NAMIC Wiki - User contributions [en]

2015 Summer Project Week:T1 mapping

2015-06-09T16:10:45Z

Kalpathy:

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

</gallery>

==Key Investigators==
* Xiao Da

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create a C++ module for T1 mapping
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Start with prostate diffusion module
* Update equations for T1 mapping

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

2015 Summer Project Week:T1 mapping

2015-06-09T16:10:11Z

Kalpathy: /* Project Description */

Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* Xiao Da

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create a C++ module for T1 mapping
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Start with prostate diffusion module
* Update equations for T1 mapping

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

2015 Summer Project Week:T1 mapping

2015-06-09T16:07:53Z

Kalpathy: Created page with 'Image:PW-Summer2015.png|Projects List </gallery> ==Key Investigators== * Xiao Da ==Project Description== <div style="margin: 20px;"> <div…'

Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* Xiao Da

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create a C++ CLI module for T1 mapping
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Start with prostate diffusion module
* Update equations for T1 mapping

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

2015 Summer Project Week:DSC

2015-06-09T16:06:30Z

Kalpathy: Created page with '<gallery> Image:PW-Summer2015.png|Projects List </gallery> ==Key Investigators== * Xiao Da ==Project Description== <div style="margin: 20…'

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

</gallery>

==Key Investigators==
* Xiao Da

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create a module for the analysis of Dynamic Susceptibility Contrast MRI (DSC)
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Start with PKmodule
* Update equations for conversion of signal to concentration

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

2015 Summer Project Week

2015-06-08T21:00:05Z

Kalpathy: /* Projects */

__NOTOC__

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

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

==Logistics==

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

==Agenda==

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

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

== '''Background''' ==

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

== '''Registrants''' ==

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

2015 Summer Project Week

2015-06-08T20:58:11Z

Kalpathy: /* Projects */

__NOTOC__

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

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

==Logistics==

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

==Agenda==

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

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

== '''Background''' ==

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

== '''Registrants''' ==

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

2015 Winter Project Week

2014-12-11T20:52:41Z

Kalpathy:

__NOTOC__

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

Welcome to the 20th Project week page!

== 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:COPD]] (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'''
|
|
|
| [[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'''l
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_SLC_Training_Workshop|Slicer Workshop (Ron Kikinis)]]
| <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 2)'' <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==
*Image-based Needle Detection from MRI (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)
*Tracked ultrasound benchtop experment system for neurosurgery (Steve Pieper, Jim Miller)
*Case review for interactive registration (Steve Pieper, Jim Miller, Alireza Mehrtash)

==Huntington's Disease==

==TBI==

==Stroke==

==Cardiac==

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

==Head and Neck Cancer / Radiotherapy ==

==[http://qiicr.org QIICR]==
* Mechanism to pull related DICOM series on derived modality load (Andrey, Csaba)
* Segmentation object and enhanced multiframe object IO in DCMTK and Slicer (Steve, Andrey, Michael)
*T1 mapping for variable flip angle (Artem, Xiao, Andrey)

==Feature Extraction==

==Additional Brain Image Analysis==

==Slicer4 Extensions==

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

==Infrastructure==

* Rulers in Markups module (Nicole Aucoin)

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. (The Registration Page is Coming Soon, so please give us a few days.)

2014 Project Week:RT FormatConversions

2014-01-10T04:54:33Z

Kalpathy:

==Key Investigators==

Jayashree Kalpathy-Cramer (MGH)

Andras

Csaba

John Evans (MGH)

Greg Sharp (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Evaluate different options for converting from DICOM-seg/NIFTI/nrrd (mask) to DICOM-RT (contours) and back.
* Compare performance of Slicer RT/plastimatch/others.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Develop a test set with range of appearance of structures
** overlapping
** donuts

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Creates python script (based on Slicer RT) for converting contours to label maps (thanks Csaba!)
* Reporting module provides conversion from label map to DICOM-SEG
* Plastimatch has DICOM-RT import export
* Will test full roundtrip conversions using QIN lung segmentation challenge datasets
* Started creating a library of test cases with known issues (donuts, overlapping structures etc)
* Will also create synthetic datasets
</div>
</div>

2014 Project Week:RT FormatConversions

2014-01-10T04:54:13Z

Kalpathy:

==Key Investigators==

Jayashree Kalpathy-Cramer (MGH)

