NAMIC Wiki - User contributions [en]

2015 Summer Project Week:LightWeightRobotIGT

2015-06-24T11:57:58Z

Tauscher:

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:FiniteStateMachine_colored.png|Finite state machine which can be operated using Slicer Module
Image:ScrennshotVFDefinitonRed.png|Screenshot of virtual fixtures in red slice
Image:ScreenShotVFOverview.png|Overview for the virtual fixtures definition
</gallery>

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

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

2015 Summer Project Week:LightWeightRobotIGT

2015-06-24T11:39:57Z

Tauscher:

File:ScrennshotVFDefinitonRed.png

2015-06-24T11:37:37Z

Tauscher:

2015 Summer Project Week:LightWeightRobotIGT

2015-06-24T11:36:32Z

Tauscher:

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

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

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

File:ScreenShotVFOverview.png

2015-06-24T11:35:27Z

Tauscher:

2015 Summer Project Week:LightWeightRobotIGT

2015-06-22T08:52:09Z

Tauscher:

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

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

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

2015 Summer Project Week:LightWeightRobotIGT

2015-06-22T08:42:08Z

Tauscher:

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

==Key Investigators==
* Sebastian Tauscher, Leibniz Universitaet Hannover, Institute of Mechatronic Systems
* Junichi Tokuda, Brigham and Women's Hospital, SPL

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

File:StatemachineColoring.jpg

2015-06-22T08:41:11Z

Tauscher:

2015 Summer Project Week:LightWeightRobotIGT

2015-06-22T08:39:43Z

Tauscher:

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

==Key Investigators==
* Sebastian Tauscher, Leibniz Universitaet Hannover, Institute of Mechatronic Systems
* Junichi Tokuda, Brigham and Women's Hospital, SPL

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

File:ScreenshotLWRIGT.jpg

2015-06-22T08:38:39Z

Tauscher:

2015 Summer Project Week:LightWeightRobotIGT

2015-06-22T08:38:04Z

Tauscher:

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:FiniteStateMachine_colored.png|Screenshot of the Slicer module and the current robot position in CT data of the Femur phantom
</gallery>

==Key Investigators==
* Sebastian Tauscher, Leibniz Universitaet Hannover, Institute of Mechatronic Systems
* Junichi Tokuda, Brigham and Women's Hospital, SPL

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

File:FiniteStateMachine colored.png

2015-06-22T08:33:33Z

Tauscher:

2015 Summer Project Week:LightWeightRobotIGT

2015-06-22T08:31:10Z

Tauscher:

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:NavGravCompSlicer_v2.png|Screenshot of the Slicer module and the current robot position in CT data of the Femur phantom
</gallery>

==Key Investigators==
* Sebastian Tauscher, Leibniz Universitaet Hannover, Institute of Mechatronic Systems
* Junichi Tokuda, Brigham and Women's Hospital, SPL

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

2015 Summer Project Week:LightWeightRobotIGT

2015-06-22T08:06:19Z

Tauscher:

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:NavGravCompSlicer_v2.png|Screenshot of the Slicer module and the current robot position in CT data of the Femur phantom
</gallery>

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

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

2015 Summer Project Week Template

2015-06-15T12:31:37Z

Tauscher: Undo revision 89402 by Tauscher (Talk)

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

==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:LightWeightRobotIGT

2015-06-15T12:31:04Z

Tauscher: Created page with '<gallery> Image:PW-Summer2015.png|Projects List Image:NavGravCompSlicer_v2.png|Screenshot of the Slicer module and the current robot positio…'

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:NavGravCompSlicer_v2.png|Screenshot of the Slicer module and the current robot position in CT data of the Femur phantom
</gallery>

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

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

2015 Summer Project Week:Equipment

2015-06-11T08:46:00Z

Tauscher:

