NAMIC Wiki - User contributions [en]

2015 Summer Project Week:LinearFeatureRegistration

2015-06-24T14:46:35Z

Mholden8: /* Project Description */

<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]
* Discussed generic module for collecting/defining/acquiring parametric features:
** Use data structure to store a set of 0D/1D/2D parametric features
** For each feature, store raw point data, as well as basic information (i.e. centroid, variance, etc.)
** Individual registration algorithms are implemented as modules using the data structure
** Individual algorithm is responsible for converting 0D/1D/2D data to points/lines/planes (if applicable)
** Methods for acquisition: tracking, models, fiducials, segmentation
* Use cases:
** Phantom registration for ultrasound calibration
** Line feature based image to tracker registration
** Fiducial frame registration
* Began implementation of generic parametric features
</div>
</div>

2015 Summer Project Week:LinearFeatureRegistration

2015-06-24T14:44:02Z

Mholden8: /* Project Description */

<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]
* Discussed generic module for collecting/defining/acquiring parametric features:
** Use data structure to store a set of 0D/1D/2D parametric features
** For each feature, store raw point data, as well as basic information (i.e. centroid, variance, etc.)
** Individual registration algorithms are implemented as modules using the data structure
** Individual algorithm is responsible for converting 0D/1D/2D data to points/lines/planes (if applicable)
** Methods for acquisition: tracking, models, fiducials, segmentation
* Use cases:
** Phantom registration for ultrasound calibration
** Line feature based image to tracker registration
* Began implementation of generic parametric features
</div>
</div>

2015 Summer Project Week:LinearFeatureRegistration

2015-06-22T12:06:30Z

Mholden8:

<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]
* Discussed generic module for collecting/defining parametric features:
** Use data structure to store a set of 0D/1D/2D parametric features
** For each feature, store raw point data, as well as basic information (i.e. centroid, variance, etc.)
** Individual registration algorithms are implemented as modules using the data structure
** Individual algorithm is responsible for converting 0D/1D/2D data to points/lines/planes (if applicable)
</div>
</div>

2015 Summer Project Week:LinearFeatureRegistration

2015-06-10T14:02:12Z

Mholden8:

2015 Summer Project Week:LinearFeatureRegistration

2015-06-10T14:01:04Z

Mholden8:

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

==Key Investigators==
* Matthew Holden

==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>

File:LinearFeatureRegistration Screenshot.jpg

2015-06-10T14:00:39Z

Mholden8:

2015 Summer Project Week:LinearFeatureRegistration

2015-06-10T13:49:19Z

Mholden8: Created page with '<gallery> Image:PW-Summer2015.png|Projects List </gallery> ==Key Investigators== * Matthew Holden ==Project Description== <div style="marg…'

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

==Key Investigators==
* Matthew Holden

==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>

2015 Summer Project Week

2015-06-10T13:38:01Z

Mholden8:

__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)
*[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_Summer_Project_Week:LinearFeatureRegistration|Linear Feature Registration]] (Matthew Holden)
==Feature Based Image Analysis==
*[[2015_Summer_Project_Week:LungCAD| LungCAD]] (Jayender Jagadeesan, Tobias Penzkofer, Sandy Wells)
*[[2015_Summer_Project_Week:QuantitativeProstate | Texture Analysis for Prostate Imaging]] (Tobias Penzkofer, Jay Jagadeesan, Tina Kapur)
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells, Tina Kapur)
*[[2015_Summer_Project_Week:USReconstruction | Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer ]] (Frank Preiswerk, Laurent Chauvin)
*[[2015_Summer_Project_Week:AutomaticCephalometric | Automatic Cephalometric Analysis ]] (J. Jesus Montufar, Marcelo Romero)
*[[2015_Summer_Project_Week:LightWeightRobotIGT | Integration of a KUKA robot using OpenIGTLink ]] (Sebastian Tauscher, Junichi Tokuda)

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

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

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

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

== '''Registrants''' ==

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

2015 Summer Project Week

2015-06-10T13:12:31Z

Mholden8:

__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)
*[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)
==Feature Based Image Analysis==
*[[2015_Summer_Project_Week:LungCAD| LungCAD]] (Jayender Jagadeesan, Tobias Penzkofer, Sandy Wells)
*[[2015_Summer_Project_Week:QuantitativeProstate | Texture Analysis for Prostate Imaging]] (Tobias Penzkofer, Jay Jagadeesan, Tina Kapur)
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells, Tina Kapur)
*[[2015_Summer_Project_Week:USReconstruction | Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer ]] (Frank Preiswerk, Laurent Chauvin)
*[[2015_Summer_Project_Week:AutomaticCephalometric | Automatic Cephalometric Analysis ]] (J. Jesus Montufar, Marcelo Romero)
*[[2015_Summer_Project_Week:LightWeightRobotIGT | Integration of a KUKA robot using OpenIGTLink ]] (Sebastian Tauscher, Junichi Tokuda)

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

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

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

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

== '''Registrants''' ==

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

2013 Summer Project Week:PerkTutorExtension

2013-06-21T13:51:02Z

Mholden8:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:PerkTutor_TransformRecorder.jpg|Screenshot of TransformRecorder module.
Image:PerkTutor_PerkEvaluator.jpg|Screenshot of PerkEvaluator module.
</gallery>

==Key Investigators==
* Queen's University: Matthew Holden, Tamas Ungi

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

<h3>Objective</h3>
Perk Tutor is an extension that is used for recording trajectories of tracked tools, and use the trajectory to give feedback for learning interventions, and to evaluate the trainee's performance.

</div>

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

<h3>Approach, Plan</h3>

Transform Recorder module records the trajectories, Workflow Segmentation analyses them, and Perk Evaluator computes motion metrics of trajectories.

Our plan for the project week is to create a MRML representation of the trajectories to be shared between modules.
* Talk to people who have been working with time series data.
* Implement chosen method.

</div>

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

<h3>Progress</h3>
* Joined time hierarchy discussion; use time hierarchy to represent tool trajectories
* Tested adding transform nodes to time hierarchy
** Need batch processing in time hierarchy to add nodes at desired frame rate
* TransformRecorder and WorkflowSegmentation modules use common interface for interacting with trajectories

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable YES
#Other (Please specify)

==References==
* Ungi T, Sargent D, Moult E, Lasso A, Pinter C, McGraw RC, Fichtinger G. Perk Tutor: an open-source training platform for ultrasound-guided needle insertions. IEEE Trans Biomed Eng. 2012 Dec;59(12):3475-81.
* Moult E, Ungi T, Welch M, Lu J, McGraw RC, Fichtinger G. Ultrasound-guided facet joint injection training using Perk Tutor. Int J Comput Assist Radiol Surg. 2013 Jan 18.

2013 Summer Project Week:PerkTutorExtension

2013-06-21T13:41:28Z

Mholden8:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:PerkTutor_TransformRecorder.jpg|Screenshot of TransformRecorder module.
Image:PerkTutor_PerkEvaluator.jpg|Screenshot of PerkEvaluator module.
</gallery>

==Key Investigators==
* Queen's University: Matthew Holden, Tamas Ungi

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

<h3>Objective</h3>
Perk Tutor is an extension that is used for recording trajectories of tracked tools, and use the trajectory to give feedback for learning interventions, and to evaluate the trainee's performance.

</div>

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

<h3>Approach, Plan</h3>

Transform Recorder module records the trajectories, Workflow Segmentation analyses them, and Perk Evaluator computes motion metrics of trajectories.

Our plan for the project week is to create a MRML representation of the trajectories to be shared between modules.
* Talk to people who have been working with time series data.
* Implement chosen method.

</div>

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

<h3>Progress</h3>
* Use time hierarchy to represent tool trajectories
* Tested adding transform nodes to time hierarchy
** Need batch processing in time hierarchy to add nodes at desired frame rate
* TransformRecorder and WorkflowSegmentation modules use common interface for interacting with trajectories

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable YES
#Other (Please specify)

==References==
* Ungi T, Sargent D, Moult E, Lasso A, Pinter C, McGraw RC, Fichtinger G. Perk Tutor: an open-source training platform for ultrasound-guided needle insertions. IEEE Trans Biomed Eng. 2012 Dec;59(12):3475-81.
* Moult E, Ungi T, Welch M, Lu J, McGraw RC, Fichtinger G. Ultrasound-guided facet joint injection training using Perk Tutor. Int J Comput Assist Radiol Surg. 2013 Jan 18.

2013 Summer Project Week:PerkTutorExtension

2013-06-03T20:20:41Z

Mholden8:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:PerkTutor_TransformRecorder.jpg|Screenshot of TransformRecorder module.
Image:PerkTutor_PerkEvaluator.jpg|Screenshot of PerkEvaluator module.
</gallery>

==Key Investigators==
* Queen's University: Matthew Holden, Tamas Ungi

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

<h3>Objective</h3>
Perk Tutor is an extension that is used for recording trajectories of tracked tools, and use the trajectory to give feedback for learning interventions, and to evaluate the trainee's performance.

</div>

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

<h3>Approach, Plan</h3>

Transform Recorder module records the trajectories, Workflow Segmentation analyses them, and Perk Evaluator computes motion metrics of trajectories.

Our plan for the project week is to create a MRML representation of the trajectories to be shared between modules.
* Talk to people who have been working with time series data.
* Implement chosen method.

</div>

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

<h3>Progress</h3>
...

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable YES
#Other (Please specify)

==References==
* Ungi T, Sargent D, Moult E, Lasso A, Pinter C, McGraw RC, Fichtinger G. Perk Tutor: an open-source training platform for ultrasound-guided needle insertions. IEEE Trans Biomed Eng. 2012 Dec;59(12):3475-81.
* Moult E, Ungi T, Welch M, Lu J, McGraw RC, Fichtinger G. Ultrasound-guided facet joint injection training using Perk Tutor. Int J Comput Assist Radiol Surg. 2013 Jan 18.

File:PerkTutor PerkEvaluator.jpg

2013-06-03T20:18:13Z

Mholden8: Screenshot of PerkEvaluator module, analyzing needle trajectory.

Screenshot of PerkEvaluator module, analyzing needle trajectory.

File:PerkTutor TransformRecorder.jpg

2013-06-03T20:17:25Z

Mholden8: Screenshot of TransformRecorder module, recording stylus and probe trajectories.

Screenshot of TransformRecorder module, recording stylus and probe trajectories.