NAMIC Wiki - User contributions [en]

2010 Winter Project Week Fast Imaging Library + Siemens EPI

2010-01-08T01:04:36Z

Shoge: /* Progress */

==Key Investigators==
* BWH: Scott Hoge
* Utah: Nick Todd, Dennis Parker

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

<h3>Objective</h3>
Incorporate improved EPI Nyquist ghost correction techniques and on-line parallel imaging reconstruction modules into the multi-shot EPI sequence used by the HiFU project at Utah.
</div>

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

<h3>Approach, Plan</h3>

Our plan for the project week is to ...
* modify the multi-shot EPI sequence to include temporal encoding
* integrate fast imaging library calls into ICE image reconstruction chain

</div>

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

<h3>Progress</h3>

* Temporal encoding of single-shot EPI complete. extending to segmented EPI sequence.
* Functor created to reconstruct acquired data in Siemens ICE framework
* Modified Functor Makefiles to link in NCIGT Fast Imaging Library

</div>
</div>

<div style="width: 97%; float: left;">

==Progress==

* On Acquisition
** Single-shot EPI pulse sequence modified to include temporal encoding.
** Data acquired on Siemens machine
** Images reconstructed using EPI-GESTE show very low Nyquist ghosts, much lower than the product reconstruction code
[[Image:Hoge_ngc_igtpw_1.jpg]]
** Double-shot EPI pulse sequence modified to include temporal encoding
** PLACE method to remove ghosts works (but with loss of temporal resolution), EPI-GESTE still needs some work.

* On Reconstruction
** EPI-GESTE Functor defined for Siemens ICE processing chain
** NCIGT Fast Imaging library linked into functor
** currently debugging the functor

==Background==

* We have a new method for self-referenced EPI ghost correction (EPI-GESTE)
* Goal for the week: implement on Siemens, both pulse sequence changes and on-line recon
** temporal encoding of EPI data acquisition
** application of parallel imaging algorithms
[[Image:hoge_ngc_igtpw_0.png]]

==References==
* [http://www.ncigt.org/pages/Research_Projects/ImagingCoreToolbox/Imaging_Toolkit Fast Imaging Library]
*
</div>

File:Hoge ngc igtpw 1.jpg

2010-01-08T00:59:55Z

Shoge:

2010 Winter Project Week Fast Imaging Library + Siemens EPI

2010-01-08T00:59:36Z

Shoge: /* Background */

==Key Investigators==
* BWH: Scott Hoge
* Utah: Nick Todd, Dennis Parker

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

<h3>Objective</h3>
Incorporate improved EPI Nyquist ghost correction techniques and on-line parallel imaging reconstruction modules into the multi-shot EPI sequence used by the HiFU project at Utah.
</div>

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

<h3>Approach, Plan</h3>

Our plan for the project week is to ...
* modify the multi-shot EPI sequence to include temporal encoding
* integrate fast imaging library calls into ICE image reconstruction chain

</div>

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

<h3>Progress</h3>

* Temporal encoding of single-shot EPI complete. extending to segmented EPI sequence.
* Functor created to reconstruct acquired data in Siemens ICE framework
* Modified Functor Makefiles to link in NCIGT Fast Imaging Library

</div>
</div>

<div style="width: 97%; float: left;">

==Progress==

[[Image:Hoge_ngc_igtpw_1.jpg]]

==Background==

* We have a new method for self-referenced EPI ghost correction (EPI-GESTE)
* Goal for the week: implement on Siemens, both pulse sequence changes and on-line recon
** temporal encoding of EPI data acquisition
** application of parallel imaging algorithms
[[Image:hoge_ngc_igtpw_0.png]]

==References==
* [http://www.ncigt.org/pages/Research_Projects/ImagingCoreToolbox/Imaging_Toolkit Fast Imaging Library]
*
</div>

2010 Winter Project Week Fast Imaging Library + Siemens EPI

2010-01-06T23:33:59Z

Shoge: /* Key Investigators */

2010 Winter Project Week Fast Imaging Library + Siemens EPI

2010-01-06T23:33:41Z

Shoge: /* Key Investigators */

2010 Winter Project Week Fast Imaging Library + Siemens EPI

2010-01-06T18:49:35Z

Shoge: /* Key Investigators */

File:Hoge ngc igtpw 0.png

2010-01-06T18:47:15Z

Shoge: uploaded a new version of "File:Hoge ngc igtpw 0.png"

2010 Winter Project Week Fast Imaging Library + Siemens EPI

2010-01-04T21:32:50Z

Shoge: /* Background */

2010 Winter Project Week Fast Imaging Library + Siemens EPI

2010-01-04T21:26:06Z

Shoge: /* Background */

2010 Winter Project Week Fast Imaging Library + Siemens EPI

2010-01-04T21:23:58Z

Shoge: /* Background */

File:Hoge ngc igtpw 0.png

2010-01-04T21:23:21Z

Shoge:

2010 Winter Project Week Fast Imaging Library + Siemens EPI

2010-01-04T21:22:50Z

Shoge: /* References */

2010 Winter Project Week

2009-11-19T20:57:27Z

Shoge: /* IGT */

Back to [[Project Events]], [[AHM_2010]], [[Events]]

__NOTOC__

==Background==

From January 4-8, 2010, the tenth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience applications will be hosted in Salt Lake City, Utah. Participant engange in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

== Dates.Venue.Registration ==

Please [[AHM_2010#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2010#Agenda|click here for the agenda for AHM 2010 and Project Week]].

==Projects==

=== Segmentation ===

=== Registration ===
*[[2010_Winter_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library Project]] (Dominik Meier, Casey Goodlett, Ron Kikinis)

=== IGT ===
* [[2010_Winter_Project_Week_Fast_Imaging_Library_%2B_Siemens_EPI]] (Scott Hoge, Nick Todd, Dennis Parker)

=== Radiotherapy ===

=== Analysis ===

=== Informatics ===

=== Diffusion ===

=== Python ===

=== NA-MIC Kit Internals ===
#Testing for Extensions (Steve, Andre, Jim, Julien Jomier)

=== Execution Model ===

=== Preparation ===

# 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]
# Starting Thursday, October 15th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 15: Engineering Infrastructure Projects
#*October 22: Funded External Collaboration Projects
#*October 29: Funded External Collaboration Projects
#*November 5: DPB Projects
#*November 19: DPB Projects
#*December 3: Other/new collaborations
#*December 10: Finalize Engineering Projects
#*December 17: Loose Ends
#By December 17, 2010: [[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 December 17, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## 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. the BIRN). 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.)
## 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. (Zack)
# 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...

2010 Winter Project Week

2009-11-19T20:57:06Z

Shoge: /* IGT */

Back to [[Project Events]], [[AHM_2010]], [[Events]]

__NOTOC__

==Background==

From January 4-8, 2010, the tenth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience applications will be hosted in Salt Lake City, Utah. Participant engange in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([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], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

== Dates.Venue.Registration ==

Please [[AHM_2010#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2010#Agenda|click here for the agenda for AHM 2010 and Project Week]].

==Projects==

=== Segmentation ===

=== Registration ===
*[[2010_Winter_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library Project]] (Dominik Meier, Casey Goodlett, Ron Kikinis)

=== IGT ===
* [[2010_Winter_Project_Week_Fast_Imaging_Library_%2B_Siemens_EPI]]

=== Radiotherapy ===

=== Analysis ===

=== Informatics ===

=== Diffusion ===

=== Python ===

=== NA-MIC Kit Internals ===
#Testing for Extensions (Steve, Andre, Jim, Julien Jomier)

=== Execution Model ===

=== Preparation ===

# 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]
# Starting Thursday, October 15th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 15: Engineering Infrastructure Projects
#*October 22: Funded External Collaboration Projects
#*October 29: Funded External Collaboration Projects
#*November 5: DPB Projects
#*November 19: DPB Projects
#*December 3: Other/new collaborations
#*December 10: Finalize Engineering Projects
#*December 17: Loose Ends
#By December 17, 2010: [[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 December 17, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## 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. the BIRN). 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.)
## 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. (Zack)
# 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...

2010 Winter Project Week Fast Imaging Library + Siemens EPI

2009-11-19T20:56:16Z

Shoge: Created page with '==Key Investigators== * BWH: Scott Hoge * Utah: Nick Todd, Dennis Parker <div style="margin: 20px;"> <div style="width: 27%; float: left; padding-right: 3%;"> <h3>Objective</h3…'

2009 Summer Project Week 3DGRASE

2009-06-26T13:14:11Z

Shoge:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project List]]
</gallery>

==Key Investigators==
* BWH: Scott Hoge
* WFU: Bob Kraft, Huan Tan
* Mediri: Mattias Guenther

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

<h3>Objective</h3>

The objective of this project is to port Dr Guenther's 3D GRASE pulse
sequence for perfusion imaging to the GE 3T scanner. Once ported, we
will seek to integrate the pulse sequence with image reconstruction
routines from the NCIGT fast imaging library.

</div>

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

<h3>Approach, Plan</h3>

Our goals for the project week are:

1. Complete development of GE EPIC version of 3D GRASE

2. Perform and evaluate performance on 3T short bore

</div>

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

<h3>Progress</h3>

3D GRASE ported to GE scanner platform, and integrated with PROPELLER EPI with NCIGT fast imaging library used for parallel imaging stage of Nyquist ghost correction step.

Prior to IGT Week:
* Perfusion ASL using PROPELLER EPI at WFU gave 5 slices, 128x128 image size, 8mm through plane resolution, with 2mm gap in roughly 6 minutes

After IGT Week:
* 3D GRASE PROPELLER PASL gives 16 slices, 128x128 image size, 5 mm through plane, with no gap, in around a 3 min scan.

</div>
</div>

[[File:2009_Summer_Project_Week_3DGRASE_img1.png]]

[[File:2009_Summer_Project_Week_3DGRASE_img2.png]]

<div style="width: 970%; float: left;">

==References==

# Matthias Gunther, Koichi Oshio, and David A Feinberg. Single-shot 3D imaging techniques improve arterial spin labeling perfusion measurements. Magn Reson Med, 54(2):491-8, 2005. [[http://dx.doi.org/10.1002/mrm.20580|DOI]]
# James G. Pipe. Motion correction with PROPELLER MRI: Application to head motion and free-breathing cardiac imaging. 42(5):963-969, 1999.
</div>

2009 Summer Project Week 3DGRASE

2009-06-26T13:08:57Z

Shoge: /* Key Investigators */

File:2009 Summer Project Week 3DGRASE img2.png

2009-06-26T13:08:34Z

Shoge:

File:2009 Summer Project Week 3DGRASE img1.png

2009-06-26T13:07:53Z

Shoge:

2009 Summer Project Week 3DGRASE

2009-06-26T13:07:28Z

Shoge: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project List]]
</gallery>

==Key Investigators==
* BWH: Scott Hoge
* WFU: Bob Kraft, Huan Tan
* Mediri: Mattias Guenther

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

<h3>Objective</h3>

The objective of this project is to port Dr Guenther's 3D GRASE pulse
sequence for perfusion imaging to the GE 3T scanner. Once ported, we
will seek to integrate the pulse sequence with image reconstruction
routines from the NCIGT fast imaging library.

</div>

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

<h3>Approach, Plan</h3>

Our goals for the project week are:

1. Complete development of GE EPIC version of 3D GRASE

2. Perform and evaluate performance on 3T short bore

</div>

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

<h3>Progress</h3>

3D GRASE ported to GE scanner platform, and integrated with PROPELLER EPI with NCIGT fast imaging library used for parallel imaging stage of Nyquist ghost correction step.

Prior to IGT Week:
* Perfusion ASL using PROPELLER EPI at WFU gave 5 slices, 128x128 image size, 8mm through plane resolution, with 2mm gap in roughly 6 minutes

After IGT Week:
* 3D GRASE PROPELLER PASL gives 16 slices, 128x128 image size, 5 mm through plane, with no gap, in around a 3 min scan.

</div>
</div>

[[Media:2009_Summer_Project_Week_3DGRASE_img1.png]]

[[Media:2009_Summer_Project_Week_3DGRASE_img2.png]]

<div style="width: 970%; float: left;">

==References==
</div>

2009 Summer Project Week 3DGRASE

2009-06-26T13:07:08Z

Shoge: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project List]]
</gallery>

==Key Investigators==
* BWH: Scott Hoge
* WFU: Bob Kraft, Huan Tan
* Mediri: Mattias Guenther

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

<h3>Objective</h3>

The objective of this project is to port Dr Guenther's 3D GRASE pulse
sequence for perfusion imaging to the GE 3T scanner. Once ported, we
will seek to integrate the pulse sequence with image reconstruction
routines from the NCIGT fast imaging library.

</div>

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

<h3>Approach, Plan</h3>

Our goals for the project week are:

1. Complete development of GE EPIC version of 3D GRASE

2. Perform and evaluate performance on 3T short bore

</div>

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

<h3>Progress</h3>

3D GRASE ported to GE scanner platform, and integrated with PROPELLER EPI with NCIGT fast imaging library used for parallel imaging stage of Nyquist ghost correction step.

Prior to IGT Week:
* Perfusion ASL using PROPELLER EPI at WFU gave 5 slices, 128x128 image size, 8mm through plane resolution, with 2mm gap in roughly 6 minutes

After IGT Week:
* 3D GRASE PROPELLER PASL gives 16 slices, 128x128 image size, 5 mm through plane, with no gap, in around a 3 min scan.

</div>
</div>

[[Media:2009_Summer_Project_Week_3DGRASE_img1.png]]

[[Media:2009_Summer_Project_Week_3DGRASE_img1.png]]

<div style="width: 970%; float: left;">

==References==
</div>

2009 Summer Project Week 3DGRASE

2009-06-25T20:33:54Z

Shoge: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project List]]
</gallery>

==Key Investigators==
* BWH: Scott Hoge
* WFU: Bob Kraft, Huan Tan
* Mediri: Mattias Guenther

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

<h3>Objective</h3>

The objective of this project is to port Dr Guenther's 3D GRASE pulse
sequence for perfusion imaging to the GE 3T scanner. Once ported, we
will seek to integrate the pulse sequence with image reconstruction
routines from the NCIGT fast imaging library.

</div>

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

<h3>Approach, Plan</h3>

Our goals for the project week are:

1. Complete development of GE EPIC version of 3D GRASE

2. Perform and evaluate performance on 3T short bore

</div>

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

<h3>Progress</h3>

3D GRASE ported to GE scanner platform, and integrated with PROPELLER EPI with NCIGT fast imaging library used for parallel imaging stage of Nyquist ghost correction step.

Prior to IGT Week:
* Perfusion ASL using PROPELLER EPI at WFU gave 5 slices, 128x128 image size, 8mm through plane resolution, with 2mm gap in roughly 6 minutes

After IGT Week:
* 3D GRASE PROPELLER PASL gives 16 slices, 128x128 image size, 5 mm through plane, with no gap, in around a 3 min scan.

</div>
</div>

<div style="width: 970%; float: left;">

==References==
</div>

File:2009 NA-MIC Project Week FastImagingLibrary.ppt

2009-06-22T21:12:43Z

Shoge:

2009 Summer Project Week

2009-06-22T21:10:44Z

Shoge: /* Tuesday */

Back to [[Project Events]], [[Events]]

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-D451 (Stata)
** Mon, noon - end
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Mon, noon-end
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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.

Active preparation begins on Thursday, April 16th 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 30-50 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], and [http://www.cimit.org CIMIT]. 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 that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
Breakout Rooms: 32-D451, 38-413

=== Monday===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
=== Tuesday ===
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper) ([[media:2009 NA-MIC Project Week Slicer3.4.ppt|Slides]], [[2009_Summer_Project_Week_Extension_Manager|Project Page]])
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge [ [[Media:2009_NA-MIC_Project_Week_FastImagingLibrary.ppt|slides]] ])
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W) (32-D451)
** noon lunch
** 2:00pm-3.00pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis) (In Griers)
** 4:30pm [http://www.cimit.org/forum-current.html CIMIT Forum (At BWH / Carl J. and Ruth Shapiro Cardiovascular Center) Open Source Software for Translational IGT Research and Commercial Use, Clif Burdette, Acoustic MedSystems, Inc. ]
** 5:30pm adjourn for day

=== Wednesday ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] ((Alexandre Gouaillard)(32-D451)
** 5:30pm adjourn for day
=== Thursday===
** 8:30am breakfast
** 9-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (Dan M.)
** 5:30pm adjourn for day
=== Friday===
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]

==Projects==

=== Segmentation ===

#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation|Lupus Lesion Segmentation]] (Mark Scully MRN)
#[[2009_Summer_Project_Week_WML_SEgmentation|White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week_Skull_Stripping|Skull Stripping]] (Snehasish Roy JHU)
#[[EMSegment|EM Segment]] (Sylvain Jaume MIT, Nicolas Rannou BWH)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation|FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_New_ITK_Level_Set_Framework|New Level Set Framework in ITK]] (Arnaud Gelas, Harvard Medical School)
#[[2009_Summer_Project_Week_TubularSurfaceSeg|Tubular Surface Segmentation in Slicer]] (Vandana Mohan, Georgia Tech)
#[[Summer2009:The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images|Segmentation of Knee Structures]] (Harish Doddi Stanford)
#[[2009 Summer Project Week Quantify VMTK seg error|Quantifying VMTK User Segmentation Error]] (Dave Welch UIowa)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Atrium_wall|Atrium Wall Segmentation]] (Behnood Gholami Georgia Tech)

=== Registration ===

#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration|Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
#[[BSpline Registration in Slicer3|BSpline Registration in Slicer3]] (Samuel Gerber Utah)
#[[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
#[[2009_Summer_project_week_prostate_registration|Prostate Registration Slicer Module]] (Yi Gao, Georgia Tech)
#[[2009_Summer_Project_Week_Slicer3_registration|Slicer 3 registration ]] (Andrew Rausch BWH PNL)
#[[EPI Correction in Slicer3|EPI Correction in Slicer3]] (Ran Tao Utah)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
#[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI)
#[[2009_Summer_Project_Week_HAMMER_Registration|HAMMER Registration]] (Guorong Wu UNC)
#[[2009_Summer_Project_Week_MCMC_Cuda_Registration|Elastic Non-Rigid Registration using MCMC and CUDA]] (Petter Risholm BWH)
#[[2009_Summer_Project_Week_Cardiac_Blood_Pool_Registration|Cardiac Blood Pool Registration]] (Michal Depa MIT)

=== IGT ===

#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)
#[[2009_Summer_Project_Week_Prostate_Robotics|Prostate Robotics]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|Demo of Neuronavigation using Brainlab, Slicer3, BioImage Suite]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)
#[[2009_Summer_Project_Week_RTHawk_MR_Navigation|Using RTHawk to Implement MR Navigation]] (Ben Schwartz BWH)
#[[2009_Summer_Project_Week_Slicer|Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer]] (Jayender Jagadeesan BWH)
#[[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
#[[Enhanced Neurosuregery navigation]] (Haytham Elhawary, Brigham and Women's Hospital)
#[[GPU accelerated FEM for simulation and segmentation]] (Megumi Nakao, Brigham and Women's Hospital)
#[[Liver EM segmentation]] (Padma Akella, Brigham and Women's Hlspital)
#[[MRI-Guided Robot-assisted Deep Brain Stimulation Electrode PLacement]] (Greg Fischer, WPI)

=== Radiotherapy ===

#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
#[[2009_Summer_Project_Week_Adaptive_RT|Adaptive Radiotherapy for Head,Neck, and Thorax]] (Ivan Kolesov GATech)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](James Balter U Michigan)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
#[[2009_Summer_project_week_adaptive_radiation_planning_visualization]](Cal Hisley, Des Moines University/Mercy Des Moines Medical Center)

=== Analysis ===

#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Linking atlas data with ontologies of brain morphology and function]] (Michael Halle BWH)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
#[[2009_Summer_Project_Week_4D_Imaging|4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer|Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
#[[2009_Summer_Project_Week_Statistical_Toolbox|multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)

=== Informatics ===

#[[2009_Summer_Project_Week_Slicer3_XNAT_UI|XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNATFS|XNAT File System with FUSE]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
#[[2009_Summer_Project_Week_GWE_XNAT|GWE-XNAT Integration]] (Marco Ruiz UCSD)
#[[2009_Summer_Project_Week_GWE_Results_Browser|GWE Results Browser Improvements]] (Marco Ruiz UCSD)
#[[Projects:ShapeCorrespondence_UNCOrthoApp|XNAT & Ortho App]] (Beatriz Paniagua UNC)

=== Diffusion ===

#[[Summer2009:VCFS|Stochastic Tractography to study VCFS and Schizophrenia]] (Sylvain Bouix BWH)
#[[2009_Summer_Project_Week_FunctionalClusteringAnalysis|Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients]] (Doug Terry BWH)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep|DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom|DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_FMTractography|Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)

=== Python ===

#[[Summer2009:Using_ITK_in_python|Using ITK in python]] (Steve Pieper BWH)
#[[Summer2009:Using_cython|Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
#[[Summer2009:Implementing_parallelism_in_python|Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
#[[Summer2009:Using_client_server_paradigm_with_python_and_slicer|Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)

=== Slicer Internals ===

#[[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Colors_Module|Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Orthogonal_Reformat_Widget|Orthogonal Planes in Reformat Widget]] (Michal Depa MIT)
#[[Slicer3 Informatics Workflow Design & XNAT updates|Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
#[[Slicer3_FlexibleLayouts | Slicer3 Flexible Layouts]] (Wendy Plesniak BWH)
#[[2009_Summer_Project_Week_Extension_Manager|Slicer3 Extension Manager]] (Katie Hayes BWH)
#[[MeshingSummer2009|IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)

=== Execution Model ===

#[[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
#[[Summer2009:Extension of the Command Line XML Syntax/Interface|Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[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 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## 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. the BIRN). 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.)
## 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. (Zack)
# 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.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-D451 (Stata)
** Mon, noon - end
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Mon, noon-end
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Attendee List==

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''
{|
|-
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{|class="wikitable"
!Number
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|
{| class="wikitable sortable"
!First
!Last
!Affiliation
|- style=&#34height:50px&#34
|John
|Melonakos
|AccelerEyes (Wed & Thu morning)
|- style=&#34height:50px&#34
|Jack
|Blevins
|Acoustic Med
|- style=&#34height:50px&#34
|Clif
|Burdette
|Acoustic Med (Mon-Wed)
|- style=&#34height:50px&#34
|Dana
|Peters
|Beth Israel Deaconess
|- style=&#34height:50px&#34
|Nicole
|Aucoin
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Giovanna
|Danagoulian
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haytham
|Elhawary
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Andriy
|Fedorov
|BWH (NAMIC Collaborator)
|- style=&#34height:50px&#34
|Daniel
|Haehn
|BWH (NAC)
|- style=&#34height:50px&#34
|Michael
|Halle
|BWH (NAC)
|- style=&#34height:50px&#34
|Nobuhiko
|Hata
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Katie
|Hayes
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Scott
|Hoge
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Tina
|Kapur
|BWH (NCIGT, NAMIC)
|- style=&#34height:50px&#34
|Ron
|Kikinis
|BWH (NAMIC, NAC, NCIGT)
|- style=&#34height:50px&#34
|Jayender
|Jagadeesan
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haying
|Liu
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Lauren
|O'Donnell
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Wendy
|Plesniak
|BWH (NAC)
|- style=&#34height:50px&#34
|Megumi
|Nakao
|BWH (NAIST)
|- style=&#34height:50px&#34
|Sonia
|Pujol
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Lei
|Qin
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Nicolas
|Rannou
|BWH (NAC)
|- style=&#34height:50px&#34
|Petter
|Risholm
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Florin
|Talos
|BWH (NAC)
|- style=&#34height:50px&#34
|Clare
|Tempany
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Junichi
|Tokuda
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Demian
|Wasserman
|BWH (INRIA)
|- style=&#34height:50px&#34
|Carl-Fredrik
|Westin
|BWH (NAC)
|- style=&#34height:50px&#34
|Sandy
|Wells
|BWH (NAC, NCIGT)
|- style=&#34height:50px&#34
|Lilla
|Zollei
|MGH (NAC)
|- style=&#34height:50px&#34
|Padma
|Akella
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Sylvain
|Bouix
|BWH (PNL)
|- style=&#34height:50px&#34
|Julien
|de Siebenthal
|BWH (PNL)
|- style=&#34height:50px&#34
|Marek
|Kubicki
|BWH (NAMIC DBP PNL)
|- style=&#34height:50px&#34
|Juhana
|Frosen
|BWH Tues only
|- style=&#34height:50px&#34
|Sun Woo
|Lee
|BWH (PNL)
|- style=&#34height:50px&#34
|Jimi
|Malcolm
|BWH (PNL)
|- style=&#34height:50px&#34
|Eric
|Melonakos
|BWH (PNL)
|- style=&#34height:50px&#34
|Yogesh
|Rathi
|BWH (PNL)
|- style=&#34height:50px&#34
|Peter
|Savadjiev
|BWH (PNL)
|- style=&#34height:50px&#34
|Doug
|Terry
|BWH (PNL)
|- style=&#34height:50px&#34
|Andrew
|Rausch
|BWH (Mon only)
|- style=&#34height:50px&#34
|Cal
|Hisley
|Des Moines Unive
|- style=&#34height:50px&#34
|Jim
|Miller
|GE
|- style=&#34height:50px&#34
|Xiaodong
|Tao
|GE
|- style=&#34height:50px&#34
|Vandana
|Mohan
|GA Tech
|- style=&#34height:50px&#34
|Yi
|Gao
|GA Tech
|- style=&#34height:50px&#34
|Ivan
|Kolosev
|GA Tech
|- style=&#34height:50px&#34
|Behnood
|Gholami
|GA Tech
|- style=&#34height:50px&#34
|Ziv
|Yaniv
|Georgetown
|- style=&#34height:50px&#34
|Alex
|Gouaillard
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Arnaud
|Gelas
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Sean
|Megason
|Harvard Systems Biology (Wed only)
|- style=&#34height:50px&#34
|Lydie
|Souhait
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Moti
|Freiman
|Hebrew University of Jerusalem
|- style=&#34height:50px&#34
|Amanda
|Peters
|Harvard SEAS
|- style=&#34height:50px&#34
|Maria Francesca
|Spadea
|Italy
|- style=&#34height:50px&#34
|Curtis
|Lisle
|KnowledgeVis
|- style=&#34height:50px&#34
|Steve
|Pieper
|Isomics
|- style=&#34height:50px&#34
|Alex
|Yarmarkovich
|Isomics
|- style=&#34height:50px&#34
|Nathan
|Cho
|JHU
|- style=&#34height:50px&#34
|Bennett
|Landman
|JHU
|- style=&#34height:50px&#34
|Snehashis
|Roy
|JHU
|- style=&#34height:50px&#34
|Sam
|Song
|JHU
|- style=&#34height:50px&#34
|Sebastien
|Barre
|Kitware
|- style=&#34height:50px&#34
|Luis
|Ibanez
|Kitware
|- style=&#34height:50px&#34
|Daniel
|Blezek
|Mayo
|- style=&#34height:50px&#34
|Yong
|Gao
|MGH
|- style=&#34height:50px&#34
|Randy
|Gollub
|MGH
|- style=&#34height:50px&#34
|Rui
|Li
|MGH
|- style=&#34height:50px&#34
|Greg
|Sharp
|MGH
|- style=&#34height:50px&#34
|Robert
|Yaffe
|MGH - Mon
|- style=&#34height:50px&#34
|Sylvain
|Jaume
|MIT
|- style=&#34height:50px&#34
|Bjoern
|Menze
|MIT
|- style=&#34height:50px&#34
|Jeremy
|Bockholt
|MRN (NAMIC Lupus DBP)
|- style=&#34height:50px&#34
|Mark
|Scully
|MRN (NAMIC Lupus DBP) Tue-Th
|- style=&#34height:50px&#34
|Joe
|Stam
|NVIDIA (Wed & Thurs)
|- style=&#34height:50px&#34
|Kimberly
|Powell
|NVIDIA (Wed)
|- style=&#34height:50px&#34
|Marta
|Peroni
|Politecnico di Milano
|- style=&#34height:50px&#34
|Andras
|Lasso
|Queen's (NAMIC DBP)
|- style=&#34height:50px&#34
|Yanling
|Liu
|SAIC/NCI-Frederick
|- style=&#34height:50px&#34
|Melanie
|Grebe
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Lining
|Yang
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Harish
|Doddi
|Stanford University
|- style=&#34height:50px&#34
|Marco
|Ruiz
|UCSD
|- style=&#34height:50px&#34
|Nathan
|Hageman
|UCLA (Mon-Thurs)
|- style=&#34height:50px&#34
|Hans
|Johnson
|U Iowa
|- style=&#34height:50px&#34
|Vincent
|Magnotta
|U Iowa
|- style=&#34height:50px&#34
|Jeffrey
|Yager
|U Iowa
|- style=&#34height:50px&#34
|Manasi
|Ramachandran
|U Iowa
|- style=&#34height:50px&#34
|Dave
|Welch
|U Iowa
|- style=&#34height:50px&#34
|Andrzej
|Przybyszewski
|UMass Med (Mon)
|- style=&#34height:50px&#34
|James
|Balter
|U Michigan
|- style=&#34height:50px&#34
|Dan
|McShan
|U Michigan
|- style=&#34height:50px&#34
|Zhou
|Shen
|U Michigan
|- style=&#34height:50px&#34
|Beatriz
|Paniagua
|UNC
|- style=&#34height:50px&#34
|Minjeong
|Kim
|UNC
|- style=&#34height:50px&#34
|Zhexing
|Liu
|UNC
|- style=&#34height:50px&#34
|Clement
|Vachet
|UNC (NAMIC DBP)
|- style=&#34height:50px&#34
|Guorong
|Wu
|UNC
|- style=&#34height:50px&#34
|Samuel
|Gerber
|SCI, Utah
|- style=&#34height:50px&#34
|Ran
|Tao
|SCI, Utah
|- style=&#34height:50px&#34
|Marcel
|Prastawa
|SCI, Utah
|- style=&#34height:50px&#34
|Ross
|Whitaker
|SCI, Utah
|- style=&#34height:50px&#34
|Curtis
|Rueden
|UW-Madison
|- style=&#34height:50px&#34
|Dan
|Marcus
|WUSTL
|- style=&#34height:50px&#34
|Misha
|Milchenko
|WUSTL
|- style=&#34height:50px&#34
|Kevin
|Archie
|WUSTL
|- style=&#34height:50px&#34
|Tim
|Olsen
|WUSTL
|- style=&#34height:50px&#34
|Mehdi
|Esteghamatian
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Diego
|Cantor
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Danielle
|Pace
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Vidya
|Rajagopalan
|VA Tech
|- style=&#34height:50px&#34
|Gregory
|Fischer
|WPI
|- style=&#34height:50px&#34
|Dominique
|Belhachemi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Alark
|Joshi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Xenios
|Papademetris
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Dustin
|Scheinost
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Michelle
|Borkin
|Harvard SEAS (Mon only)
|- style=&#34height:50px&#34
|Renxin
|Chu
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Ben
|Schwartz
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Marianna
|Jakab
|BWH (NCIGT, NAC) (Mon, Tue)
|- style=&#34height:50px&#34
|Viswanath
|Avasarala
|GE (Wed, Thurs)
|- style=&#34height:50px&#34
|}
|}

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''

The following was used to convert from excel to mediawiki markup: http://area23.brightbyte.de/csv2wp.php

2009 Summer Project Week 3DGRASE

2009-06-17T19:11:44Z

Shoge:

2009 Summer Project Week 3DGRASE

2009-06-11T15:33:22Z

Shoge: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page </gallery> ==Key Investigators== * BWH: Scott Hoge * WFU: Bob Kraft, Huan Tan * Medi...'

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Scott Hoge
* WFU: Bob Kraft, Huan Tan
* Mediri: Mattias Guenther

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

<h3>Objective</h3>

The objective of this project is to port Dr Guenther's 3D GRASE pulse
sequence for perfusion imaging to the GE 3T scanner.

</div>

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

<h3>Approach, Plan</h3>

Our goals for the project week are:

1. Complete development of GE EPIC version of 3D GRASE

2. Perform and evaluate performance on 3T short bore

</div>

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

<h3>Progress</h3>

</div>

<div style="width: 970%; float: left;">

</div>
</div>
==References==

2009 Summer Project Week

2009-06-11T15:27:25Z

Shoge:

Back to [[Project Events]], [[Events]]

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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.

Active preparation will begin on''' Thursday, April 16th 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 30-50 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], and [http://www.cimit.org CIMIT]. 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 that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (Dan M.)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]

== Projects ==

#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi Tokuda BWH)
# Need Lupus Project here
#[[Summer2009:VCFS| Pipeline development for VCFS]] (Marek Kubicki BWH)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]] (Saikat Pal Stanford)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Snehasish Roy JHU)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Segmentation of thalamic nuclei from DTI]] (Ion-Florin Talos BWH)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao Utah)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
# [[EMSegment|EM Segment]] (Sylvain Jaume BWH)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu UNC)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber Utah)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve Pieper BWH)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)
# [[Summer2009:Using_cython| Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
#[[2009_Summer_Project_Week_Slicer3_registration| Slicer 3 registration ]] (Andrew Rausch)
#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)

===CUDA Projects===

This is a list of candidate cuda projects that will be discussed with Joe Stam shortly:

#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins Acousticmed)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen U Michigan)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)
#acceleration of parallel real time processing of strain and elasticity images for monitoring of ablative therapy (Clif Burdette Acousticmed)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[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 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## 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. the BIRN). 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.)
## 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. (Zack)
# 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.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
#Clare Tempany, BWH (NCIGT)
#Tina Kapur, BWH (NA-MIC, NCIGT)
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Randy Gollub, MGH
#Nicole Aucoin, BWH (NA-MIC) (Attending Tuesday-Friday)
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH (NCIGT)
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc (Attending: Monday/Tuesday/Wednesday)
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH (NAC)
#Haiying Liu BWH (NCIGT)
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH (NA-MIC)
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH (NCIGT)
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH (NA-MIC)
#Sonia Pujol, BWH (NA-MIC)
#Andras Lasso, Queen's University
#Yong Gao, MGH
#Minjeong Kim, UNC-Chapel Hill
#Guorong Wu, UNC-Chapel Hill
#Jeffrey Yager, UIowa
#Yanling Liu, SAIC/NCI-Frederick
#Ziv Yaniv, Georgetown
#Bjoern Menze, MIT
#Vidya Rajagopalan, Virginia Tech
#Sandy Wells, BWH (NAC, NCIGT)
#Lilla Zollei, MGH (NAC)
#Lauren O'Donnell, BWH
#Florin Talos, BWH (NAC)
#Nobuhiko Hata, BWH (NCIGT)
#Alark Joshi, Yale
#Yogesh Rathi, BWH
#Jimi Malcolm, BWH
#Dustin Scheinost, Yale
#Dominique Belhachemi, Yale
#Sam Song, JHU
#Nathan Cho, JHU
#Julien de Siebenthal, BWH
#Peter Savadjiev, BWH
#Carl-Fredrik Westin, BWH
#John Melonakos, AccelerEyes (Wed & Thu morning)
#Yi Gao, Georgia Tech
#Sylvain Bouix, BWH
#Zhexing Liu, UNC-CH
#Eric Melonakos, BWH
#Lei Qin, BWH
#Giovanna Danagoulian, BWH
#Andrew Rausch, BWH (1st day only)
#Haytham Elhawary, BWH
#Jayender Jagadeesan, BWH
#Marek Kubicki, BWH
#Doug Terry, BWH
#Nathan Hageman, LONI (UCLA)
#Dana Peters, Beth Israel Deaconess
#Sun Woo Lee, BWH
# Melanie Grebe, Siemens Corporate Research
# Megumi Nakao, BWH/NAIST
# Moti Freiman, The Hebrew Univ. of Jerusalem
#Jack Blevins, Acoustic Med Systems
#Michael Halle, BWH
#Amanda Peters, Harvard SEAS
#Joe Stam, NVIDIA (Wednesday, Thursday)
#Petter Risholm, BWH (NCIGT)
#Kimberly Powell, NVIDIA (Wednesday)
#Padma Akella, BWH (NCIGT)
#Clif Burdette, Acousticmed (Mon, Tue, Wed)

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

2009 Summer Project Week

2009-04-30T20:20:14Z

Shoge:

Back to [[Project Events]], [[Events]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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.

Active preparation will begin on''' Thursday, April 16th 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 30-50 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], and [http://www.cimit.org CIMIT]. 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 that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]]
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 4D+T Microscopy Cell Dataset Segmentation]] (Alex G.)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11pm Tutorial Contest Presentations
** noon lunch
** 2:30pm: Breakout Session: TBD
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Tutorial Contest Winner Announcement and Project Progress using update [[#Projects|Project Wiki pages]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]

== Projects ==

The list of projects for this week will go here.

*Prostate Robotics (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
*4D Imaging - currently used for Lung Perfusion (Junichi, Dan Blezek?, Steve, Alex G?)
*Liver Ablation in Slicer (Haiying, Georgetown?)
*SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)
*Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
*gpu based registration acceleration (James Balter, Greg Sharp, Alark Joshi?, Aditya K., Yogesh Rathi?, Jimi Malcolm, Sandy Wells, Tina Kapur)
*Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
*Xnat user interface improvements for NA-MIC (Dan M, Tina, Florin, Ron, Wendy)
*xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
*Xnat user clinic - combine with data clinic
*xnat programmer clinic
*Grid Wizard+xnat clinic (Clement)
*?Fluid Mechanincs Module (Nathan Hageman)
*?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)
*Cortical Thickness Pipeline (Clement, Ipek)
*Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)

IGT Projects:
*port 4d gated ultrasound code to Slicer - (Danielle)
*integration of stereo video into Slicer (Mehdi)
*multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego, sylvain jaume, nicholas, noby)
*neuroendoscope workflow presentation (sebastien barre)
*slicer integration of mri compatible prostate biopsy robot(sid, queens)
*breakout session on Dynamic Patient Models (James Balter)
*gpu acceleration of 2d-3d registration (james balter, greg sharp, sandy wells, noby hata, terry peters proxy)

NA-MIC Engineering Projects
* DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
* Using ITK in python (Steve, Demian, Jim)
* VTK 3d Widgets in Slicer3 (Nicole, Will/Karthik)
* Update to Slicer3 Colors module (Nicole)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[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 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## 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. the BIRN). 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.)
## 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. (Zack)
# 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...

==Attendee List==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH
#Ferenc Jolesz, BWH
#Clare Tempany, BWH
#Tina Kapur, BWH
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Bill Lorensen, EAB
#Randy Gollub, MGH
#Nicole Aucoin, BWH
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc
#Vincent Magnotta, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH
#Haiying Liu BWH
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

2008 IGT Project Week Fast Imaging Library

2008-12-12T15:30:38Z

Shoge:

Back to [[2008_IGT_Project_Week#Projects]]

Team: Scott Hoge, Bob Kraft

Goals: Further integrate algorithms from the Fast Imaging Library (doc here: http://www.spl.harvard.edu/publications/item/view/1393) to enable interactive EPI measurements for perfusion, fMRI, and temperature monitoring using accelerated and efficient EPI-based MR acquisitions

Approach:
* complete a mechanism to maintain the phase in our pMRI-UNFOLD-EPI-PROPELLER acquisition technique, which is required for both temperature change estimation and EPI distortion correction
* incorporate real-time hooks into EPI sequence, to provide interactive acquisitions
* start investigations into radial EPI

Other Notes:

* This team will spend significant time on the MR scanner. Schedule here: http://calendar.yahoo.com/YYY,5107b4/srt,0/lmrc_ms_scanner/?v=2&t=1228608000

Results (to be completed and presented at the end of the week):
* extended accelerate short axis propeller epi to use partial Fourier
** issues w/ recon pending due to susceptibility distortion from blade to blade
* implemented both double-sampled and 'racetrack' trajectory in epi psd, to collect self-ref data for b0 field map estimation
** able to calculate relative phase changes using racetrack reference data
** may be incompatible with unfold nyquist ghost removal method
* wfu epi psd updated to 3d
* modified fgre to use modular rthawk implementation
* rt epi not accomplished, due to difficulty getting rthawk to run on scanner

[[Image:igtweek08_fil_racetrack.png]]
Fig 1 from Roopchansingh MRM 50:839, 2003

[[Image:igtweek08_grad_kx.png]]

[[Image:igtweek08_grad_ky.png]]

File:Igtweek08 fil racetrack.png

2008-12-12T15:28:23Z

Shoge: uploaded a new version of "Image:Igtweek08 fil racetrack.png": Fig 1 from Roopchansingh, et. al. MRM 50:829, 2003.

File:Igtweek08 grad ky.png

2008-12-12T15:26:59Z

Shoge:

2008 IGT Project Week Fast Imaging Library

2008-12-12T15:26:41Z

Shoge:

Back to [[2008_IGT_Project_Week#Projects]]

Team: Scott Hoge, Bob Kraft

Goals: Further integrate algorithms from the Fast Imaging Library (doc here: http://www.spl.harvard.edu/publications/item/view/1393) to enable interactive EPI measurements for perfusion, fMRI, and temperature monitoring using accelerated and efficient EPI-based MR acquisitions

Approach:
* complete a mechanism to maintain the phase in our pMRI-UNFOLD-EPI-PROPELLER acquisition technique, which is required for both temperature change estimation and EPI distortion correction
* incorporate real-time hooks into EPI sequence, to provide interactive acquisitions
* start investigations into radial EPI

Other Notes:

* This team will spend significant time on the MR scanner. Schedule here: http://calendar.yahoo.com/YYY,5107b4/srt,0/lmrc_ms_scanner/?v=2&t=1228608000

Results (to be completed and presented at the end of the week):
* extended accelerate short axis propeller epi to use partial Fourier
** issues w/ recon pending due to susceptibility distortion from blade to blade
* implemented both double-sampled and 'racetrack' trajectory in epi psd, to collect self-ref data for b0 field map estimation
** able to calculate relative phase changes using racetrack reference data
** may be incompatible with unfold nyquist ghost removal method
* wfu epi psd updated to 3d
* modified fgre to use modular rthawk implementation
* rt epi not accomplished, due to difficulty getting rthawk to run on scanner

[[Image:igtweek08_fil_racetrack.png]]
[[Image:igtweek08_grad_kx.png]]
[[Image:igtweek08_grad_ky.png]]

File:Igtweek08 grad kx.png

2008-12-12T15:25:59Z

Shoge:

2008 IGT Project Week Fast Imaging Library

2008-12-12T15:25:38Z

Shoge:

File:Igtweek08 fil racetrack.png

2008-12-12T15:25:05Z

Shoge:

2008 IGT Project Week Fast Imaging Library

2008-12-12T15:24:46Z

Shoge:

2008 IGT Project Week Fast Imaging Library

2008-12-12T03:45:12Z

Shoge:

2008 IGT Project Week Fast Imaging Library

2008-12-12T03:44:07Z

Shoge:

Back to [[2008_IGT_Project_Week#Projects]]

Team: Scott Hoge, Bob Kraft

Goals: Further integrate algorithms from the Fast Imaging Library (doc here: http://www.spl.harvard.edu/publications/item/view/1393) to enable interactive EPI measurements for perfusion, fMRI, and temperature monitoring using accelerated and efficient EPI-based MR acquisitions

Approach:
* complete a mechanism to maintain the phase in our pMRI-UNFOLD-EPI-PROPELLER acquisition technique, which is required for both temperature change estimation and EPI distortion correction
* incorporate real-time hooks into EPI sequence, to provide interactive acquisitions
* start investigations into radial EPI

Other Notes:

* This team will spend significant time on the MR scanner. Schedule here: http://calendar.yahoo.com/YYY,5107b4/srt,0/lmrc_ms_scanner/?v=2&t=1228608000

Results (to be completed and presented at the end of the week):
* extended accelerate short axis propeller epi to use partial Fourier
** issues w/ recon pending due to susceptibility distortion from blade to blade
* implemented both double-sampled and 'racetrack' trajectory in epi psd, to collect self-ref data for b0 field map estimation
* able to calculate relative phase changes using racetrack reference data
* wfu epi psd updated to 3d
* modified fgre to use modular rthawk implementation
* rt epi not accomplished, due to difficulty getting rthawk to run on scanner

2008 IGT Project Week Fast Imaging Library

2008-12-12T03:38:44Z

Shoge:

Back to [[2008_IGT_Project_Week#Projects]]

Team: Scott Hoge, Bob Kraft

Goals: Further integrate algorithms from the Fast Imaging Library (doc here: http://www.spl.harvard.edu/publications/item/view/1393) to enable interactive EPI measurements for perfusion, fMRI, and temperature monitoring using accelerated and efficient EPI-based MR acquisitions

Approach:
* complete a mechanism to maintain the phase in our pMRI-UNFOLD-EPI-PROPELLER acquisition technique, which is required for both temperature change estimation and EPI distortion correction
* incorporate real-time hooks into EPI sequence, to provide interactive acquisitions
* start investigations into radial EPI

Other Notes:

* This team will spend significant time on the MR scanner. Schedule here: http://calendar.yahoo.com/YYY,5107b4/srt,0/lmrc_ms_scanner/?v=2&t=1228608000

Results (to be completed and presented at the end of the week):
* extended accelerate short axis propeller epi to use partial Fourier
** issues w/ recon pending due to susceptibility distortion from blade to blade
* implemented 'racetrack' trajectory in epi psd.
* able to calculate relative phase changes using racetrack reference data
* wfu epi psd updated to 3d
* modified fgre to use modular rthawk implementation
* rt epi not accomplished, due to difficulty getting rthawk to run on scanner

2008 IGT Project Week Dynamic control of the MRI acquisition

2008-12-08T19:09:14Z

Shoge:

Back to [[2008_IGT_Project_Week#Projects]]

Team:Nathan McDannold, Ben Schwartz, Scott Hoge

Goals: Dynamic control of the MRI acquisition based on US-based signals. This would be to apply existing technologies developed for IGT such as optical-based tracking of a biopsy or ablation probe.

Needs:
# want to move FUS treatments to dynamic target (liver, kidney)

Approach:
# use ultrasound navigators
# how many sensors does one need?
# different ways to manipulate the MR scan

Results (to be completed and presented at the end of the week):

2008 IGT Project Week Fast Imaging Library

2008-12-08T19:00:42Z

Shoge:

2008 IGT Project Week Fast Imaging Library

2008-12-08T18:54:33Z

Shoge:

Back to [[2008_IGT_Project_Week#Projects]]

Team: Scott Hoge, Bob Kraft

Goals: Further develop tools to enable interactive EPI measurements for perfusion, fMRI, and temperature monitoring using accelerated and efficient EPI-based MR acquisitions

Integrating algorithms from the Fast Imaging Library (doc here: http://www.spl.harvard.edu/publications/item/view/1393) into interactive EPI.