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

==Equipment==

===Steve Pieper===

* TeleMed MicrUs USB US scanner and probe (MicrUs EXT-1H Kit with L12-5L40S-3 transducer)
* NDI tracker
* Microsoft Surface Pro 3 (US)
* Galaxy Gear VR and Galaxy Note 4
* Structure Sensor & ipad mini
* Ultrasound Phantom (elephantom) & scans CT, MR, microCT

===Javier Pascau===

* Ascension 3D Guidance medSAFE (3DGM) EM tracker with three sensors (1 x Model 800, 2 x Model 180)

===Sebastian Tauscher===

*Light Weight Robot LWR iiwa (KUKA Roboter GmbH)
*Sawbone Femur Phantom with fiducials

2015 Summer Project Week Template

2015-06-10T08:45:40Z

Tauscher:

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:NavGravCompSlicer_v2.png|Screenshot of the Slicer module and the current robot position in CT data of the Femur phantom
</gallery>

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

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

2015 Summer Project Week

2015-06-10T08:32:54Z

Tauscher:

__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

2015 Summer Project Week

2015-06-10T08:25:34Z

Tauscher:

__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)

==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

2013 Summer Project Week:kukarobot

2013-06-21T13:12:32Z

Tauscher:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:NavGravCompSlicer_v2.png|Screenshot of the Slicer module and the current robot position in CT data of the Femur phantom
Image:DataDescription_LWRIGT.png|Protocol description for the current Version of LightWeightRobotIGT in start_up stage
Image:DataDescription_LWRIGT_2.png|Protocol description for the current Version of LightWeightRobotIGT in targetting stage
</gallery>

==Key Investigators==
* imes: Sebastian Tauscher
* KUKA: Thomas Neff
* BWH: Junichi Tokuda
* BWH: Nobuhiko Hata

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

<h3>Objective</h3>
Within this cooperative project of the KUKA Laboratories GmbH and the Institute for Mechatronic Systems we are developing a interface concept for the integration of the Light Weight Robot (KUKA) in an image-guided therapy system. Therefor we developed an interfae concept using OpenIGTLink which will be tested and validated by integrating the KUKA LWR into the MediLAB environment in the medical technology laboratory of the institute. For Further Information visit [http://www.imes.uni-hannover.de/35.html?&L=1&categorie=6&no_cache=1 imes] or [http://www.kuka-labs.com/de/medical_robotics/projects_studies/ KUKA Laboratories] page.
</div>

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

<h3>Approach, Plan</h3>
The aim is to use this OpenIGTLink interface to control the Leight Weight Robot (LWR) with a Slicer Modul and visualize the current position in CT image data. Therefor a state machine is running on the robot controller. Implemented states so far are registration, sending registrations points, receiving transform, gravitation compensation (GravComp) mode, navigated GravComp and a virtual fixtures (Plane/Cone). These State machine will be extended during this project with states e.g move to point.

</div>

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

<h3>Progress</h3>
A Slicer module was implemented with which Commands and Transformation can be send to the robot and the current position of the robot can be shown in CT data.
The Slicer extension is available at :
https://github.com/SNRLab/LightWeightRobotIGT

</div>
</div>

File:DataDescription LWRIGT 2.png

2013-06-21T13:09:00Z

Tauscher: Protocol Description for the LightWeightRobotIGT first version for the targetting phase

Protocol Description for the LightWeightRobotIGT first version for the targetting phase

File:DataDescription LWRIGT.png

2013-06-21T13:07:58Z

Tauscher: Protocl Description of the first Version of the LightWeightRobotIGT and the state machine

Protocl Description of the first Version of the LightWeightRobotIGT and the state machine

2013 Summer Project Week:kukarobot

2013-06-21T12:46:48Z

Tauscher:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:NavGravCompSlicer_v2.png|Screenshot of the Slicer module and the current robot position in CT data of the Femur phantom
</gallery>

==Key Investigators==
* imes: Sebastian Tauscher
* KUKA: Thomas Neff
* BWH: Junichi Tokuda
* BWH: Nobuhiko Hata

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

<h3>Objective</h3>
Within this cooperative project of the KUKA Laboratories GmbH and the Institute for Mechatronic Systems we are developing a interface concept for the integration of the Light Weight Robot (KUKA) in an image-guided therapy system. Therefor we developed an interfae concept using OpenIGTLink which will be tested and validated by integrating the KUKA LWR into the MediLAB environment in the medical technology laboratory of the institute. For Further Information visit [http://www.imes.uni-hannover.de/35.html?&L=1&categorie=6&no_cache=1 imes] or [http://www.kuka-labs.com/de/medical_robotics/projects_studies/ KUKA Laboratories] page.
</div>

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

<h3>Approach, Plan</h3>
The aim is to use this OpenIGTLink interface to control the Leight Weight Robot (LWR) with a Slicer Modul and visualize the current position in CT image data. Therefor a state machine is running on the robot controller. Implemented states so far are registration, sending registrations points, receiving transform, gravitation compensation (GravComp) mode, navigated GravComp and a virtual fixtures (Plane/Cone). These State machine will be extended during this project with states e.g move to point.

</div>

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

<h3>Progress</h3>
A Slicer module was implemented with which Commands and Transformation can be send to the robot and the current position of the robot can be shown in CT data.
The Slicer extension is available at :
https://github.com/SNRLab/LightWeightRobotIGT

</div>
</div>

File:NavGravCompSlicer v2.png

2013-06-21T11:11:22Z

Tauscher: Screenshot of the LightWeightRobotIGT Module in Slice with the current robot position shown in the CT data of an femur sawbone phantom

Screenshot of the LightWeightRobotIGT Module in Slice with the current robot position shown in the CT data of an femur sawbone phantom

2013 Summer Project Week:kukarobot

2013-06-21T03:04:28Z

Tauscher: /* Key Investigators */

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

==Key Investigators==
* imes: Sebastian Tauscher
* KUKA: Thomas Neff
* BWH: Junichi Tokuda
* BWH: Nobuhiko Hata

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

<h3>Objective</h3>
Within this cooperative project of the KUKA Laboratories GmbH and the Institute for Mechatronic Systems we are developing a interface concept for the integration of the Light Weight Robot (KUKA) in an image-guided therapy system. Therefor we developed an interfae concept using OpenIGTLink which will be tested and validated by integrating the KUKA LWR into the MediLAB environment in the medical technology laboratory of the institute. For Further Information visit [http://www.imes.uni-hannover.de/35.html?&L=1&categorie=6&no_cache=1 imes] or [http://www.kuka-labs.com/de/medical_robotics/projects_studies/ KUKA Laboratories] page.
</div>

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

<h3>Approach, Plan</h3>
The aim is to use this OpenIGTLink interface to control the Leight Weight Robot (LWR) with a Slicer Modul and visualize the current position in CT image data. Therefor a state machine is running on the robot controller. Implemented states so far are registration, sending registrations points, receiving transform, gravitation compensation (GravComp) mode, navigated GravComp and a virtual fixtures (Plane/Cone). These State machine will be extended during this project with states e.g move to point.

</div>

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

<h3>Progress</h3>
A Slicer module was implemented with which Commands and Transformation can be send to the robot and the current position of the robot can be shown in CT data.
The Slicer extension is available at :
https://github.com/SNRLab/LightWeightRobotIGT

</div>
</div>

2013 Summer Project Week

2013-06-17T12:39:24Z

Tauscher:

Back to [[Events]]
[[image:PW-MIT2013.png|300px]]

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] (Steve Pieper) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans Johnson, Brad Lowekamp)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina Kapur)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|<br>----------------------------------------<br>'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Projects''' ==

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template this template] to create wiki pages for your project. Then link the page here with a list of key personnel.

