* [[ProstateNavigation workflow | Workflow for prostate navigation and its components]] (Peter Behringer, Andriy Fedorov)
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[Needle Finder Tutorial | Needle Finder Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*[[VR Radiology | Application of consumer virtual reality devices in creating environments for diagnostic radiology]] (Franklin King, Steve Pieper)
*[[Distribution modeling | Summary statistics versus distributions: evaluating improved ability to detect clinical differences using DTI]] (Anuja Sharma, Guido Gerig)
*[[Valve Replacement | Aortic valve replacement using tracked 3D ultrasound]] (Adam Rankin)
*[[2015_Winter_Project_Week:CommunicationProtocolForOpticalTrackingWithSurfaceScan| Communication Protocol for Optical Tracking with Surface Scan]] (Junichi Tokuda, Sangyong Kim, ByungHyun Cho, Brian Nini, Nobuhiko Hata)

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

==CTE==
* [[Slicer_Tract_Analysis | Measurement and visualization using white matter hierarchies in Slicer]] (Alexander Yarmarkovich, Lauren O'Donnell)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Fissure Enhancement | Supervised fissure enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)
== Lung ==
*[[ Small lung nodule differential diagnosis using 3D Slicer | Small lung nodule differential diagnosis using 3D Slicer]] (Li Ming, Jay Jagadeesan)

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

==Feature Extraction==
* [[3D_SIFT_VIEW| 3D SIFT Feature Visualization in Slicer]] (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)
* [[Cortex_Clustering| Experimental tract-based cortical clustering ]] (Lauren O'Donnell, William Wells)

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

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

==Infrastructure==

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

== '''Registrants''' ==

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

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

2015 Winter Project Week

2015-01-06T23:54:28Z

Raul: /* Agenda */

__NOTOC__

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

Welcome to the 20th Project week page!

== Note of Remembrance ==

[[file:ferenc.jpg|right]]
This project week is dedicated to Ferenc Jolesz, leader and mentor to many in the image guided therapy community. There is a [http://ferenc.jolesz.muchloved.com/ tribute page to Ferenc] for people who want to share their thoughts.

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

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

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

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

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

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

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

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

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

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

==Image-Guided Therapy==
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
* [[User:Yli|Quantitative Evaluation of Digitally Registered Pre and Post op DTI by 3D ROI Segmentation]] (Li Ye, Sonia Pujol, Steve Pieper, Alireza Mehrtash)
* [[New Distance|A new modified Frechet distance for measuring the similarity between fiber tracts]] (Ruizhi Liao, Lauren O'Donnell)
* [[UKF Edema|Performance of UKF tractography in edema]] (Ruizhi Liao, Lauren O'Donnell)
* [[ProstateNavigation workflow | Workflow for prostate navigation and its components]] (Peter Behringer, Andriy Fedorov)
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[Needle Finder Tutorial | Needle Finder Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*[[VR Radiology | Application of consumer virtual reality devices in creating environments for diagnostic radiology]] (Franklin King, Steve Pieper)
*[[Distribution modeling | Summary statistics versus distributions: evaluating improved ability to detect clinical differences using DTI]] (Anuja Sharma, Guido Gerig)
*[[Valve Replacement | Aortic valve replacement using tracked 3D ultrasound]] (Adam Rankin)
*[[2015_Winter_Project_Week:CommunicationProtocolForOpticalTrackingWithSurfaceScan| Communication Protocol for Optical Tracking with Surface Scan]] (Junichi Tokuda, Sangyong Kim, ByungHyun Cho, Brian Nini, Nobuhiko Hata)

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

==CTE==
* [[Slicer_Tract_Analysis | Measurement and visualization using white matter hierarchies in Slicer]] (Alexander Yarmarkovich, Lauren O'Donnell)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Fissure Enhancement | Supervised fissure enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)
== Lung ==
*[[ Small lung nodule differential diagnosis using 3D Slicer | Small lung nodule differential diagnosis using 3D Slicer]] (Li Ming, Jay Jagadeesan)

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

==Feature Extraction==
* [[3D_SIFT_VIEW| 3D SIFT Feature Visualization in Slicer]] (Matthew Toews, Steve Pieper, Nicole Aucoin, Andriy Fedorov, Raul San Jose, William Wells)
* [[Cortex_Clustering| Experimental tract-based cortical clustering ]] (Lauren O'Donnell, William Wells)

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

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

==Infrastructure==

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

== '''Registrants''' ==

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

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

2015 Winter Project Week COPD Breakout

2015-01-06T17:03:53Z

Raul: /* Modules Categories */

== Introduction==
Chest Imaging Platform (CIP) and SlicerCIP is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD).
The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA]
=== Project Goals ===
* AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.

* AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.

* AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.

=== History ===
* 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
* Lung Imaging Platform (Jan 2009 - March 2012): Initial consolidation of our developments for high-throughput image analysis in [https://www.copdgene.org COPDGene].
* April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
* April 2013 - January 2014: Port to github and further consolidation under a private repository.
* Today: Release 0.0.0 of the [https://github.com/acil-bwh/ChestImagingPlatform Chest Imaging Platform]

=== Brief intro to COPD ===

=== Team ===
* Raul San Jose
* James Ross
* Rola Harmouche
* Jorge Onieva
* German Gonzalez
* Alex Yarmakovich

Collaborators
* George Washko
* Alejandro Diaz

== Architecture ==
[[File:CIPArchitecture.png]]

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components [http://www.na-mic.org/Wiki/images/0/0b/CipTools.pptx slides]
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

2015 Winter Project Week COPD Breakout

2015-01-06T17:03:40Z

Raul: /* Modules Categories */

== Introduction==
Chest Imaging Platform (CIP) and SlicerCIP is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD).
The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA]
=== Project Goals ===
* AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.

* AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.

* AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.

=== History ===
* 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
* Lung Imaging Platform (Jan 2009 - March 2012): Initial consolidation of our developments for high-throughput image analysis in [https://www.copdgene.org COPDGene].
* April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
* April 2013 - January 2014: Port to github and further consolidation under a private repository.
* Today: Release 0.0.0 of the [https://github.com/acil-bwh/ChestImagingPlatform Chest Imaging Platform]

=== Brief intro to COPD ===

=== Team ===
* Raul San Jose
* James Ross
* Rola Harmouche
* Jorge Onieva
* German Gonzalez
* Alex Yarmakovich

Collaborators
* George Washko
* Alejandro Diaz

== Architecture ==
[[File:CIPArchitecture.png]]

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components [http://www.na-mic.org/Wiki/images/0/0b/CipTools.pptx slides]
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Modules Categories ===
* Toolkit
* Densitometry
* Airway Sizing
* Lesion Sizing
* PA/A
* Probing Tools
* Intervention
** Trachea stent planning
** Hilum Planning

=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

2015 Winter Project Week COPD Breakout

2015-01-06T16:23:35Z

Raul: /* Architecture */

== Introduction==
Chest Imaging Platform (CIP) and SlicerCIP is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD).
The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA]
=== Project Goals ===
* AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.

* AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.

* AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.

=== History ===
* 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
* Lung Imaging Platform (Jan 2009 - March 2012): Initial consolidation of our developments for high-throughput image analysis in [https://www.copdgene.org COPDGene].
* April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
* April 2013 - January 2014: Port to github and further consolidation under a private repository.
* Today: Release 0.0.0 of the [https://github.com/acil-bwh/ChestImagingPlatform Chest Imaging Platform]

=== Brief intro to COPD ===

=== Team ===
* Raul San Jose
* James Ross
* Rola Harmouche
* Jorge Onieva
* German Gonzalez
* Alex Yarmakovich

Collaborators
* George Washko
* Alejandro Diaz

== Architecture ==
[[File:CIPArchitecture.png]]

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Modules Categories ===

=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

2015 Winter Project Week COPD Breakout

2015-01-06T16:23:21Z

Raul: /* Architecture */

== Introduction==
Chest Imaging Platform (CIP) and SlicerCIP is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD).
The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA]
=== Project Goals ===
* AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.

* AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.

* AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.

=== History ===
* 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
* Lung Imaging Platform (Jan 2009 - March 2012): Initial consolidation of our developments for high-throughput image analysis in [https://www.copdgene.org COPDGene].
* April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
* April 2013 - January 2014: Port to github and further consolidation under a private repository.
* Today: Release 0.0.0 of the [https://github.com/acil-bwh/ChestImagingPlatform Chest Imaging Platform]

=== Brief intro to COPD ===

=== Team ===
* Raul San Jose
* James Ross
* Rola Harmouche
* Jorge Onieva
* German Gonzalez
* Alex Yarmakovich

Collaborators
* George Washko
* Alejandro Diaz

== Architecture ==
[ [Image:CIPArchitecture.png]]

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Modules Categories ===

=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

2015 Winter Project Week COPD Breakout

2015-01-06T16:22:56Z

Raul: /* Architecture */

== Introduction==
Chest Imaging Platform (CIP) and SlicerCIP is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD).
The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA]
=== Project Goals ===
* AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.

* AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.

* AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.

=== History ===
* 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
* Lung Imaging Platform (Jan 2009 - March 2012): Initial consolidation of our developments for high-throughput image analysis in [https://www.copdgene.org COPDGene].
* April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
* April 2013 - January 2014: Port to github and further consolidation under a private repository.
* Today: Release 0.0.0 of the [https://github.com/acil-bwh/ChestImagingPlatform Chest Imaging Platform]

=== Brief intro to COPD ===

=== Team ===
* Raul San Jose
* James Ross
* Rola Harmouche
* Jorge Onieva
* German Gonzalez
* Alex Yarmakovich

Collaborators
* George Washko
* Alejandro Diaz

== Architecture ==
[Image:CIPArchitecture.png]

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Modules Categories ===

=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

2015 Winter Project Week COPD Breakout

2015-01-06T16:22:44Z

Raul: /* Architecture */

== Introduction==
Chest Imaging Platform (CIP) and SlicerCIP is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD).
The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA]
=== Project Goals ===
* AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.

* AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.

* AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.

=== History ===
* 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
* Lung Imaging Platform (Jan 2009 - March 2012): Initial consolidation of our developments for high-throughput image analysis in [https://www.copdgene.org COPDGene].
* April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
* April 2013 - January 2014: Port to github and further consolidation under a private repository.
* Today: Release 0.0.0 of the [https://github.com/acil-bwh/ChestImagingPlatform Chest Imaging Platform]

=== Brief intro to COPD ===

=== Team ===
* Raul San Jose
* James Ross
* Rola Harmouche
* Jorge Onieva
* German Gonzalez
* Alex Yarmakovich

Collaborators
* George Washko
* Alejandro Diaz

== Architecture ==
[File:CIPArchitecture.png]

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Modules Categories ===

=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

File:CIPArchitecture.png

2015-01-06T16:22:04Z

Raul: uploaded a new version of "File:CIPArchitecture.png": CIPArchitecture

2015 Winter Project Week COPD Breakout

2015-01-06T16:20:24Z

Raul: /* Team */

== Introduction==
Chest Imaging Platform (CIP) and SlicerCIP is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD).
The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA]
=== Project Goals ===
* AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.

* AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.

* AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.

=== History ===
* 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
* Lung Imaging Platform (Jan 2009 - March 2012): Initial consolidation of our developments for high-throughput image analysis in [https://www.copdgene.org COPDGene].
* April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
* April 2013 - January 2014: Port to github and further consolidation under a private repository.
* Today: Release 0.0.0 of the [https://github.com/acil-bwh/ChestImagingPlatform Chest Imaging Platform]

=== Brief intro to COPD ===

=== Team ===
* Raul San Jose
* James Ross
* Rola Harmouche
* Jorge Onieva
* German Gonzalez
* Alex Yarmakovich

Collaborators
* George Washko
* Alejandro Diaz

== Architecture ==

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Modules Categories ===

=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

2015 Winter Project Week COPD Breakout

2015-01-06T10:41:13Z

Raul: /* History */

== Introduction==
Chest Imaging Platform (CIP) and SlicerCIP is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD).
The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA]
=== Project Goals ===
* AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.

* AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.

* AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.

=== History ===
* 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
* Lung Imaging Platform (Jan 2009 - March 2012): Initial consolidation of our developments for high-throughput image analysis in [https://www.copdgene.org COPDGene].
* April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
* April 2013 - January 2014: Port to github and further consolidation under a private repository.
* Today: Release 0.0.0 of the [https://github.com/acil-bwh/ChestImagingPlatform Chest Imaging Platform]

=== Brief intro to COPD ===

=== Team ===
* James Ross
* Rola Harmouche
* Jorge Onieva
* German Gonzalez
* Alex Yarmakovich

== Architecture ==

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Modules Categories ===

=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

2015 Winter Project Week COPD Breakout

2015-01-06T10:39:56Z

Raul: /* Introduction */

== Introduction==
Chest Imaging Platform (CIP) and SlicerCIP is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD).
The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA]
=== Project Goals ===
* AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.

* AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.

* AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.

=== History ===
* 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
* Lung Imaging Platform (Jan 2009 - March 2012): First consolidate of our development for high-throughput image analysis in [www.copdgene.org COPDGene] with dependencies to Slicer3.
* April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
* April 2013 - January 2014: Port to github and further consolidation under a private repository.
* Today: Release 0.0.0 of the [https://github.com/acil-bwh/ChestImagingPlatform Chest Imaging Platform]

=== Brief intro to COPD ===

=== Team ===
* James Ross
* Rola Harmouche
* Jorge Onieva
* German Gonzalez
* Alex Yarmakovich

== Architecture ==

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Modules Categories ===

=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

2015 Winter Project Week COPD Breakout

2015-01-06T10:39:14Z

Raul: /* History */

== Introduction==
Chest Imaging Platform is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD).
The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA]
=== Project Goals ===
* AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.

* AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.

* AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.

=== History ===
* 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
* Lung Imaging Platform (Jan 2009 - March 2012): First consolidate of our development for high-throughput image analysis in [www.copdgene.org COPDGene] with dependencies to Slicer3.
* April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
* April 2013 - January 2014: Port to github and further consolidation under a private repository.
* Today: Release 0.0.0 of the [https://github.com/acil-bwh/ChestImagingPlatform Chest Imaging Platform]

=== Brief intro to COPD ===

=== Team ===
* James Ross
* Rola Harmouche
* Jorge Onieva
* German Gonzalez
* Alex Yarmakovich

== Architecture ==

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Modules Categories ===

=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

2015 Winter Project Week COPD Breakout

2015-01-06T10:38:18Z

Raul: /* Introduction */

== Introduction==
Chest Imaging Platform is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD).
The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA]
=== Project Goals ===
* AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.

* AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.

* AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.

=== History ===
* 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
* Lung Imaging Platform (Jan 2009 - March 2012): First consolidate of our development for high-throughput image analysis in [www.copdgene.org COPDGene] with dependencies to Slicer3.
* April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
* April 2013 - January 2014: Port to github and further consolidation under a private repository.
* Today: Release 0.1 of the Chest Imaging Platform

=== Brief intro to COPD ===

=== Team ===
* James Ross
* Rola Harmouche
* Jorge Onieva
* German Gonzalez
* Alex Yarmakovich

== Architecture ==

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Modules Categories ===

=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

2015 Winter Project Week COPD Breakout

2015-01-06T10:08:15Z

Raul: /* New Developments: Organ Detection */

== Introduction==

=== Project Goals and Funding ===

=== History ===

=== Brief intro to COPD ===

=== Team ===

== Architecture ==

== Chest Imaging Platform (CIP) ==
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository]
=== Code Structure ===
CIP has four main components
*Common: base library
*Utilities: third party libraries
*Command Line Tools: Slicer execution model tools
*cip_python: python library

=== Building CIP ===
git clone https://github.com/acil-bwh/ChestImagingPlatform.git
mkdir ChestImagingPlatform-build
cd ChestImagingPlatoform-build
ccmake ../ChestImagingPlatform

=== Components and Data type ===

* [https://github.com/acil-bwh/ChestImagingPlatform/blob/release/Common/cipChestConventions.h CIP conventions]

* Region/Type structure for labelmaps

=== Python and CIP ===
[https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python cip_python] provides the following functionality:
* Code base for scale-space particles [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/particles]
* Phenotype computation framework [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/phentoypes]
* Nipype interfaces for CLIS [https://github.com/acil-bwh/ChestImagingPlatform/tree/release/cip_python/nipype]

=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]

== Testing Infrastructure ==

* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides]

* [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard]

== Slicer CIP ==
[https://github.com/acil-bwh/SlicerCIP Git Repository]

=== MRML Types ===
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/RegionTypeDisplay RegionType]
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles]

=== Modules Categories ===

=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]

== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

File:BreakoutSession-CIP-NextDevelopment.pptx

2015-01-06T10:05:51Z

Raul: BreakoutSession-CIP-NextDevelopment

BreakoutSession-CIP-NextDevelopment

2015 Winter Project Week COPD Breakout

2015-01-06T10:05:05Z

Raul: