NAMIC Wiki - User contributions [en]

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2009-08-21T15:55:47Z

Vidyaraj:

Back to [[NA-MIC_External_Collaborations]]
==Abstract==
Alcohol abuse continues to be a major problem in the United States with an estimated 14 million adults
meeting the clinical criteria for a diagnosis of alcohol abuse or alcoholism at an estimated cost of $185
billion. Chronic alcohol exposure has been shown to impact structure and function of the brain. Since
most of what is known of alcohol's effects on the brain is based on studies of individuals who have
abused for a long time, it is unclear whether some of the effects might occur early in the abuse process.
Additionally, human studies are often complicated by many factors incuding polydrug abuse, poor
nutritional states and other medical conditions. Another complicating factor is the interaction of stress
and alcohol.

Using magnetic resonance imaging (MRI), we will examine the the effects of chronic alcohol self-
administration on brain structure and function in a group of monkeys that have been mother-reared or
nursery-reared. MRI scans will be acquired to determine whether there are differences in stucture or
functions as a result of alcohol exposure and whether rearing conditions play a role in these effects.
MRI techniques will also be used to examine how chronic alcohol consumption affects cerebral blood
flow, which is a measure of neuronal activity. Because we will conduct these measures both before
and after alcohol exposure in the same "young adult" animals, we will be able to track any changes that
might occur early in alcohol abuse which is something that cannot be accomplished in human studies.
Another goal is to adapt imaging tools and computer software that are used to measure the brains of
humans to the monkey brain. To accomplish this, we will collaborate with the National Alliance for
Medical Computing (NA-MIC), an existing NIH Center for Biomedical Computing.

We can control all variables associated with alcohol self-administration in these monkeys. They will be
monitored both before and after exposure to alcohol, thus, we will be able to monitor the progression of
any changes in structure or function that directly result from alcohol exposure. These studies will help
identify how exposure to long-term alcohol might affect how the brain works.

==Grant #==
1R01AA016748-01

==Key Personnel==
Wake Forest University: Jim Daunais, Bob Kraft

Virginia Tech: Chris Wyatt, Vidya Rajagopalan, Xiaojing Long

NAMIC: Kilian Pohl, Sandy Wells, Andriy Fedorov

==Projects==
Active projects in this collaboration are:

=== Tutorials on using EMSegmenter to segment nonhuman primate images ===
#Slicer3 based tutorial
##[http://www.na-mic.org/Wiki/index.php/Image:EMSegment_TrainingTutorial.pdf Tutorial Slide Handouts (PDF)]
##[http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Vervet Atlas]
##[http://www.na-mic.org/Wiki/images/c/c9/SlicerTutorialData_Vervet.tar.gz Example Data]
#[http://bsl.ece.vt.edu/download/NHP-EMSTut.zip older Slicer2.x based tutorial]
## [http://www.na-mic.org/Wiki/index.php/Image:EMSegment_Vervet_TrainingTutorial_Slicer2.pdf Vervet segmentation with Slicer2] (extracted from above for convenience)

=== Nonhuman Primate Atlas Development ===
Vervet Probabalistic Atlas - Adult
# [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Vervet Probabilistic Atlas (VPA-10)]

Rhesus Probabalistic Atlas - Adult
#[[Rhesus_WMGM_Atlas|WM/GM Atlas]]
#[[Rhesus_Subcortical_Atlas|Subcortical Atlas]]

Rhesus Probabalistic Atlas - Juvenile
#[[Rhesus_Juvenile_WMGM_Atlas|WM/GM Atlas]]

Cyno Probabalistic Atlas - Adult
#[[Cyno_WMGM_Atlas|WM/GM Atlas]]

=== Segmentation ===
#[[Rhesus_ICV_Extraction | Rhesus ICV Extraction]]
#[[Rhesus_EM_Segmentation | Rhesus EM Segmentation]]

=== Documentation ===

==Publications==
==Meetings and Events Specific to this Collaboration==
*[[2007_Programming/Project_Week_MIT|2007 Summer Programming/Project Week at MIT]]
*[[AHM_2008|2008 NA-MIC AHM]]
*[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction|2008 NA-MIC Summer Project Week Page]]
*2009 NA-MIC Winter Project Week Pages: [[2009_Winter_Project_Week_WFU1|Project 1]]
* [http://wiki.na-mic.org/Wiki/index.php/Measuring_Alcohol_Stress_Interaction 2009 Summer project week Boston]

==Resource Links==

* [http://www.slicer.org slicer]
* [http://www.bsl.ece.vt.edu Bioimaging Systems Lab at VT]

Measuring Alcohol Stress Interaction

2009-06-26T14:29:48Z

Vidyaraj:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:MonkeyProject09Slicer.png|Segmentation of Vervet Subcortical Structures

</gallery>

==Key Investigators==
* VT: Chris Wyatt, Vidya Rajagopalan
* BWH: Andrey Fedorov, Ron Kikinis, Nicolas Rannou, Sylvain Jaume

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

<h3>Objective</h3>
* To improve cortical segmentation of Vervet segmentation Results
* Use Change tracker module in Slicer to study hippocampal changes between subjects at two time points

</div>

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

<h3>Approach, Plan</h3>
* Improve rigid registration results by optimizing parameters
* Add bias correction to workflow to improve segmentation results
* Study hippocampal changes between subjects at two time points using Change Tracker

</div>

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

<h3>Progress</h3>
* ChangeTracker augmented with the capability to accept externally-defined segmentation ([http://svn.na-mic.org/NAMICSandBox/trunk/ChangeTrackerExtra/ChangeTrackerVT/ ChangeTrackerVT] in NAMIC Sandbox)
* [http://svn.na-mic.org/NAMICSandBox/trunk/MRIBiasCorrectionFilter/ MRIBiasCorrectionFilter] module by Nicolas Rannou available in NAMIC SandBox, initial testing on rhesus data done
* GWE set up on SPL Cluster for registration parameter exploration
* ChangerTracker used to detect change between hippocampus of State0 and State1 of first vervet subject.
{|
|[[Image:ChangeTracker_3dScreenShot_0.png|thumb|220px|ChangerTracker output for hippocampus changes between state0 and state1]]

|}

* MRIBiasCorrection Module parameter exploration being set up in GWE of SPL cluster.

{|
|[[Image:Hugo_ICC_SagSlice128_BiasC_5.nii.base.png‎ |thumb|220px|Before bias correction ]]
|[[Image:Hugo_ICC_SagSlice128_BiasC_5.nii.diff.png‎|thumb|220px|After bias correction]]
|}
<h3>In Progress</h3>
* Working with Xioadong to adapt SkullStripper Module for Vervet Images
* Explore use of ACPC align prior to rigid registration.
</div>
</div>
<div style="width: 97%; float: left;">

==References==
* [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction NA-MIC NCBC Collaboration: Measuring alcohol and stress interaction]
* [http://wiki.na-mic.org/Wiki/index.php/EMSegment EM Segment project by Sylvain Jaume and Nicolas Rannou]
* Tustison N., Gee J. "N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction" InsightJournal, 2009 January - June, [http://www.insight-journal.org/browse/publication/640]

Measuring Alcohol Stress Interaction

2009-06-26T13:26:31Z

Vidyaraj:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:MonkeyProject09Slicer.png|Segmentation of Vervet Subcortical Structures

</gallery>

==Key Investigators==
* VT: Chris Wyatt, Vidya Rajagopalan
* BWH: Andrey Fedorov, Ron Kikinis, Nicolas Rannou, Sylvain Jaume

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

<h3>Objective</h3>
* To improve cortical segmentation of Vervet segmentation Results
* Use Change tracker module in Slicer to study hippocampal changes between subjects at two time points

</div>

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

<h3>Approach, Plan</h3>
* Improve rigid registration results by optimizing parameters
* Add bias correction to workflow to improve segmentation results
* Study hippocampal changes between subjects at two time points using Change Tracker

</div>

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

<h3>Progress</h3>
* ChangeTracker augmented with the capability to accept externally-defined segmentation ([http://svn.na-mic.org/NAMICSandBox/trunk/ChangeTrackerExtra/ChangeTrackerVT/ ChangeTrackerVT] in NAMIC Sandbox)
* [http://svn.na-mic.org/NAMICSandBox/trunk/MRIBiasCorrectionFilter/ MRIBiasCorrectionFilter] module by Nicolas Rannou available in NAMIC SandBox, initial testing on rhesus data done
* GWE set up on SPL Cluster for registration parameter exploration
* ChangerTracker used to detect change between hippocampus of State0 and State1 of first vervet subject.
{|
|[[Image:ChangeTracker_3dScreenShot_0.png|thumb|220px|ChangerTracker output for hippocampus changes between state0 and state1]]

|}

* MRIBiasCorrection Module parameter exploration being set up in GWE of SPL cluster.