===Huntington's Disease===
* [[Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data]] (Hans, Demian)
* [[Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation]] (Hans)
* [[2013_Summer_Project_Week:SinglePrecisionRegistrationITK| Single Precision Registration]] (Hans, Brad Lowekamp, Dave, Ali Ghayoor)
* [[Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend]] (Dave)
* [[DWIConvert]] (Dave, Kent Williams)
* [[Enhance and update SPL atlas]] (Dave, Hans)
* [[Linear Mixed-effects shape model to explore Huntington's Disease Data]] (Dave, Manasi, Hans, Ross)

===Traumatic Brain Injury===
* [[Visualization and quantification of peri-contusional white matter bundles in traumatic brain injury using diffusion tensor imaging]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[Clinically oriented assessment of local changes in the properties of white matter affected by intra-cranial hemorrhage]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[Exploring multi-modal registration for improved longitudinal modeling of patient-specific 4D DTI data]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[2013_Summer_Project_Week: A Portable Ultrasound Device for Intracranial Hemorrhage Detection|A Portable Ultrasound Device for Intracranial Hemorrhage Detection]] (Jason White, Vicki Noble, Kirby Vosburgh)

===Atrial Fibrillation and Cardiac Image Analysis===
* [[2013_Summer_Project_Week:Fibrosis_analysis|Fibrosis distribution analysis]] (Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:CARMA_workflow_wizard|Cardiac MRI Toolkit LA segmentation and enhancement quantification workflow wizard]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Documentataion|Cardiac MRI Toolkit Documentation Project]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Visualization|LA model visualization]] (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_AutoLASeg|Cardiac MRI Toolkit: Automatic LA Segmentation with Graph Cuts Module]] (Salma Bengali, Alan Morris, Josh Cates, Gopal, Ross Whitaker, Rob MacLeod)
* [[2013_Summer_Project_Week:Sobolev_Segmenter|Medical Volume Segmentation Using Sobolev Active Contours]] (Arie Nakhmani, Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:Left_Ventricle_Motion_Analysis_using_Tagged_MRI|Left Ventricle Motion Analysis using Tagged MRI]] (Yang Yu, Shaoting Zhang, Dimitris Metaxas)

===Radiation Therapy===
* [[2013_Summer_Project_Week:Landmark_Registration| Landmark Registration]] (Steve, Nadya, Greg, Paolo, Erol)
* [[2013_Summer_Project_Week:Slicer_RT:_DICOM-RT_Export | SlicerRT: Dicom-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]] (Greg Sharp, Kevin Wang, Maxime Desplanques)
* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, Kevin Wang, Andrey Fedorov, anyone else?)
* [[2013_Summer_Project_Week:Deformable_transforms | Deformable transform handling in Transforms module]] (Csaba Pinter, Alex Yarmarkovich, Andras Lasso, ?)
* [[2013_Summer_Project_Week:Brachy_HDR_Ultrasound | Using ultrasound for prostate HDR brachytherapy]] (Adam Rankin)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Christian Wachinger, Karl Fritscher, Greg Sharp, Matthew Brennan)

===IGT and Device Integration with Slicer===
* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering for Neurosurgery]] (Lauren O'Donnell)
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Stephen Aylward, Isaiah Norton, Tamas Ungi)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:LabelMapStatistics| Label map statistics]] (Laurent Chauvin, Csaba Pinter)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
* [[2013_Summer_Project_Week:3D_prostate_segmentation_of_Ultrasound_image| Segmentation of Prostate Gland from 3D US for Prostate Interventions]] (Xu Li, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:3D_prostate_registration_of_Ultrasound_image_using_MRI| Registration of an MRI delineated image of the Prostate Gland ot a 3D US for Prostate Interventions]] (Demian Wassermann, Andriy Fedorov, Tina Kapur, William Wells)

===Chronic Obstructive Pulmonary Disease===
* [[2013_Summer_Project_Week:Airway_Inspector_Porting | Porting Airway Inspector to Slicer 4]] (Raul San Jose, Demian Wassermann, Rola Harmouche)
* [[2013_Summer_Project_Week:MRML_Infrastructure_Airway_Inspector | Airway Inspector: Slicer Extension and MRML Infrastructure]] (Demian Wassermann, Raul San Jose, Rola Harmouche)
* [[2013_Summer_Project_Week:Nipype_CLI_Integration | Integration of Nipype with CLI modules in the Chest Imaging Platform Library ]] (Rola Harmouche,Demian Wassermann, Raul San Jose)

=== '''Additional Collaborations'''===
* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ivan Kolesov, Allen Tannenbaum, Ron Kikinis)
* [[2013_Summer_Project_Week:XNAT 3D Viewer| XNAT 3D Viewer]] (Amanda Hartung, Steve Pieper, Daniel Haehn)
* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpenIGTLink]] (Sebastian Tauscher, Thomas Neff, Junichi Tokuda, Nobuhiko Hata)
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
* [[2013_Summer_Project_Week: Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease| Individualized Neuroimaging Content Analysis using 3D Slicer]] (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
* [[2013_Summer_Project_Week:CMFReg | Cranio-Maxillofacial Registration]] (Vinicius Boen)
* [[2013_Summer_Project_Week:DTIPipelineExtensions | DTI Analysis Pipeline as Slicer4 Extensions]] (Vinicius Boen)
*[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Daniel Haehn, Steve Pieper, Rudolph Pienaar, Lilla Zollei, Nathaniel Reynolds)
* [[2013_Summer_Project_Week:Biomedical_Image_Computing_Teaching_Modules|3D Slicer based Biomedical image computing teaching modules]] (A. Vilchis, J-C. Avila-Vilchis, S. Pujol)
* [[2013_Summer_Project_Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer|Analyzing Breast Tumor Heterogeneity Using 3D Slicer]] (Sneha Durgapal, Jayender Jagadeesan, Tobias Penzkofer, Vivek Narayan)
* [[2013_Summer_Project_Week:WMH Segmentation for Stroke|WMH Segmentation for Stroke]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin, Ron Kikinis)
* [[2013_Summer_Project_Week:Patient_hierarchy | Patient hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Andras Lasso, Csaba Pinter, Jc, Steve, Jim, ?)
* [[2013_Summer_Project_Week:CLI_Matlab | CLI module implementation in Matlab]] (Andras Lasso, Jc, Steve, Jim, ?)
* [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
* [[Plastimatch in NiPype]] (Paolo, Dave, Hans)
* [[2013_Summer_Project_Week:Optimizing start time of slicer| Optimizing start time of slicer]] (Jc, Steve)
* [[Common resampling and conversion utility functions in Slicer]] (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)
* [[2013_Summer_Project_Week:SimpleITK_GUI| Common Usage GUI for SimpleITK]] (Hans Johnson, Dave Welch, Brad Lowekamp)
* [[2013_Summer_Project_Week:Extension_dependencies| Extension dependencies]] (Jc, Adam Rankin)
* [[2013_Summer_Project_Week:Parameter_heirarchy| Parameter Hierarchy]] (Adam Rankin, ??)

== '''Background''' ==

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 25th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], [http://www.cimit.org CIMIT], and OCAIRO. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== '''Logistics''' ==

*'''Dates:''' June 17-21, 2013.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' http://www.regonline.com/namic2013summerprojweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list before May 27th. See [[2013_Summer_Project_Week/RoomSharing|here]]

== '''Preparation''' ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. Participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 13: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1233699 Please click here to register.])

#Parth Amin, WIT, aminp@wit.edu
#Charles Anderson, BWH, canderson26@partners.org
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
#Juan Carlos Avila Vilchis, Univ del Estado de Mexico, jc.avila.vilchis@hotmail.com
#Salma Bengali, Univ UT, salma.bengali@carma.utah.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Matthew Brennan, MIT, brennanm@mit.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Ivan Buzurovic, BWH/HMS, ibuzurovic@lroc.harvard.edu
#Josh Cates, Univ UT, cates@sci.utah.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Laurent Chauvin, BWH - SPL, lchauvin@bwh.harvard.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Adrian Dalca, MIT, adalca@MIT.EDU
#Matthew D'Artista, BWH - SPL, mdartista7@gmail.com
#Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
#Sneha Durgapal, BWH, durgapalsneha@gmail.com
#Luping Fang, Zhejiang Univ of Technology (China), flp@zjut.edu.cn
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Gregory Fischer, WPI, gfischer@wpi.edu
#Barton Fiske, zSpace Inc, bfiske@zspace.com
#Matthew Flynn, WIT, flynnm3@wit.edu
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Maria Gonzalez-Puente, WIT, gonzalezpuentem@wit.edu
#Daniel Haehn, Boston Childrens Hospital, daniel.haehn@childrens.harvard.edu
#Michael Halle, BWH-SPL, mhalle@bwh.harvard.edu
#Rola Harmouche, BWH, rharmo@bwh.harvard.edu
#Amanda Hartung, Rochester Inst of Tech, amh1646@rit.edu
#Nobuhiko Hata, BWH, hata@bwh.harvard.edu
#Nicholas Herlambang, AZE Technology Inc, nicholas.herlambang@azetech.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Andrei Irimia, UCLA, andrei.irimia@loni.ucla.edu
#Jayender Jagadeesan, BWH-SPL, jayender@bwh.harvard.edu
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Alex Kikinis, BWH, alexkikinis@gmail.com
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Nils Klarlund, IEEE, klarlund@ieee.org
#Daniel Kostro, BWH, dkostro@bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
#Rui Li, GE Global Research, li.rui@ge.com
#Xu Li, BWH, lixu0103@gmail.com
#Lichen Liang, MGH, lichenl@nmr.mgh.harvard.edu
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
#Nikos Makris, MGH, nikos@nmr.mgh.harvard.edu
#Katie Mastrogiacomo, BWH - SPL, kmast@bwh.harvard.edu
#Alireza Mehrtash, BWH - SPL, mehrtash@bwh.harvard.edu
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Isaiah Norton, BWH, inorton@bwh.harvard.edu
#Lauren O'Donnell, BWH, odonnell@bwh.harvard.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Jian Pan, Zhejiang Univ of Technology (China), pj@zjut.edu.cn
#George Papadimitriou, MGH, georgep@nmr.mgh.harvard.edu
#Tobias Penzkofer, BWH - SPL, pt@bwh.harvard.edu
#Rudolph Pienaar, Boston Childrens Hospital, Rudolph.Pienaar@childrens.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
#Nathaniel Reynolds, MGH, reynolds@nmr.mgh.harvard.edu
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
#Peter Savadjiev, BWH, petersv@bwh.harvard.edu
#Anuja Sharma, Univ UT-SCI Institute, anuja@cs.utah.edu
#Greg Sharp, MGH, gcsharp@partners.org
#Nadya Shusharina, MGH, nshusharina@partners.org
#Sebastian Tauscher, Leibniz Univ Hannover (Germany), sebastian.tauscher@imes.uni-hannover.de
#Clare Tempany, BWH, ctempanyafdhal@partners.org
#Cyrill von Tiesenhausen, KUKA Laboratories (Germany), cyrill.tiesenhausen@kuka.com
#Gaurie Tilak, BWH, gaurie_tilak@hms.harvard.edu
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Junichi Tokuda, BWH, tokuda@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
#Kirby Vosburgh, BWH, kirby@bwh.harvard.edu
#Christian Wachinger, MIT, wachinge@mit.edu
#Bo Wang, Univ UT-SCI Institute, bowang@sci.utah.edu
#Demian Wassermann, BWH, demian@bwh.harvard.edu
#David Welch, Univ Iowa, david-welch@uiowa.edu
#William Wells, BWH/HMS, sw@bwh.harvard.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Alex Yarmarkovich, Isomics Inc, alexy@bwh.harvard.edu
#Kitaro Yoshimitsu, BWH, kitarof1@bwh.harvard.edu
#Yang Yu, Rutgers Univ, yyu@cs.rutgers.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
#Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu

2013 Summer Project Week:kukarobot

2013-06-17T12:38:36Z

Tauscher:

2013 Summer Project Week:kukarobot

2013-06-11T17:57:35Z

Tauscher: Created page with '__NOTOC__ <gallery> Image:PW-MIT2013.png|Projects List </gallery> ==Key Investigators== * imes: Sebastian Tauscher * BWH: Nobuhiko Hata <d…'

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

==Key Investigators==
* imes: Sebastian Tauscher
* BWH: Nobuhiko Hata

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

<h3>Objective</h3>
Within this cooperative project of the KUKA Laboratories GmbH and the Institute for Mechatronic Systems we are developing a interface concept for the integration of the Light Weight Robot (KUKA) in an image-guided therapy system. Therefor we developed an interfae concept using OpenIGTLink which will be tested and validated by integrating the KUKA LWR into the MediLAB environment in the medical technology laboratory of the institute. For Further Information visit [http://www.imes.uni-hannover.de/35.html?&L=1&categorie=6&no_cache=1 imes] or [http://www.kuka-labs.com/de/medical_robotics/projects_studies/ KUKA Laboratories] page.
</div>

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

<h3>Approach, Plan</h3>

</div>

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

<h3>Progress</h3>

</div>
</div>

2013 Summer Project Week

2013-06-11T16:46:23Z

Tauscher:

Back to [[Events]]
[[image:PW-MIT2013.png|300px]]

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Projects''' ==

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template this template] to create wiki pages for your project. Then link the page here with a list of key personnel.

===Huntington's Disease===
* [[Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend]] (Dave)
* [[DWIConvert]] (Kent)
* [[Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data]] (Hans, Demian)
* [[Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation]] (Hans)
* [[Enhance and update SPL atlas]] (Dave, Hans)

===Traumatic Brain Injury===
* Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury (Andrei Irimia, Micah Chambers, Bo Wang, Marcel Prastawa, Guido Gerig, Jack van Horn)
* Visualization and quantification of peri-contusional white matter bundles in traumatic brain injury using diffusion tensor imaging (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* Clinically oriented assessment of local changes in the properties of white matter affected by intra-cranial hemorrhage (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* Investigation of the peri-lesional penumbra in traumatic brain injury using diffusion tensor imaging to isolate longitudinal changes in white matter integrity (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* Reconstruction and visualization of the corticospinal tract in traumatic brain injury in the presence of severe hematoma and CSF-perfused edematous tissue using diffusion tensor imaging (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)

===Atrial Fibrillation===
* [[2013_Summer_Project_Week:CARMA_workflow_wizard|Cardiac MRI Toolkit LA segmentation and enhancement quantification workflow wizard]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Documentataion|Cardiac MRI Toolkit Documentation Project]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Visualization|LA model visualization]] (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_AutoLASeg|Cardiac MRI Toolkit: Automatic LA Segmentation with Graph Cuts Module]] (Salma Bengali, Alan Morris, Josh Cates, Gopal, Ross Whitaker, Rob MacLeod)
* [[2013_Summer_Project_Week:Sobolev_Segmenter|Medical Volume Segmentation Using Sobolev Active Contours]] (Arie Nakhmani, Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:Fibrosis_analysis|Fibrosis distribution analysis]] (Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)

===Radiation Therapy===
* [[2013_Summer_Project_Week:Landmark_Registration| Landmark Registration]] (Steve, Nadya, Greg, Paolo, Erol)
* [[2013_Summer_Project_Week:Slicer_RT:_DICOM-RT_Export | SlicerRT: Dicom-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]] (Greg Sharp, Kevin Wang, Maxime Desplanques)
* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, Kevin Wang, Andrey Fedorov, anyone else?)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Christian Wachinger, Karl Fritscher, Greg Sharp, Matthew Brennan)
* [[2013_Summer_Project_Week:Deformable_transforms | Deformable transform handling in Transforms module]] (Csaba Pinter, Alex Yarmarkovich, Andras Lasso, ?)
* [[2013_Summer_Project_Week:CMFReg | Cranio-Maxillofacial Registration]] (Vinicius Boen)

===Device Integration with Slicer===
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpnIGTLink]] (Sebastian Tauscher, Nobuhiko Hata)

===IGT===
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas, Junichi, Laurent)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Steven Aylward, Tamas Ungi)
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent, Junichi)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent, Junichi)
* [[2013_Summer_Project_Week: Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease| Individualized Neuroimaging Content Analysis using 3D Slicer]] (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ron Kikinis)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)

=== '''Informatics'''===
* [[2013_Summer_Project_Week:Biomedical_Image_Computing_Teaching_Modules|3D Slicer based Biomedical image computing teaching modules]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin)
* Provenance
* [[2013_Summer_Project_Week:Patient_hierarchy | Patient hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Csaba Pinter, Andras Lasso, Jc, Steve, Jim, ?)
* [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
* [[Plastimatch in NiPype]] (Paolo, Dave, Hans)
** look for commonalities/reuse of CompareVolumes
* iPython in Slicer (Hans, Jc, Dave)
* Optimizing start time of slicer (Jc, Steve)
* [[Common resampling and conversion utility functions in Slicer]] (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)

==='''Brain Segmentation'''===
* [[2013_Summer_Project_Week:Multi_Atlas_Based_Multi_Image_Segmentation | Multi-Atlas-Based Multi-Image Segmentation for Brain MR Images]] (Minjeong Kim, Xiaofeng Liu, Jim Miller, Dinggang Shen)

== '''Background''' ==

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 25th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], [http://www.cimit.org CIMIT], and OCAIRO. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== '''Logistics''' ==

*'''Dates:''' June 17-21, 2013.
*'''Location:''' MIT.
*'''REGISTRATION:''' http://www.regonline.com/namic2013summerprojweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list before May 27th. See [[2013_Summer_Project_Week/RoomSharing|here]]

== '''Preparation''' ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. Participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 13: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1233699 Please click here to register.])

#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
#Juan Carlos Avila Vilchis, Univ del Estado de Mexico, jc.avila.vilchis@hotmail.com
#Salma Bengali, Univ UT, salma.bengali@carma.utah.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Matthew Brennan, MIT, brennanm@mit.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Josh Cates, Univ UT, cates@sci.utah.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Daniel Haehn, Boston Childrens Hospital, daniel.haehn@childrens.harvard.edu
#Rola Harmouche, BWH, rharmo@bwh.harvard.edu
#Nobuhiko Hata, BWH, hata@bwh.harvard.edu
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Daniel Kostro, BWH, dkostro@bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
#Rui Li, GE Global Research, li.rui@ge.com
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
#Alireza Mehrtash, BWH - SPL, mehrtash@bwh.harvard.edu
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Isaiah Norton, BWH, inorton@bwh.harvard.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
#Nathaniel Reynolds, MGH, reynolds@nmr.mgh.harvard.edu
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
#Anuja Sharma, Univ UT-SCI Institute, anuja@cs.utah.edu
#Greg Sharp, MGH, gcsharp@partners.org
#Nadya Shusharina, MGH, nshusharina@partners.org
#Sebastian Tauscher, Leibniz Univ Hannover (Germany), sebastian.tauscher@imes.uni-hannover.de
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
#Christian Wachinger, MIT, wachinge@mit.edu
#Bo Wang, Univ UT-SCI Institute, bowang@sci.utah.edu
#Demian Wassermann, BWH, demian@bwh.harvard.edu
#David Welch, Univ Iowa, david-welch@uiowa.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Yang Yu, Rutgers Univ, yyu@cs.rutgers.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
#Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu