NAMIC Wiki - User contributions [en]

2016 Winter Project Week/Projects/SlicerROSIntegration

2016-01-05T03:15:36Z

Nirav:

__NOTOC__
<gallery>
Image:PW-MIT2016.png|[[2016_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Junichi Tokuda (Brigham and Women's Hospital)
* Axel Krieger (Children's National Medical Center)
* Simon Leonard (Johns Hopkins University)
* Tobias Frank (University Hannover, Germany)
* Jayender Jagadeesan (BWH)
*Niravkumar Patel(Worcester Polytechnic Institute)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Define requirements and system architecture for medical robotics software system based on 3D Slicer and Robot Operating System (ROS)
|
* Needs for 3D Slicer / ROS integration in ongoing research projects (presentations by participants) (See [[2016_Winter_Project_Week/Breakout_Sessions/SlicerForMedicalRoboticsResearch|Breakout session]])
** Axel (Autonomous Surgery using the KUKA LWR)
** Simon (dVRK?)
** Junichi (OpenIGTLink and medical robotics research)
** Tobias (OCT robot / Integration of KUKA robot and 3D Slicer
* Brainstorming 1: Requirements
** Applications (e.g. endoscopic surgery, percutaneous interventions, catheterization, etc.)
** Platforms -- Linux, Windows, MAC
** Roles for 3D Slicer -- visualization, image processing, etc.
** Roles for ROS -- vision, sensors, devices, etc.
* Brainstorming 2: Architecture for 3D Slicer-ROS integration
** Types of data exchanged between ROS and 3D Slicer
** Communication scheme between ROS and 3D Slicer
** Software package to provide
*** Independent middleware?
*** 3D Slicer plug-in modules
*** ROS modules
* Brainstorming 3: Collaborative tools / teams
** Platforms to support (ROS mainly support Linux)
** Repository
|
*
|}

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-27T01:54:51Z

Nirav:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* [[User:Gfischer|Greg Fischer (WPI)]]
* [[User:Nirav|Nirav Patel (WPI)]]
* [[User:Tokuda|Junichi Tokuda (BWH/SPL)]]
* [[User:Lasso|Andras Lasso (PerkLab, Queen's)]]

==Project Description==
<div style="margin: 20px;">
* This Project is to further develop a workflow and communication protocol for interfacing robots with image-guided therapy systems using OpenIGTLink.
* Also, we would like to enhance JAVA implementation of IGTLink and support more message types.
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Some of the supported standard messages in OpenIGTLink for JAVA are Position, Status, String and Transform. During this week we would like to add support for other message types like NDArray, Sensor and any other useful messages for controlling the robot using IGTLink.
* Also, would like to collaborate with team working on MATLAB interface for IGTLink and test it with JAVA implementation.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Taking BRP Robot Application as base and extending it for any other robot applications.
* Testing it for MATLAB and standard C++ implementation.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* We have tested IGTLink communication with the clinical workflow described at http://www.na-mic.org/Wiki/index.php/ProstateBRP_OpenIGTLink_Communication_June_2013 which was implemented during 2013 Summer Project Week.
* String, NDArray and Transform messages tested between JAVA OpenIGTLink Server and MATLAB client.
* MATLAB OpenIGTLink code by Andras Lasso is made more modular and easy to use. Supports STRING, TRANSFORM and 1D Float arrays fromm MATLAB to other clients and MATLAB client can receive STRING and TRANSFORM messages.
* XML Based string messages may be used for getting and setting parameter values. Tested it with MATLAB sending a STRING message to JAVA application to set value of a parameter using STRING command like ''<Command Name='SetVar' theta='23.5'/>''. Similarly we can define such commands with more arguments.
* Still working on other message types, especially IMAGE message might be of interest to many.
</div>
</div>

