NAMIC Wiki - User contributions [en]

NA-MIC/Projects/Collaboration/SARP phantom

2008-06-27T13:22:47Z

Kegunder:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:phantomSeg.jpg|thumb|320px|Segmentation of a section of the modified catphan 600 phantom.]]
|}

__NOTOC__

===Key Investigators===
* U. of Iowa: Eric Hoffman, Janice Cook Granroth, Keith Gunderson
* Kitware, Luis Ibanez

<div style="margin: 20px;">

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

<h1>Objective</h1>
The research is funded by SARP -- Severe Asthma Research Program
<BR>
Severe asthma affects a small subset of asthma patients but uses a disproportionate amount of health care resources. It is also responsible for a significant amount of the morbidity and mortality associated with asthma. The purpose of this study to establish a collaborative program to investigate the mechanistic basis for severe asthma and how it differs from mild-to-moderate asthma.

<H2> Technical specifics </H2>

#Compare the results of different scanner brands and kernels quantitatively
#Investigate homoegeneity (w/ respect to objective 1)
#Investigage MTF (w/ respect to objective 1)
#Investigate airway size and wall thickness algorithms (w/ respect to objective 1)

</div>

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

<h1>Approach, Plan</h1>
[http://www.i-clic.org/projects/SARP-UI-PHANTOM.short.ppt Results-to-date]

Add rotational registration feature. <br>
Investigate porting issues <br>

</div>

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

<h1>Progress</h1>
<H2> Pre-NAMIC status </H2>

Objective 1,2,3 completed<br>
Objective 4 is in progress

<H2> Post-NAMIC updates </H2>

# Registration details understood, coding underway
# Two new segmentation approaches to be investigated (Model-based & Projection/HoughTransform2DCircles)
# CMake improvents & CTest/ CDash integration begun (i.e. introduction to CMake-ish tools)
# Regression & Uniting testing being added

</div>

<br style="clear: both;" />

</div>

===References===
*

NA-MIC/Projects/Collaboration/SARP phantom

2008-06-26T20:33:42Z

Kegunder:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:phantomSeg.jpg|thumb|320px|Segmentation of a section of the modified catphan 600 phantom.]]
|}

__NOTOC__

===Key Investigators===
* U. of Iowa: Eric Hoffman, Janice Cook Granroth, Keith Gunderson
* Kitware, Luis Ibanez

<div style="margin: 20px;">

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

<h1>Objective</h1>
The research is funded by SARP -- Severe Asthma Research Program
<BR>
Severe asthma affects a small subset of asthma patients but uses a disproportionate amount of health care resources. It is also responsible for a significant amount of the morbidity and mortality associated with asthma. The purpose of this study to establish a collaborative program to investigate the mechanistic basis for severe asthma and how it differs from mild-to-moderate asthma.

<H2> Technical specifics </H2>

#Compare the results of different scanner brands and kernels quantitatively
#Investigate homoegeneity (w/ respect to objective 1)
#Investigage MTF (w/ respect to objective 1)
#Investigate airway size and wall thickness algorithms (w/ respect to objective 1)

</div>

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

<h1>Approach, Plan</h1>
[http://www.i-clic.org/projects/SARP-UI-PHANTOM.short.ppt Results-to-date]

Add rotational registration feature. <br>
Investigate porting issues <br>

</div>

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

<h1>Progress</h1>
<H2> Pre-NAMIC status </H2>

Objective 1,2,3 completed<br>
Objective 4 is in progress

<H2> Post-NAMIC updates </H2>

# Registration details understood, coding underway
# Two new segmentation approaches to be investigated (Model-based & Projection/HoughTransform2DCircles)
# CMake improvents & CTest/ CDash integration begun
# Regression & Uniting testing being added

</div>

<br style="clear: both;" />

</div>

===References===
*

NA-MIC/Projects/Collaboration/SARP phantom

2008-06-23T18:15:37Z

Kegunder:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:phantomSeg.jpg|thumb|320px|Segmentation of a section of the modified catphan 600 phantom.]]
|}

__NOTOC__

===Key Investigators===
* U. of Iowa: Eric Hoffman, Janice Cook Granroth, Keith Gunderson
* Kitware, Luis Ibanez

<div style="margin: 20px;">

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

<h1>Objective</h1>
The research is funded by SARP -- Severe Asthma Research Program
<BR>
Severe asthma affects a small subset of asthma patients but uses a disproportionate amount of health care resources. It is also responsible for a significant amount of the morbidity and mortality associated with asthma. The purpose of this study to establish a collaborative program to investigate the mechanistic basis for severe asthma and how it differs from mild-to-moderate asthma.

<H2> Technical specifics </H2>

#Compare the results of different scanner brands and kernels quantitatively
#Investigate homoegeneity (w/ respect to objective 1)
#Investigage MTF (w/ respect to objective 1)
#Investigate airway size and wall thickness algorithms (w/ respect to objective 1)

</div>

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

<h1>Approach, Plan</h1>
[http://www.i-clic.org/projects/SARP-UI-PHANTOM.short.ppt Results-to-date]

Add rotational registration feature. <br>
Investigate porting issues <br>

</div>

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

<h1>Progress</h1>
Objective 1,2,3 completed<br>
Objective 4 is in progress

</div>

<br style="clear: both;" />

</div>

===References===
*

NA-MIC/Projects/Collaboration/SARP phantom

2008-06-23T17:54:36Z

Kegunder:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:phantomSeg.jpg|thumb|320px|Segmentation of a section of the modified catphan 600 phantom.]]
|}

__NOTOC__

===Key Investigators===
* U. of Iowa: Eric Hoffman, Janice Cook Granroth, Keith Gunderson

<div style="margin: 20px;">

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

<h1>Objective</h1>
The research is funded by SARP -- Severe Asthma Research Program
<BR>
Severe asthma affects a small subset of asthma patients but uses a disproportionate amount of health care resources. It is also responsible for a significant amount of the morbidity and mortality associated with asthma. The purpose of this study to establish a collaborative program to investigate the mechanistic basis for severe asthma and how it differs from mild-to-moderate asthma.