Approach:
* complete a mechanism to maintain the phase in our pMRI-UNFOLD-EPI acquisition technique, which is required for both temperature change estimation and EPI distortion correction
* incorporate real-time hooks into EPI sequence, to provide interactive acquisitions
* start investigations into radial EPI

Other Notes:

* This team will spend significant time on the MR scanner. Schedule here: http://calendar.yahoo.com/YYY,5107b4/srt,0/lmrc_ms_scanner/?v=2&t=1228608000

Results (to be completed and presented at the end of the week):

2008 IGT Project Week Fast Imaging Library

2008-12-04T17:26:21Z

Shoge:

Back to [[2008_IGT_Project_Week#Projects]]

Team: Scott Hoge, Bob Kraft

Goals: Further develop tools to enable interactive EPI measurements for perfusion, fMRI, and temperature monitoring using accelerated and efficient EPI-based MR acquisitions

Approach:
* complete a mechanism to maintain the phase in our pMRI-UNFOLD-EPI acquisition technique, which is required for both temperature change estimation and EPI distortion correction
* incorporate real-time hooks into EPI sequence, to provide interactive acquisitions
* start investigations into radial EPI

Other Notes:

* This team will spend significant time on the MR scanner. Schedule here: http://calendar.yahoo.com/YYY,5107b4/srt,0/lmrc_ms_scanner/?v=2&t=1228608000

Results (to be completed and presented at the end of the week):

2008 IGT Project Week Fast Imaging Library

2008-12-03T22:37:00Z

Shoge:

Back to [[2008_IGT_Project_Week#Projects]]

Team: Scott Hoge, Bob Kraft

Goals: Further develop tools to enable interactive EPI measurements for perfusion, fMRI, and temperature monitoring using accelerated and efficient EPI-based MR acquisitions

Approach:
* complete a mechanism to maintain the phase in our pMRI-UNFOLD-EPI acquisition technique, which is required for both temperature change estimation and EPI distortion correction
* incorporate real-time hooks into EPI sequence, to provide interactive acquisitions
* start investigations into radial EPI

Results (to be completed and presented at the end of the week):

2008 IGT Project Week

2008-10-30T04:48:53Z

Shoge: /* Tentative Projects */

=Introduction=
<gallery perrow="2" widths="200px">
Image:NCIGTlogo.gif|[http://www.ncigt.org National Center for Image Guided therapy]
Image:NAMIC 380x463.jpg|[http://www.na-mic.org National Alliance for Medical Image Computing]
Image:Nac.png|[http://nac.spl.harvard.edu/ Neuroimage Analysis Center]
Image:Cimit_logo.gif|[http://www.cimit.org CIMIT]
</gallery>
'''Dates: Monday, December 8th to Friday, December 12th'''

Location: SPL facility at 1249 Boylston Street, Boston MA

IGT Project Week is a hands-on event that will involve various scientific, clinical, and engineering activities that are part of building image-guided therapy systems. Please note that is not a week long session of lectures and/or slide presentations. Instead, active researchers in the field will gather for a week to get actual work done on projects that they have identified ahead of time. A fair amount of effort will be put into teleconferences in the month leading upto the event to ensure that every participant belongs to a project that makes sense to be pursued in such a collaborative setting. Depending on the needs of the projects, the hosts, NCIGT at Brigham and Women's Hospital, will reserve time at appropriate research imaging and therapy equipment.

About a month before the event, a teleconference will be held with interested participants to determine the scope of the work that they will collaboratively pursue during this week. The event itself will start with short presentation by each project team to allows all participants to be acquainted with others who are doing similar work. In the rest of the week, most of the time will be spent doing hands-on programming, imaging, algorithm design, phantom or animal experiments or other validation in small project teams. Given that this is the first stand-alone IGT event of this kind, we expect to have about 5-10 teams of size 3-4 each. To facilitate this work, a conference room will be setup with several tables, with internet and power access, to allow teams to either work on their own laptops. Based on the project requirements, times will also be reserved on the research imaging equipment and therapy equipment at Brigham and Women's Hospital. 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 modeled after the NA-MIC Project Week and its main goal is to foster a hand-on image-guided therapy systems community. The first event is being organized by NCIGT and several other NIH funded grants, and the outcome at this meeting will determine the format and frequency of future events. Unfortunately, no travel support is available from NCIGT for this event; it must be sponsored by their host institution/grant.

If you are interested in joining this event, please send an email to Tina Kapur: tkapur at bwh.harvard.edu

=Agenda=

Monday
*1:30-3:30pm: Presentation of all Projects
*3:30-5pm: Start Working
Tuesday
*9-5: Work

Wednesday
*9-5: Work

Thursday
*9-5: Work

Friday
*10am: Review of Progress
*12pm: lunch and adjourn

=Tentative Projects=
This list will be populated shortly...

* Fast Imaging Library (Hoge, Madore)

=Confirmed Attendees=
#Kevin Cleary, Georgetown
#Ziv Yaniv, Georgetown
#Stephen Aylward, Kitware
#Luis Ibanez, Kitware
#Xenios Papademetris, Yale
#Sandy Wells, BWH
#Tina Kapur, BWH
#Noby Hata, BWH
#Steve Pieper, BWH
#Katie Hayes, BWH
#Scott Hoge, BWH
#Nathan McDannold, BWH
#Ron Kikinis, BWH
#Clare Tempany, BWH
#Ferenc Jolesz, BWH

=Tentative Attendees=
#Mike Miga, Vanderbilt
#Bob Kraft, Wake Forest Univ

2008 IGT Project Week

2008-10-30T04:48:30Z

Shoge:

=Introduction=
<gallery perrow="2" widths="200px">
Image:NCIGTlogo.gif|[http://www.ncigt.org National Center for Image Guided therapy]
Image:NAMIC 380x463.jpg|[http://www.na-mic.org National Alliance for Medical Image Computing]
Image:Nac.png|[http://nac.spl.harvard.edu/ Neuroimage Analysis Center]
Image:Cimit_logo.gif|[http://www.cimit.org CIMIT]
</gallery>
'''Dates: Monday, December 8th to Friday, December 12th'''

Location: SPL facility at 1249 Boylston Street, Boston MA

IGT Project Week is a hands-on event that will involve various scientific, clinical, and engineering activities that are part of building image-guided therapy systems. Please note that is not a week long session of lectures and/or slide presentations. Instead, active researchers in the field will gather for a week to get actual work done on projects that they have identified ahead of time. A fair amount of effort will be put into teleconferences in the month leading upto the event to ensure that every participant belongs to a project that makes sense to be pursued in such a collaborative setting. Depending on the needs of the projects, the hosts, NCIGT at Brigham and Women's Hospital, will reserve time at appropriate research imaging and therapy equipment.

About a month before the event, a teleconference will be held with interested participants to determine the scope of the work that they will collaboratively pursue during this week. The event itself will start with short presentation by each project team to allows all participants to be acquainted with others who are doing similar work. In the rest of the week, most of the time will be spent doing hands-on programming, imaging, algorithm design, phantom or animal experiments or other validation in small project teams. Given that this is the first stand-alone IGT event of this kind, we expect to have about 5-10 teams of size 3-4 each. To facilitate this work, a conference room will be setup with several tables, with internet and power access, to allow teams to either work on their own laptops. Based on the project requirements, times will also be reserved on the research imaging equipment and therapy equipment at Brigham and Women's Hospital. 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 modeled after the NA-MIC Project Week and its main goal is to foster a hand-on image-guided therapy systems community. The first event is being organized by NCIGT and several other NIH funded grants, and the outcome at this meeting will determine the format and frequency of future events. Unfortunately, no travel support is available from NCIGT for this event; it must be sponsored by their host institution/grant.

If you are interested in joining this event, please send an email to Tina Kapur: tkapur at bwh.harvard.edu

=Agenda=

Monday
*1:30-3:30pm: Presentation of all Projects
*3:30-5pm: Start Working
Tuesday
*9-5: Work

Wednesday
*9-5: Work

Thursday
*9-5: Work

Friday
*10am: Review of Progress
*12pm: lunch and adjourn

=Tentative Projects=
This list will be populated shortly...

* Fast Imaging Library (Hoge)

=Confirmed Attendees=
#Kevin Cleary, Georgetown
#Ziv Yaniv, Georgetown
#Stephen Aylward, Kitware
#Luis Ibanez, Kitware
#Xenios Papademetris, Yale
#Sandy Wells, BWH
#Tina Kapur, BWH
#Noby Hata, BWH
#Steve Pieper, BWH
#Katie Hayes, BWH
#Scott Hoge, BWH
#Nathan McDannold, BWH
#Ron Kikinis, BWH
#Clare Tempany, BWH
#Ferenc Jolesz, BWH

=Tentative Attendees=
#Mike Miga, Vanderbilt
#Bob Kraft, Wake Forest Univ

2008 Summer Project Week

2008-06-06T19:40:13Z

Shoge: /* Attendee List */

Back to [[Engineering:Programming_Events|Programming/Project Events]]

[[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]

== Logistics ==

'''Dates:''' June 23-27, 2008

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139

'''Registration Method''' Please add your name to the attendee list below (create namic wiki account if you don't have one, by clicking on the "login/create account" link on the top right corner of this page), and then mail a check to Donna Kaufman at the address above.