<h2>OpenIGTLink XML command specification</h2>
* Command message:
** Type: ''STRING''
** Device name: ''CMD_uid''
*** The _uid part is optional, it's for matching requests and responses. The uid is a unique string to identify the request, such as a counter or timestamp.)
** Content: ''Command'' XML element
*** ''Name'' attribute contains the command name
*** Any number of additional attributes and/or child elements to specify further parameters for the command can be added.
* Command response message:
** Type: ''STRING''
** Device name: ''ACK_uid''
*** uid matches the uid in the command message's device name
** Content: ''CommandReply'' XML element
*** ''Status'' attribute containing the status of the command; allowed values: ''SUCCESS'' or ''FAIL''
*** ''Message'' attribute containing a human-readable status of the command completion
*** Any number of additional attributes and/or child elements to specify further return values can be added.
** Example command and response content:
*** Command: <Command Name="SomeCommandName" SomeAttribute1="attribute value 1" SomeAttribute2="123" />
****'''Should we specify type of the attribute??OR if its got any alphabet then its should be string otherwise numeric value'''
****'''Should we specify that this is a read/write request, may be should we specify some standard commands??'''
*** Response: <CommandReply Status="SUCCESS" SomeReturnValue1="123" SomeReturnValue1="abc" />

String message send/receive in Matlab: https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/src/MatlabCommander/commandserver/cli_commandserver.m

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-25T18:41:21Z

Nirav: /* Project Description */

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* [[User:Gfischer|Greg Fischer (WPI)]]
* [[User:Nirav|Nirav Patel (WPI)]]
* [[User:Tokuda|Junichi Tokuda (BWH/SPL)]]
* [[User:Lasso|Andras Lasso (PerkLab, Queen's)]]

==Project Description==
<div style="margin: 20px;">
* This Project is to further develop a workflow and communication protocol for interfacing robots with image-guided therapy systems using OpenIGTLink.
* Also, we would like to enhance JAVA implementation of IGTLink and support more message types.
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Some of the supported standard messages in OpenIGTLink for JAVA are Position, Status, String and Transform. During this week we would like to add support for other message types like NDArray, Sensor and any other useful messages for controlling the robot using IGTLink.
* Also, would like to collaborate with team working on MATLAB interface for IGTLink and test it with JAVA implementation.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Taking BRP Robot Application as base and extending it for any other robot applications.
* Testing it for MATLAB and standard C++ implementation.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* We have tested IGTLink communication with the clinical workflow described at http://www.na-mic.org/Wiki/index.php/ProstateBRP_OpenIGTLink_Communication_June_2013 which was implemented during 2013 Summer Project Week.
* NDArray is tested for 1D float arrays.
* String, NDArray and Transform messages tested between JAVA OpenIGTLink Server and MATLAB client.
</div>
</div>

<h2>OpenIGTLink XML command specification</h2>
* Command message:
** Type: ''STRING''
** Device name: ''CMD_uid''
*** The _uid part is optional, it's for matching requests and responses. The uid is a unique string to identify the request, such as a counter or timestamp.)
** Content: ''Command'' XML element
*** ''Name'' attribute contains the command name
*** Any number of additional attributes and/or child elements to specify further parameters for the command can be added.
* Command response message:
** Type: ''STRING''
** Device name: ''ACK_uid''
*** uid matches the uid in the command message's device name
** Content: ''CommandReply'' XML element
*** ''Status'' attribute containing the status of the command; allowed values: ''SUCCESS'' or ''FAIL''
*** ''Message'' attribute containing a human-readable status of the command completion
*** Any number of additional attributes and/or child elements to specify further return values can be added.
** Example command and response content:
*** Command: <Command Name="SomeCommandName" SomeAttribute1="attribute value 1" SomeAttribute2="123" />
****'''Should we specify type of the attribute??OR if its got any alphabet then its should be string otherwise numeric value'''
****'''Should we specify that this is a read/write request, may be should we specify some standard commands??'''
*** Response: <CommandReply Status="SUCCESS" SomeReturnValue1="123" SomeReturnValue1="abc" />

String message send/receive in Matlab: https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/src/MatlabCommander/commandserver/cli_commandserver.m

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-24T13:03:08Z

Nirav:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* [[User:Gfischer|Greg Fischer (WPI)]]
* [[User:Nirav|Nirav Patel (WPI)]]
* [[User:Tokuda|Junichi Tokuda (BWH/SPL)]]
* [[User:Lasso|Andras Lasso (PerkLab, Queen's)]]

==Project Description==
<div style="margin: 20px;">
* This Project is to further develop a workflow and communication protocol for interfacing robots with image-guided therapy systems using OpenIGTLink.
* Also, we would like to enhance JAVA implementation of IGTLink and support more message types.
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Some of the supported standard messages in OpenIGTLink for JAVA are Position, Status, String and Transform. During this week we would like to add support for other message types like NDArray, Sensor and any other useful messages for controlling the robot using IGTLink.
* Also, would like to collaborate with team working on MATLAB interface for IGTLink and test it with JAVA implementation.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Taking BRP Robot Application as base and extending it for any other robot applications.
* Testing it for MATLAB and standard C++ implementation.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* We have tested IGTLink communication with the clinical workflow described at http://www.na-mic.org/Wiki/index.php/ProstateBRP_OpenIGTLink_Communication_June_2013 which was implemented during 2013 Summer Project Week.
* NDArray is being implemented but not yet tested.
* Sensor message yet to be implemented.
</div>
</div>

<h2>OpenIGTLink XML command specification</h2>
* Command message:
** Type: ''STRING''
** Device name: ''CMD_uid''
*** The _uid part is optional, it's for matching requests and responses. The uid is a unique string to identify the request, such as a counter or timestamp.)
** Content: ''Command'' XML element
*** ''Name'' attribute contains the command name
*** Any number of additional attributes and/or child elements to specify further parameters for the command can be added.
* Command response message:
** Type: ''STRING''
** Device name: ''ACK_uid''
*** uid matches the uid in the command message's device name
** Content: ''CommandReply'' XML element
*** ''Status'' attribute containing the status of the command; allowed values: ''SUCCESS'' or ''FAIL''
*** ''Message'' attribute containing a human-readable status of the command completion
*** Any number of additional attributes and/or child elements to specify further return values can be added.
** Example command and response content:
*** Command: <Command Name="SomeCommandName" SomeAttribute1="attribute value 1" SomeAttribute2="123" />
****'''Should we specify type of the attribute??OR if its got any alphabet then its should be string otherwise numeric value'''
****'''Should we specify that this is a read/write request, may be should we specify some standard commands??'''
*** Response: <CommandReply Status="SUCCESS" SomeReturnValue1="123" SomeReturnValue1="abc" />

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-23T19:42:23Z

Nirav:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* [[User:Gfischer|Greg Fischer (WPI)]]
* [[User:Nirav|Nirav Patel (WPI)]]
* [[User:Tokuda|Junichi Tokuda (BWH/SPL)]]
* [[User:Lasso|Andras Lasso (PerkLab, Queen's)]]

==Project Description==
<div style="margin: 20px;">
* This Project is to further develop a workflow and communication protocol for interfacing robots with image-guided therapy systems using OpenIGTLink.
* Also, we would like to enhance JAVA implementation of IGTLink and support more message types.
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Some of the supported standard messages in OpenIGTLink for JAVA are Position, Status, String and Transform. During this week we would like to add support for other message types like NDArray, Sensor and any other useful messages for controlling the robot using IGTLink.
* Also, would like to collaborate with team working on MATLAB interface for IGTLink and test it with JAVA implementation.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Taking BRP Robot Application as base and extending it for any other robot applications.
* Testing it for MATLAB and standard C++ implementation.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* We have tested IGTLink communication with the clinical workflow described at http://www.na-mic.org/Wiki/index.php/ProstateBRP_OpenIGTLink_Communication_June_2013 which was implemented during 2013 Summer Project Week.
* NDArray is being implemented but not yet tested.
* Sensor message yet to be implemented.
</div>
</div>

<h2>OpenIGTLink XML command specification</h2>
* Command message:
** Type: ''STRING''
** Device name: ''CMD_uid''
*** The _uid part is optional, it's for matching requests and responses. The uid is a unique string to identify the request, such as a counter or timestamp.)
** Content: ''Command'' XML element
*** ''Name'' attribute contains the command name
*** Any number of additional attributes and/or child elements to specify further parameters for the command can be added.
* Command response message:
** Type: ''STRING''
** Device name: ''ACK_uid''
*** uid matches the uid in the command message's device name
** Content: ''CommandReply'' XML element
*** ''Status'' attribute containing the status of the command; allowed values: ''SUCCESS'' or ''FAIL''
*** ''Message'' attribute containing a human-readable status of the command completion
*** Any number of additional attributes and/or child elements to specify further return values can be added.
** Example command and response content:
*** Command: <Command Name="SomeCommandName" SomeAttribute1="attribute value 1" SomeAttribute2="123" />
****'''Should we specify type of the attribute??'''
****'''Should we specify that this is a read/write request??'''
*** Response: <CommandReply Status="SUCCESS" SomeReturnValue1="123" SomeReturnValue1="abc" />

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-23T19:01:55Z

Nirav:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* [[User:Gfischer|Greg Fischer (WPI)]]
* [[User:Nirav|Nirav Patel (WPI)]]
* [[User:Tokuda|Junichi Tokuda (BWH/SPL)]]
* [[User:Lasso|Andras Lasso (PerkLab, Queen's)]]

==Project Description==
<div style="margin: 20px;">
* This Project is to further develop a workflow and communication protocol for interfacing robots with image-guided therapy systems using OpenIGTLink.
* Also, we would like to enhance JAVA implementation of IGTLink and support more message types.
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Some of the supported standard messages in OpenIGTLink for JAVA are Position, Status, String and Transform. During this week we would like to add support for other message types like NDArray, Sensor and any other useful messages for controlling the robot using IGTLink.
* Also, would like to collaborate with team working on MATLAB interface for IGTLink and test it with JAVA implementation.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Taking BRP Robot Application as base and extending it for any other robot applications.
* Testing it for MATLAB and standard C++ implementation.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* We have tested IGTLink communication with the clinical workflow described at http://www.na-mic.org/Wiki/index.php/ProstateBRP_OpenIGTLink_Communication_June_2013 which was implemented during 2013 Summer Project Week.
* NDArray is being implemented but not yet tested.
* Sensor message yet to be implemented.
</div>
</div>

<h2>OpenIGTLink XML command specification</h2>
* Command message:
** Type: ''STRING''
** Device name: ''CMD_uid''
*** The _uid part is optional, it's for matching requests and responses. The uid is a unique string to identify the request, such as a counter or timestamp.)
** Content: ''Command'' XML element
*** ''Name'' attribute contains the command name
*** Any number of additional attributes and/or child elements to specify further parameters for the command can be added.
* Command response message:
** Type: ''STRING''
** Device name: ''ACK_uid''
*** uid matches the uid in the command message's device name
** Content: ''CommandReply'' XML element
*** ''Status'' attribute containing the status of the command; allowed values: ''SUCCESS'' or ''FAIL''
*** ''Message'' attribute containing a human-readable status of the command completion
*** Any number of additional attributes and/or child elements to specify further return values can be added.
** Example command and response content:
*** Command: <Command Name="SomeCommandName" SomeAttribute1="attribute value 1" SomeAttribute2="123" />
****'''Should we specify type of the attribute??'''

*** Response: <CommandReply Status="SUCCESS" SomeReturnValue1="123" SomeReturnValue1="abc" />
**** '''How to associate requested and returned values???'''

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-23T16:06:26Z

Nirav:

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-23T14:22:57Z

Nirav:

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-23T14:22:24Z

Nirav:

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-23T14:14:39Z

Nirav:

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-23T12:36:30Z

Nirav:

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-23T12:35:21Z

Nirav:

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-23T04:46:13Z

Nirav:

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-23T04:20:17Z

Nirav:

2014 Summer Project Week/RoomSharing

2014-06-20T19:44:06Z

Nirav:

Please put your name here if you are interested in a room share.