{|
|[[Image:Hugo_ICC_SagSlice128_BiasC_5.nii.base.png‎ |thumb|220px|Before bias correction ]]
|[[Image:Hugo_ICC_SagSlice128_BiasC_5.nii.diff.png‎|thumb|220px|After bias correction]]
|}
<h3>In Progress</h3>
* Working with Xioadong to adapt SkullStripper Module for Vervet Images
</div>
</div>
<div style="width: 97%; float: left;">

==References==
* [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction NA-MIC NCBC Collaboration: Measuring alcohol and stress interaction]
* [http://wiki.na-mic.org/Wiki/index.php/EMSegment EM Segment project by Sylvain Jaume and Nicolas Rannou]
* Tustison N., Gee J. "N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction" InsightJournal, 2009 January - June, [http://www.insight-journal.org/browse/publication/640]

Measuring Alcohol Stress Interaction

2009-06-26T13:23:59Z

Vidyaraj:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:MonkeyProject09Slicer.png|Segmentation of Vervet Subcortical Structures

</gallery>

==Key Investigators==
* VT: Chris Wyatt, Vidya Rajagopalan
* BWH: Andrey Fedorov, Ron Kikinis, Nicolas Rannou, Sylvain Jaume

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

<h3>Objective</h3>
* To improve cortical segmentation of Vervet segmentation Results
* Use Change tracker module in Slicer to study hippocampal changes between subjects at two time points

</div>

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

<h3>Approach, Plan</h3>
* Improve rigid registration results by optimizing parameters
* Add bias correction to workflow to improve segmentation results
* Study hippocampal changes between subjects at two time points using Change Tracker

</div>

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

<h3>Progress</h3>
* ChangeTracker augmented with the capability to accept externally-defined segmentation ([http://svn.na-mic.org/NAMICSandBox/trunk/ChangeTrackerExtra/ChangeTrackerVT/ ChangeTrackerVT] in NAMIC Sandbox)
* [http://svn.na-mic.org/NAMICSandBox/trunk/MRIBiasCorrectionFilter/ MRIBiasCorrectionFilter] module by Nicolas Rannou available in NAMIC SandBox, initial testing on rhesus data done
* GWE set up on SPL Cluster for registration parameter exploration
* ChangerTracker used to detect change between hippocampus of State0 and State1 of first vervet subject.
{|[[Image:ChangeTracker_3dScreenShot_0.png|ChangerTracker output for hippocampus changes between state0 and state1]]|}

* MRIBiasCorrection Module parameter exploration being set up in GWE of SPL cluster.

{|
|[[Image:Hugo_ICC_SagSlice128_BiasC_5.nii.base.png‎ |thumb|220px|Before bias correction ]]
|[[Image:Hugo_ICC_SagSlice128_BiasC_5.nii.diff.png‎|thumb|220px|After bias correction]]
|}
<h3>In Progress</h3>
* Working with Xioadong to adapt SkullStripper Module for Vervet Images
</div>
</div>
<div style="width: 97%; float: left;">

==References==
* [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction NA-MIC NCBC Collaboration: Measuring alcohol and stress interaction]
* [http://wiki.na-mic.org/Wiki/index.php/EMSegment EM Segment project by Sylvain Jaume and Nicolas Rannou]
* Tustison N., Gee J. "N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction" InsightJournal, 2009 January - June, [http://www.insight-journal.org/browse/publication/640]

File:Hugo ICC SagSlice128 BiasC 5.nii.diff.png

2009-06-26T13:23:00Z

Vidyaraj:

File:Hugo ICC SagSlice128 BiasC 5.nii.base.png

2009-06-26T13:22:36Z

Vidyaraj:

Measuring Alcohol Stress Interaction

2009-06-26T13:18:34Z

Vidyaraj:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:MonkeyProject09Slicer.png|Segmentation of Vervet Subcortical Structures

</gallery>

==Key Investigators==
* VT: Chris Wyatt, Vidya Rajagopalan
* BWH: Andrey Fedorov, Ron Kikinis, Nicolas Rannou, Sylvain Jaume

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

<h3>Objective</h3>
* To improve cortical segmentation of Vervet segmentation Results
* Use Change tracker module in Slicer to study hippocampal changes between subjects at two time points

