NAMIC Wiki - User contributions [en]

2015 Summer Project Week:SordinaLinacPath

2015-06-24T15:11:16Z

Nenetto: /* Key Investigators */

==Key Investigators==
* Eugenio Marinetto UC3M, Madrid
* Sebastian Tauscher, Hannover
* Javier Pascau UC3M, Madrid
* David García UC3M, Madrid
* Laura Sanz UC3M, Madrid

[[File:SordinaTool.png|200px|thumb|left|Sordina tool]]

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create a Sordina LINAC movements simulator on Slicer using models from the vendor.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a Python-based module that load the models and need transformations
* Add the degrees of freedom to some parts of the model
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Models are loaded properly and starting transformations
* A slider was added to control a rotation angle
</div>
</div>

2015 Summer Project Week:SordinaLinacPath

2015-06-24T15:09:56Z

Nenetto: /* Key Investigators */

==Key Investigators==
* Eugenio Marinetto UC3M, Madrid
* Sebastian Tauscher, Hannover
* Javier Pascau UC3M, Madrid
* David García UC3M, Madrid

[[File:SordinaTool.png|200px|thumb|left|Sordina tool]]

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create a Sordina LINAC movements simulator on Slicer using models from the vendor.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a Python-based module that load the models and need transformations
* Add the degrees of freedom to some parts of the model
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Models are loaded properly and starting transformations
* A slider was added to control a rotation angle
</div>
</div>

2015 Summer Project Week:SordinaLinacPath

2015-06-24T15:04:09Z

Nenetto: /* Key Investigators */

==Key Investigators==
* Eugenio Marinetto UC3M, Madrid
* Javier Pascau UC3M, Madrid
* David García UC3M, Madrid

[[File:SordinaTool.png|200px|thumb|left|Sordina tool]]

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create a Sordina LINAC movements simulator on Slicer using models from the vendor.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a Python-based module that load the models and need transformations
* Add the degrees of freedom to some parts of the model
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Models are loaded properly and starting transformations
* A slider was added to control a rotation angle
</div>
</div>

2015 Summer Project Week:SordinaLinacPath

2015-06-24T15:01:52Z

Nenetto: /* Key Investigators */

==Key Investigators==
* Eugenio Marinetto UC3M, Madrid
* Javier Pascau UC3M, Madrid
* David García UC3M, Madrid

[[File:File.png|200px|thumb|left|Sordina tool]]

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create a Sordina LINAC movements simulator on Slicer using models from the vendor.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a Python-based module that load the models and need transformations
* Add the degrees of freedom to some parts of the model
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Models are loaded properly and starting transformations
* A slider was added to control a rotation angle
</div>
</div>

File:SordinaTool.png

2015-06-24T15:01:01Z

Nenetto:

2015 Summer Project Week:SordinaLinacPath

2015-06-24T14:58:30Z

Nenetto: /* Project Description */

==Key Investigators==
* Eugenio Marinetto UC3M, Madrid
* Javier Pascau UC3M, Madrid
* David García UC3M, Madrid

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create a Sordina LINAC movements simulator on Slicer using models from the vendor.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a Python-based module that load the models and need transformations
* Add the degrees of freedom to some parts of the model
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Models are loaded properly and starting transformations
* A slider was added to control a rotation angle
</div>
</div>

2015 Summer Project Week:SordinaLinacPath

2015-06-24T14:56:12Z

Nenetto: /* Key Investigators */

==Key Investigators==
* Eugenio Marinetto UC3M, Madrid
* Javier Pascau UC3M, Madrid
* David García UC3M, Madrid

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Allow the new [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/Segmentations Segmentation node] to be used in the Editor
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Merge vtkMRMLSegmentationNode into SlicerRT
* Create a new Editor module main GUI (using Segmentation node widgets)
* Make plugins compatible with both vtkMRMLSegmentationNode and vtkMRMLLabelMapVolumeNode
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* vtkMRMLLabelMapVolume node is merged into the trunk
</div>
</div>

2015 Summer Project Week:SordinaLinacPath

2015-06-24T14:55:20Z

Nenetto: Created page with '==Key Investigators== * Andras Lasso * Steve Pieper ==Project Description== <div style="margin: 20px;"> <div style="width: 27%; float: left; padding-right: 3%;"> <h3>Objective</…'

==Key Investigators==
* Andras Lasso
* Steve Pieper

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Allow the new [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/Segmentations Segmentation node] to be used in the Editor
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Merge vtkMRMLSegmentationNode into SlicerRT
* Create a new Editor module main GUI (using Segmentation node widgets)
* Make plugins compatible with both vtkMRMLSegmentationNode and vtkMRMLLabelMapVolumeNode
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* vtkMRMLLabelMapVolume node is merged into the trunk
</div>
</div>

2015 Summer Project Week

2015-06-24T14:54:08Z

Nenetto: /* Image-Guided Therapy */

__NOTOC__

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

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

==Logistics==

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

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

==Agenda==

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

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

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

== '''Background''' ==

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

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

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

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

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

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

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

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

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

==Equipment==

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

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

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

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

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

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

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

== '''Registrants''' ==

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

2015 Summer Project Week

2015-06-24T14:53:58Z

Nenetto: /* Image-Guided Therapy */

__NOTOC__

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

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

==Logistics==

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

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

==Agenda==

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

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

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

== '''Background''' ==

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

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

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

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

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

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

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

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

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

==Equipment==

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

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

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

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

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

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

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

== '''Registrants''' ==

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

2015 Orthognathic Surgery

2015-06-22T09:14:46Z

Nenetto: /* Key Investigators */

__NOTOC__
<gallery>
Image:ResultsFigure.jpg|Orthognathic registration result
Image:3Dsurfacemodel.jpg|3D rendering
</gallery>

==Key Investigators==
*Dženan Zukić, PhD, Kitware
*Tung Nguyen, PhD, MD, UNC Chapel Hill
*Ricardo Ortiz, PhD, Kitware
*Beatriz Paniagua, PhD, UNC Chapel Hill
*Andinet Enquobahrie, PhD, Kitware
*Laura Sanz, UC3M, Madrid

==Collaborators==
*Andras Lasso, PhD, Queen's University
*Tamas Ungi, PhD, Queen's University

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*Use ultrasound to verify proper position of mandibular condyle during orthognatic surgery
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*Use tracking to create 3D ultrasound image and register it with preop CT
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*Preliminary results available
*Paper submitted to a MICCAI/AECAI2015 workshop.
</div>
</div>

==Meeting goals==
<div style="float: left">
Project week goals are discussions for improvement of
*3D reconstruction algorithm parameters
*Ultrasound image post-processing
*Scanning aspects related to repeatability
*Bone segmentation considerations
</div>

2015 Summer Project Week:LinearFeatureRegistration

2015-06-22T09:13:38Z

Nenetto: /* Key Investigators */

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:LinearFeatureRegistration_Screenshot.jpg|Screenshot of LinearFeatureRegistration module
</gallery>

==Key Investigators==
* Matthew Holden
* Nicole Aucoin, BWH (fiducials)
* Eugenio Marinetto, UC3M Madrid (Line-Based Registration, Reg. Algorithm)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Add module for registration using linear features
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Investigate module use cases:
** Ultrasound calibration for PLUS
** ...
* Use Fiducial Registration Wizard module as a template
* Investigate whether linear features can be treated in the same way as fiducials
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* See: [https://github.com/mholden8/LinearObjectRegistration LinearObjectRegistration]
</div>
</div>