* Jean-Christophe Fillion-Robin ( jchris.fillionr@kitware.com ): Double room booked at Residence Inn Boston Cambridge
** Address: Six Cambridge Center, 120 Broadway Cambridge
** [http://www.marriott.com/hotels/fact-sheet/travel/boscm-residence-inn-boston-cambridge/ hotel]
** [https://www.google.com/maps/place/Residence+Inn+Boston+Cambridge/@42.363858,-71.088143,17z/data=!3m1!4b1!4m2!3m1!1s0x89e370af1cc250e7:0xef4a28b1b62d1d38 map]
** When: From Monday to Friday
** Status: Available

If any one is willing to share a room please email accoringinly.

User:Nirav

2014-06-20T16:03:09Z

Nirav:

==Personal Website==
*Please see: http://aimlab.wpi.edu/people/Nirav_Patel

==Contact==
*Email: napatel@wpi.edu
*Address: AIMLab, WPI, 100 Institute Road, Higgins Lab, Rm 045, Worcester, MA 01609

User:Nirav

2014-06-20T16:01:42Z

Nirav: Created page with 'Please see: http://aimlab.wpi.edu/people/Nirav_Patel [edit]Contact Email: napatel@wpi.edu Address: AIMLab, WPI, 100 Institute Road, Higgins Lab, Rm 045, Worcester, MA 01609'

Please see: http://aimlab.wpi.edu/people/Nirav_Patel

[edit]Contact

Email: napatel@wpi.edu
Address: AIMLab, WPI, 100 Institute Road, Higgins Lab, Rm 045, Worcester, MA 01609

2014 Summer Project Week:Robot Control With OpenIGTLink

2014-06-18T21:36:21Z

Nirav:

2014 Summer Project Week/RoomSharing

2014-06-15T02:56:07Z

Nirav:

Please put your name here if you are interested in a room share.

* Nirav Patel( napatel@wpi.edu ) : I have a double room booked at Midtown Hotel( Address : 220 Huntington Ave., 02115, Boston ), if any one is willing to share the room please email me.

2014 Summer Project Week

2014-06-11T23:52:31Z

Nirav:

__NOTOC__

[[image:PW-MIT2014.png|300px]]

Dates: June 23-27, 2014.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 23
!style="width:18%" |Tuesday, June 24
!style="width:18%" |Wednesday, June 25
!style="width:18%" |Thursday, June 26
!style="width:18%" |Friday, June 27
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT 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'''
|
|'''10-11:30pm''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: DICOM|DICOM]] (Steve Pieper)
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|
|
'''9:00-10:30am''' [[2014_Tutorial_Contest|Tutorial Contest Presentations (Sonia Pujol)]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Neuro|Image-Guided Therapy - Neurosurgery]] (Alexandra Golby, Tina Kapur) <br>
[[MIT_Project_Week_Rooms#Star|Star]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
'''12pm''' [[Events:TutorialContestJune2014|Tutorial Contest Winner Announcement]]
[[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''' [[2014 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:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: QIICR|QIICR]] (Andrey Fedorov)
[[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-2:30pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: Contours|Contours]] (Adam Rankin, Csaba Pinter)
TBD [[MIT_Project_Week_Rooms#Kiva|Kiva]]
|'''1-3pm:''' <font color="#503020">Breakout Session:'''</font><br>[[2014 Project Week Breakout Session: IGT Prostate|Image-Guided Therapy - Prostate Interventions]] (Clare Tempany, Noby Hata)
<br>----------------------------------------<br>
|
|-
|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
|
|}

== '''Background''' ==

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all NA-MIC members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. 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 NA-MIC coverage for all. Subsequent teleconferences 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 are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

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

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

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==TBI==

==Atrial Fibrillation==

==Huntington's Disease==

==Head and Neck Cancer==
*[[2014_Summer_Project_Week:Interactive_DIR| Interactive DIR]] (Greg, Ivan)
*[[2014_Summer_Project_Week:DIR_validation_tools| DIR validation tools]] (Greg, Ivan)
*[[2014_Summer_Project_Week:Upload_HN_data| Upload H&N data]] (Greg, Paolo)

==Slicer4 Extensions==

*[[2014_Summer_Project_Week:Multidim Data| Multidim Data]] (Kevin Wang, Andras, ?)
*[[2014_Summer_Project_Week:DICOM-SRO import| DICOM-SRO import]] (Kevin Wang)
*[[2014_Summer_Project_Week:PLM_engineering| Plastimatch extension re-engineering]] (Greg Sharp)

==Cardiac==

==Stroke==

==Brain Segmentation==

==Image-Guided Therapy==

* SlicerIGT extension: testing, tutorials, website (Tamas Ungi, Junichi Tokuda)
* Gestural Point of Care Interface for IGT (Saskia, Franklin, Tobias)
*[[2014_Summer_Project_Week:MR-Ultrasound_Registration_for_Prostate_Interventions | MR-Ultrasound Registration for Prostate Interventions]] (Chenxi Zhang, Andriy Fedorov, Andras)
*[[2014_Summer_Project_Week:Surface_approximation_from_contour_points | Surface approximation from contour points]] (Chenxi Zhang, Csaba Pinter, Andrey Fedorov)
* Steered image registration using intelligent interfaces for minimal user interaction (Marcel Prastawa, Jim Miller, Steve Pieper)
* Image To Mesh Conversion for Brain MRI (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov, Ron Kikinis, Nikos Chrisochoides)
* An ITK implementation of Physics-Based Non-Rigid Registration method for Brain Shift (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz, Ron Kikinis, Nikos Chrisochoides)

==Radiation Therapy==
*[[2014_Summer_Project_Week:External Beam Planning| External Beam Planning]] (Kevin Wang, Greg, ?)

==Chronic Obstructive Pulmonary Disease ==

==[http://qiicr.org QIICR]==
* Real world value mapping support (Andrey, Andras, Steve, Jim, ...)
* Segmentation object support (Andrey, Csaba, Steve, ...)
* [[2014_Summer_Project_Week: CLI Derived DICOM Data| Proper formatting of DICOM Derived Data from CLI]] (Steve, Andrey, Jim, {Michael and David remotely})

==Infrastructure==
*Slicer 4.4 Release (JC, Steve, Nicole)
* [[2014_Summer_Project_Week: Chronicle| Chronicle]] (Steve)
* [[2014_Summer_Project_Week: Volume Registration|Volume Registration]] (Steve, Greg, Marcel, Jim)
* [[2014_Summer_Project_Week:Markups | Markups]] (Nicole Aucoin)
*Pluggable Label Statistics (Andrey , Ethan, Steve, Brad?, Jim? Dirk?)
*[[2014_Summer_Project_Week:Subject_hierarchy_integration | Subject hierarchy integration]] (Csaba, Steve, Jc, Andras?, ?)
*[[2014_Summer_Project_Week:Contours | Contours]] (Adam Rankin, Csaba, Andras, Steve, Jc, ?)
*[[2014_Summer_Project_Week:Parameter Node Serialization | Parameter Node Serialization]] (Kevin Wang, Andras, Steve, Jim, Csaba, ?)
*[[2014_Summer_Project_Week:Self-tests for non-linear transforms | Self-tests for non-linear transforms]] (Xining Du)

==Feature Extraction==
*Breast Tumor Segmentation and Heterogeneity Analysis (Vivek Narayan, Jay Jagadeesan)
*Quantitative image feature extraction in Non-Small Cell Lung Cancer (Hugo Aerts)

==Other==
*[[2014_Summer_Project_Week:Slicer_Murin_Shape_Analysis | Shape Analysis for the developing murine skull]] (Murat Maga, Ryan Young, Seattle Chidren's Hospital).
*[[2014_Summer_Project_Week:Slicer_LDDMM_Shape_Analysis | Slicer Interface to LDDMM shape anlaysis]] (Saurabh Jain, JHU; Steve Pieper, Isomics; Josh Cates, SCI, Utah; Hans Johnson, Iowa; Martin Styner, UNC)
*[[2014_Summer_Project_Week:Image_Registration_with_Sliding_Motion_Constraints | Image Registration with Sliding Motion Constraints]] (Alexander Derksen, Kanglin Chen, Gregory Sharp, Danielle Pace?)
*[[2014_Summer_Project_Week:Atlas Selection | Atlas Selection]] (Kanglin Chen, Gregory Sharp)
*[[2014_Summer_Project_Week:Multiscale_Non_Local_Means_filter_(NLM)_for_chest_CT_images | Multiscale Non Local Means filter (NLM) for chest CT images]] (Pietro Nardelli, University College Cork (UCC), Ireland)
*Robot Control using OpenIGTLink ( Gregory Fischer(WPI), Nirav Patel(WPI), Junichi Tokuda(BWH))
== '''Logistics''' ==

*'''Dates:''' June 23-27, 2014.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' https://www.regonline.com/namic2014summerprojectweek. 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: [[2014_Summer_Project_Week/RoomSharing|here]]

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([https://www.regonline.com/namic2014summerprojectweek Please click here to register.])

#Hugo Aerts, Dana Farber/Harvard, hugo_aerts@dfci.harvard.edu
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, Brigham & Women's Hospital, nicole@bwh.harvard.edu
#Kanglin Chen, Fraunhofer MEVIS, kanglin.chen@mevis.fraunhofer.de
#Adrian Dalca, MIT CSAIL, adalca@mit.edu
#Alexander Derksen, Fraunhofer MEVIS, alexander.derksen@mevis.fraunhofer.de
#Fotis Drakopoulos, Old Dominion University, fdrakopo@gmail.com
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Saurabh Jain, Johns Hopkins University, saurabh@cis.jhu.edu
#Hans Johnson, University of Iowa, hans-johnson@uiowa.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Yangming Li, University of Washington, ymli81@uw.edu
#Siqi Liu, University of Sydney, sliu4512@uni.sydney.edu.au
#Bradley Lowekamp, National Institutes of Health, blowekamp@mail.nih.gov
#Murat Maga, Seattle Children's Research Institute, maga@uw.edu
#Katie Mastrogiacomo, SPL/BWH, kmast@bwh.harvard.edu
#Alireza Mehrtash, SPL/BWH, mehrtash@bwh.harvard.edu
#Jim Miller, GE Research, millerjv@ge.com
#Pietro Nardelli, University College Cork, pietro@bwh.harvard.edu
#Yangming Ou, MGH, yangming.ou@uphs.upenn.edu
#Nirav Patel, WPI, napatel@wpi.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's University, csaba.pinter@queensu.ca
#Marcel Prastawa, GE Research, marcel.prastawa@ge.com
#Somia Pujol, Harvard Medical School, spujol@bwh.harvard.edu
#Adam Rankin, Queen's University, rankin@queensu.ca
#Ramesh Sridharan, MIT CSAIL, rameshvs@csail.mit.edu
#Ethan Ulrich, University of Iowa, ethan-ulrich@uiowa.edu
#David Welch, University of Iowa, david-welch@uiowa.edu
#Ryan Young, Seattle Children's Research Institute, ryan.young@seattlechildrens.org
#Paolo Zaffino, University Magna Graecia of Catanzaro, p.zaffino@unicz.it
#Chenxi Zhang, Brigham & Women's Hospital, chenxizhang@fudan.edu.cn
#Fan Zhang, University of Sydney, fzha8048@uni.sydney.edu.au

2014 Summer Project Week/RoomSharing

2014-06-09T20:14:13Z

Nirav:

Please put your name here if you are interested in a room share.

Nirav Patel: napatel@wpi.edu