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&key=4FD1B Please click here to reserve.]This rate is good only through June 1.

Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

==Introduction to NA-MIC Project Week==

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. 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).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process
** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]]
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])

== Preparation ==

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

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/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 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## 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. the BIRN). 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.)
## 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. (Zack)
# 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...

== A History in Wiki Links ==

A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##EPI-DWI Distortion correction (Sylvain Bouix BWH, Tauseef Rehman GATech)
##[[2008_Summer_Project_Week:EddyCurrentCorrection|EPI-DWI Eddy Current distortion correction]] (Sylvain Bouix BWH, Ran Tao Utah)
##Lobe Parcellation of 3T MR data - need help parametrization (Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
##Finsler method (John Melonakos GATech, Marek Kubicki BWH)
##Group Analysis on DTI (Casey Goodlett Utah, Marek Kubicki BWH)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##Work Flow Tool for regional cortical thickness pipeline (Clement Vachet UNC)
##NITRC registration of cortical thickness modules (Clement Vachet UNC)
##DTI tools for a) DWI preparation and b) DTI atlas building (Zhexing Liu UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[DBP2:MIND:RoadmapProject|Finish Roadmap Project]]
##[[DBP2:MIND:LongitudinalRegistrationProject|Longitudinal Registration]]
##[[DBP2:MIND:BeyondLesionsProject|Beyond Lesions]]
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)
##[[DBP2:JHU:Roadmap|Trans-Rectal Prostate Biopsy module (David Gobbi, Gabor Fichtinger, Queens/JHU)]]
##[[Projects:ProstateSegmentation|Prostate Segmentation and Registration (Yi Gao GATech, Gabor Fichtinger JHU)]]
##Hardware/software overlay for percutaneous intervention (Siddharth Vikal, Gabor Fichtinger, Queens/JHU)

===Other Projects===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#Integraton of groupwise b-spline registration into atlas building (Casey Goodlett, Serdar Balci)
# CVS / SVN auto synchronization
# 3D Widgets in Slicer
## Issues with existing widgets
## Design of new widgets
# Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
# Module Chaining (Marco, Jim, Steve, Dan B., Luca)
# Nonlinear transforms (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# Slicer3, XNAT integration, and desigining XCEDE Web Services (Dan M., Steve, Julien)
## Review and enrich use cases
# Python in Slicer (Dan B., Michael Halle, Steve, Luca)
# Performance Tuning of Fiducials using the EventBroker and other tools (Nicole, Alex, Steve, Will)
# GUI Tweaking (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#NIREP: Non-rigid Image Registration Evaluation (Gary Christensen Group)
#Lung Atlas (Gary Christensen Group)
#Non-rigid image registration (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
#FMA (Protege) links to Slicer (Vish, Mike, Florin, Jim, Steve, Wendy)
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]]
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga)
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)

===Non-Medical Collaborations===
#[[NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine|Astronomical Medicine]] (Harvard IIC: Douglas Alan, Michael Halle)

==Attendee List==
# Ron Kikinis, BWH
# Carl-Fredrik Westin, BWH
# Gary Christensen, The University of Iowa
# Jeffrey Hawley, Gary Christensen's student
# Kate Raising, Gary Christensen's student
# Nathan Fritze, Gary Christensen's student
# Paul Song, Gary Christensen's student
# Cheng Zhang, Gary Christensen's student
# Ying Wei, Gary Christensen's student
# Nathan Burnette, The University of Iowa
# Hans Johnson, The University of Iowa
# Vincent Magnotta, The University of Iowa
# Keith Gunderson, The University of Iowa
# Steve Pieper, Isomics, Core 2/6
# Dana C. Peters, BIDMC Harvard Medical
# Jason Taclas, BIDMC Harvard Medical
# Nicole Aucoin, BWH, Core 2
# Will Schroeder, Kitware, Cores 2/4
# Sebastien Barre, Kitware, Core 2
# Julien Jomier, Kitware, Core 2
# Luis Ibanez, Kitware, Core 2
# Curtis Lisle, KnowledgeVis, Core 2
# Katie Hayes, BWH, Core 2
# Randy Gollub, MGH, Core 5
# Clement Vachet, UNC, Core 3
# Zhexing Liu, UNC, Core 1/3
# Casey Goodlett, Utah, Core 1
# Marcel Prastawa, Utah, Core 1
# Jeffrey Grethe, UCSD, Core 2
# Marco Ruiz, UCSD, Core 2
# Zhen Qian, Rutgers University
# Jinghao Zhou, Rutgers University
# Luca Antiga, Mario Negri Institute
# Adam Wittek, The University of Western Australia
# Grand Joldes, The University of Western Australia
# Jamie Berger, The University of Western Australia
# Serdar Balci, MIT, Core 1
# Bryce Kim, MIT, Core1
# Tina Kapur, BWH, Core 6
# Carling Cheung, Robarts Research Institute / The University of Western Ontario
# Danielle Pace, Robarts Research Institute / The University of Western Ontario
# Sean Megason, Dept of Systems Biology, Harvard Medical School
# Alex Gouaillard, Dept of Systems Biology, Harvard Medical School
# Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School
# Arnaud Gelas, Dept of Systems Biology, Harvard Medical School
# Sonia Pujol, Surgical Planning Laboratory, BWH
# Bjoern Menze, (then) Surgical Planning Laboratory, BWH
# Alex Yarmarkovich, Isomics, Core 2
# Sylvain Bouix, BWH, Core 3
# Priya Srinivasan, BWH, Core 3
# Chris Churas, UCSD, Core 2
# John Melonakos, Georgia Tech, Core 1
# Yi Gao, Georgia Tech, Core 1
# Tauseef Rehman, Georgia Tech, Core 1
# Clare Poynton, MIT, Core 1
# H. Jeremy Bockholt, MRN Lupus DBP Core 3
# Mark Scully, MRN Lupus DBP Core 3
# Gabor Fichtinger, Queen's, Core 3
# David Gobbi, Queen's, Core 3
# Purang Abolmaesumi, Queen's, Core 3
# Siddharth Vikal, Queen's, Core 3
# Daniel Blezek, Mayo
# Csaba Csoma, JHU, Core 3
# Ran Tao, University of Utah, Core 1
# Jim Miller, GE Research, Core 2
# Xiaodong Tao, GE Research, Core 2
# Dirk Padfield, GE Research, Core 2
# Viswanath Avasarala, GE Research, NAC
# Dan Marcus, Washington University
# Tim Olsen, Washington University
# Kevin Archie, Washington University
# Misha Milchenko, Washington University
# Wendy Plesniak, BWH, Core 2
# Demian Wasserman, INRIA, LMI-collaborator
# Xenophon Papademetris, Yale, Collaborator
# Xenophon P's postdoc, Yale, Collaborator
# Xenophon P's student, Yale, Collaborator
# Vidya Rajagopalan, Virginia Tech, Student of Chris Wyatt, External Collaborator
# Greg Sharp, MGH, External Collaborator
# Marta Peroni, MGH, External Collaborator
# Toru Higaki, Hiroshima Univ., Japan, External collaborator (Hata)
# Jacek Kukluk, BWH,
# Nobuhiko Hata, BWH
# Junichi Tokuda, BWH
# Haying Liu, BWH
# Ragini Verma, UPenn (June 24)
# Luke Bloy, UPenn (Ragini Verma's student) (June 24)
# Yang Li, UPenn (Ragini's postdoc) (June 24)
# Jack Blevins, Acoustic Med, Collaborator
# Nikos Chrisochoides, College of William and Mary, External collaborator (June 23)
# Andriy Fedorov, College of William and Mary, External collaborator
# Carlos Sánchez Mendoza, BWH
# Kilian Pohl, BWH
# Pratik Patel, Brainlab, Collaborator
# Marianna Jakab, BWH
# Nathan Hageman, UCLA
# Douglas Alan, Harvard IIC, External Collaborator
# Tammy Riklin Raviv, MIT
# Peter Kazanzides, JHU, Collaborator
# Scott Hoge, BWH, (Wed, Jun 25)

==Pictures==