</div>

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

<h3>Approach, Plan</h3>
* Improve rigid registration results by optimizing parameters
* Add bias correction to workflow to improve segmentation results
* Study hippocampal changes between subjects at two time points using Change Tracker

</div>

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

<h3>Progress</h3>
* ChangeTracker augmented with the capability to accept externally-defined segmentation ([http://svn.na-mic.org/NAMICSandBox/trunk/ChangeTrackerExtra/ChangeTrackerVT/ ChangeTrackerVT] in NAMIC Sandbox)
* [http://svn.na-mic.org/NAMICSandBox/trunk/MRIBiasCorrectionFilter/ MRIBiasCorrectionFilter] module by Nicolas Rannou available in NAMIC SandBox, initial testing on rhesus data done
* GWE set up on SPL Cluster for registration parameter exploration
* ChangerTracker used to detect change between hippocampus of State0 and State1 of first vervet subject.
{|[[Image:ChangeTracker_3dScreenShot_0.png|ChangerTracker output for hippocampus changes between state0 and state1]]|}

* MRIBiasCorrection Module parameter exploration being set up in GWE of SPL cluster.

{|
|[[Image:CheckerB4Reg_Screenshot.jpg |thumb|220px|Before bias correction ]]
|[[Image:CheckerAfterreg_Screenshot.png|thumb|220px|After bias correction]]
|}
<h3>In Progress</h3>
* Working with Xioadong to adapt SkullStripper Module for Vervet Images
</div>
</div>
<div style="width: 97%; float: left;">

==References==
* [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction NA-MIC NCBC Collaboration: Measuring alcohol and stress interaction]
* [http://wiki.na-mic.org/Wiki/index.php/EMSegment EM Segment project by Sylvain Jaume and Nicolas Rannou]
* Tustison N., Gee J. "N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction" InsightJournal, 2009 January - June, [http://www.insight-journal.org/browse/publication/640]

Measuring Alcohol Stress Interaction

2009-06-26T02:57:35Z

Vidyaraj:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:MonkeyProject09Slicer.png|Segmentation of Vervet Subcortical Structures
Image:ChangeTracker_3dScreenShot_0.png|ChangerTracker output for hippocampus changes between state0 and state1
</gallery>

==Key Investigators==
* VT: Chris Wyatt, Vidya Rajagopalan
* BWH: Andrey Fedorov, Ron Kikinis, Nicolas Rannou, Sylvain Jaume

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

<h3>Objective</h3>
* To improve cortical segmentation of Vervet segmentation Results
* Use Change tracker module in Slicer to study hippocampal changes between subjects at two time points

</div>

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

<h3>Approach, Plan</h3>
* Improve rigid registration results by optimizing parameters
* Add bias correction to workflow to improve segmentation results
* Study hippocampal changes between subjects at two time points using Change Tracker

</div>

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

<h3>Progress</h3>
* ChangeTracker augmented with the capability to accept externally-defined segmentation ([http://svn.na-mic.org/NAMICSandBox/trunk/ChangeTrackerExtra/ChangeTrackerVT/ ChangeTrackerVT] in NAMIC Sandbox)
* [http://svn.na-mic.org/NAMICSandBox/trunk/MRIBiasCorrectionFilter/ MRIBiasCorrectionFilter] module by Nicolas Rannou available in NAMIC SandBox, initial testing on rhesus data done
* GWE set up on SPL Cluster for registration parameter exploration
* ChangerTracker used to detect change between hippocampus of State0 and State1 of first vervet subject.
* MRIBiasCorrection Module parameter exploration being set up in GWE of SPL cluster.
<h3>In Progress</h3>
* Working with Xioadong to adapt SkullStripper Module for Vervet Images
</div>
</div>
<div style="width: 97%; float: left;">

==References==
* [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction NA-MIC NCBC Collaboration: Measuring alcohol and stress interaction]
* [http://wiki.na-mic.org/Wiki/index.php/EMSegment EM Segment project by Sylvain Jaume and Nicolas Rannou]
* Tustison N., Gee J. "N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction" InsightJournal, 2009 January - June, [http://www.insight-journal.org/browse/publication/640]

File:ChangeTracker 3dScreenShot 0.png

2009-06-26T02:56:03Z

Vidyaraj:

Measuring Alcohol Stress Interaction

2009-06-26T02:53:16Z

Vidyaraj:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:MonkeyProject09Slicer.png|Segmentation of Vervet Subcortical Structures
</gallery>