<H2> Technical specifics </H2>

#Compare the results of different scanner brands and kernels quantitatively
#Investigate homoegeneity (w/ respect to objective 1)
#Investigage MTF (w/ respect to objective 1)
#Investigate airway size and wall thickness algorithms (w/ respect to objective 1)

</div>

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

<h1>Approach, Plan</h1>
[http://www.i-clic.org/projects/SARP-UI-PHANTOM.short.ppt Results-to-date]

Add rotational registration feature. <br>
Investigate porting issues <br>

</div>

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

<h1>Progress</h1>
Objective 1,2,3 completed<br>
Objective 4 is in progress

</div>

<br style="clear: both;" />

</div>

===References===
*

NA-MIC/Projects/Collaboration/SARP phantom

2008-06-10T19:41:36Z

Kegunder:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:phantomSeg.jpg|thumb|320px|Segmentation of a section of the modified catphan 600 phantom.]]
|}

__NOTOC__

===Key Investigators===
* U. of Iowa: Eric Hoffman, Janice Cook Granroth, Keith Gunderson

<div style="margin: 20px;">

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

<h1>Objective</h1>
The research is funded by SARP -- Severe Asthma Research Program
<BR>
Severe asthma affects a small subset of asthma patients but uses a disproportionate amount of health care resources. It is also responsible for a significant amount of the morbidity and mortality associated with asthma. The purpose of this study to establish a collaborative program to investigate the mechanistic basis for severe asthma and how it differs from mild-to-moderate asthma.

<H2> Technical specifics </H2>

#Compare the results of different scanner brands and kernels quantitatively
#Investigate homoegeneity (w/ respect to objective 1)
#Investigage MTF (w/ respect to objective 1)
#Investigate airway size and wall thickness algorithms (w/ respect to objective 1)

</div>

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

<h1>Approach, Plan</h1>
[http://www.i-clic.org/projects/SARP-UI-PHANTOM.short.ppt Results-to-date]

</div>

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

<h1>Progress</h1>
Objective 1,2,3 completed<br>
Objective 4 is in progress

</div>

<br style="clear: both;" />

</div>

===References===
*

NA-MIC/Projects/Collaboration/SARP phantom

2008-06-10T19:35:44Z

Kegunder:

NA-MIC/Projects/Collaboration/SARP phantom

2008-06-10T19:34:11Z

Kegunder:

NA-MIC/Projects/Collaboration/SARP phantom

2008-06-10T19:27:24Z

Kegunder:

NA-MIC/Projects/Collaboration/SARP phantom

2008-06-10T19:26:52Z

Kegunder:

NA-MIC/Projects/Collaboration/SARP phantom

2008-05-29T17:17:04Z

Kegunder:

File:PhantomSeg.jpg

2008-05-29T17:15:36Z

Kegunder: CT image of the modified catphan 600 phantom used in the SARP project.

CT image of the modified catphan 600 phantom used in the SARP project.

NA-MIC/Projects/Collaboration/SARP phantom

2008-05-29T17:11:24Z

Kegunder:

NA-MIC/Projects/Collaboration/SARP phantom

2008-05-29T17:09:25Z

Kegunder: New page: {| |Project Week Main Page ]] |[[Image:genuFAp.jpg|thumb|320px|Scatter plot of the original FA data through ...

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:genuFAp.jpg|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]
|[[Image:genuFA.jpg|thumb|320px|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.]]
|}

__NOTOC__

===Key Investigators===
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

<div style="margin: 20px;">

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

<h1>Objective</h1>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

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

<h1>Approach, Plan</h1>

Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...
</div>

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

<h1>Progress</h1>

Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>

<br style="clear: both;" />

</div>

===References===
*

2008 Summer Project Week

2008-05-29T17:08:02Z

Kegunder:

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

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)
##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)
##Add Projects for this DBP here...
#[[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)
##Add Projects for this DBP here...

===Structural Analysis===

===Diffusion Image Analysis===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]]

===Calibration/Validation===

===NA-MIC Kit - Slicer 3===

===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)

===Non-Medical Collaborations===

==Attendee List==
# Ron Kikinis, 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
# Casey Goodlett, 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 2
# David Gobbi, Queen's, Core 2
# Purang Abolmaesumi, Queen's, Core 2
# Siddharth Vikal, Queen's, Core 2
# Daniel Blezek, Mayo
# Csaba Csoma, JHU, Core 2
# Ran Tao, University of Utah, Core 1
# Jim Miller, GE Research, Core 2
# Viswanath Avasarala, GE Research, NAC

==Pictures==

2008 Summer Project Week

2008-05-28T17:18:47Z

Kegunder:

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

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)
##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)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##Add Projects for this DBP here...
#[[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)
##Add Projects for this DBP here...

===Structural Analysis===

===Diffusion Image Analysis===

===Calibration/Validation===

===NA-MIC Kit - Slicer 3===

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)

===Non-Medical Collaborations===

==Attendee List==
# Ron Kikinis, 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
# Casey Goodlett, 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 2
# David Gobbi, Queen's, Core 2
# Purang Abolmaesumi, Queen's, Core 2
# Siddharth Vikal, Queen's, Core 2
# Daniel Blezek, Mayo
# Csaba Csoma, JHU, Core 2

==Pictures==