Andras

Csaba

John Evans (MGH)

Greg Sharp (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Evaluate different options for converting from DICOM-seg/NIFTI/nrrd (mask) to DICOM-RT (contours) and back.
* Compare performance of Slicer RT/plastimatch/others.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Develop a test set with range of appearance of structures
** overlapping
** donuts

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Creates python script (based on Slicer RT) for converting contours to label maps (thanks Csaba!)
* Reporting module provides conversion from label map to DICOM-SEG
* Plastimatch had DICOM-RT import export
* Will test full roundtrip conversions using QIN lung segmentation challenge datasets
* Started creating a library of test cases with known issues (donuts, overlapping structures etc)
* Will also create synthetic datasets
</div>
</div>

2014 Project Week:RT FormatConversions

2014-01-10T04:53:40Z

Kalpathy:

==Key Investigators==

Jayashree Kalpathy-Cramer (MGH)

Andras

Csaba

John Evans (MGH)

Greg Sharp (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Evaluate different options for converting from DICOM-seg/NIFTI/nrrd (mask) to DICOM-RT (contours) and back.
* Compare performance of Slicer RT/plastimatch/others.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Develop a test set with range of appearance of structures
** overlapping
** donuts

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Csaba prepared a python script (based on Slicer RT) for converting contours to label maps.
* Reporting module provides conversion from label map to DICOM-SEG
* Plastimatch had DICOM-RT import export
* Will test full roundtrip conversions using QIN lung segmentation challenge datasets
* Started creating a library of test cases with known issues (donuts, overlapping structures etc)
* Will also create synthetic datasets
</div>
</div>

2014 Project Week:RT FormatConversions

2014-01-06T20:22:32Z

Kalpathy:

2014 Project Week:4D NIfTI Multivolume

2013-12-26T21:35:39Z

Kalpathy: Created page with '==Key Investigators== Jayashree Kalpathy-Cramer (MGH) Andrey Fedorov (BWH) Jim John Evans (MGH) ==Project Description== <div style="margin: 20px;"> <div style="width: 27%; …'

==Key Investigators==

Jayashree Kalpathy-Cramer (MGH)

Andrey Fedorov (BWH)

Jim

John Evans (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Support for 4D nifti in multivolume (needed as input to PK modeling)

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

2014 Project Week:RT FormatConversions

2013-12-26T21:27:15Z

Kalpathy:

==Key Investigators==

Jayashree Kalpathy-Cramer (MGH)

Andras

Csaba

John Evans (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Evaluate different options for converting from DICOM-seg/NIFTI/nrrd (mask) to DICOM-RT (contours) and back.
* Compare performance of Slicer RT/plastimatch/others.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Develop a test set with range of appearance of structures
** overlapping
** donuts

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

2014 Project Week:RT FormatConversions

2013-12-26T21:26:37Z

Kalpathy:

==Key Investigators==

Jayashree Kalpathy-Cramer (MGH)

Andras

Csaba

John Evans (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Evaluate different options for converting from NIFTI/nrrd (mask) to DICOM-RT (Contours) and back.
* Compare performance of Slicer RT/plastimatch/others.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Develop a test set with range of appearance of structures
** overlapping
** donuts

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

2014 Project Week:RT FormatConversions

2013-12-26T21:26:20Z

Kalpathy:

==Key Investigators==

Jayashree Kalpathy-Cramer (MGH)
Andras
Csaba
John Evans (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Evaluate different options for converting from NIFTI/nrrd (mask) to DICOM-RT (Contours) and back.
* Compare performance of Slicer RT/plastimatch/others.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Develop a test set with range of appearance of structures
** overlapping
** donuts

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

2014 Project Week:RT FormatConversions

2013-12-26T21:26:06Z

Kalpathy: Created page with '==Key Investigators== Jayashree Kalpathy-Cramer (MGH) Andras Csaba John Evans (MGH) ==Project Description== <div style="margin: 20px;"> <div style="width: 27%; float: left;…'

==Key Investigators==

Jayashree Kalpathy-Cramer (MGH)

Andras

Csaba

John Evans (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Evaluate different options for converting from NIFTI/nrrd (mask) to DICOM-RT (Contours) and back.
* Compare performance of Slicer RT/plastimatch/others.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Develop a test set with range of appearance of structures
** overlapping
** donuts

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