==Key Investigators==
* VT: Chris Wyatt, Vidya Rajagopalan
* BWH: Andrey Fedorov, Ron Kikinis, Nicolas Rannou, Sylvain Jaume

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

<h3>Objective</h3>
* To improve cortical segmentation of Vervet segmentation Results
* Use Change tracker module in Slicer to study hippocampal changes between subjects at two time points

</div>

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

<h3>Approach, Plan</h3>
* Improve rigid registration results by optimizing parameters
* Add bias correction to workflow to improve segmentation results
* Study hippocampal changes between subjects at two time points using Change Tracker

</div>

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

<h3>Progress</h3>
* ChangeTracker augmented with the capability to accept externally-defined segmentation ([http://svn.na-mic.org/NAMICSandBox/trunk/ChangeTrackerExtra/ChangeTrackerVT/ ChangeTrackerVT] in NAMIC Sandbox)
* [http://svn.na-mic.org/NAMICSandBox/trunk/MRIBiasCorrectionFilter/ MRIBiasCorrectionFilter] module by Nicolas Rannou available in NAMIC SandBox, initial testing on rhesus data done
* GWE set up on SPL Cluster for registration parameter exploration
* ChangerTracker used to detect change between hippocampus of State0 and State1 of first vervet subject.
* MRIBiasCorrection Module parameter exploration being set up in GWE of SPL cluster.
<h3>In Progress</h3>
* Working with Xioadong to adapt SkullStripper Module for Vervet Images
</div>
</div>
<div style="width: 97%; float: left;">

==References==
* [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction NA-MIC NCBC Collaboration: Measuring alcohol and stress interaction]
* [http://wiki.na-mic.org/Wiki/index.php/EMSegment EM Segment project by Sylvain Jaume and Nicolas Rannou]
* Tustison N., Gee J. "N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction" InsightJournal, 2009 January - June, [http://www.insight-journal.org/browse/publication/640]

Measuring Alcohol Stress Interaction

2009-06-01T19:30:29Z

Vidyaraj: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page Image:MonkeyProject09Slicer.png|[[thumb|Segmentation of Vervet Subcortical Structures]...'

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:MonkeyProject09Slicer.png|[[thumb|Segmentation of Vervet Subcortical Structures]]
</gallery>

==Key Investigators==
* VT: Chris Wyatt, Vidya Rajagopalan
* BWH: Andrey Fedorov

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

<h3>Objective</h3>
* To improve cortical segmentation of Vervet segmentation Results
* Use Change tracker module in Slicer to study hippocampal changes between subjects at two time points

</div>

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

<h3>Approach, Plan</h3>
* Improve rigid registration results by optimizing parameters
* Add bias correction to workflow to improve segmentation results
* Study hippocampal changes between subjects at two time points using Change Tracker

</div>

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

<h3>Progress</h3>

</div>
</div>

==References==

2009 Summer Project Week

2009-06-01T19:13:19Z

Vidyaraj: /* Collaboration Projects */

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) ([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
** 9-11pm Tutorial Contest Presentations
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT]] (Dan M.)
** 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.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)
#Liver Ablation in Slicer (Haiying, Ziv)
#SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Grid Wizard+xnat clinic (Clement Vachet)
#?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 Vachet, Ipek Oguz)
#Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)
#Skull Stripping (Xiaodong, Snehashis Roy)
#FastMarching for brain tumor segmentation (Fedorov, GeorgiaTech)
#Meningioma growth simulation for validation (Fedorov, Marcel, Ron)
#Automatic brain MRI processing pipeline (Marcel, Hans)
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#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)
#breakout session on Dynamic Patient Models (James Balter)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)

===NA-MIC Engineering Projects===
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# EM Segmenter (Sylvain, Nicolas)
# Plug-in 3D Viewer based on XIP (Lining)
# IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien Siebenthal)
# Fix [http://www.na-mic.org/Bug/view.php?id=416 bug 416] in registration (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)

== 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)
#Ferenc Jolesz, BWH (NCIGT, NAC)
#Clare Tempany, BWH (NCIGT)
#Tina Kapur, BWH (NA-MIC, NCIGT)
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Bill Lorensen, EAB
#Randy Gollub, MGH
#Nicole Aucoin, BWH (NA-MIC)
#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
#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

== 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

2009-06-01T15:36:40Z

Vidyaraj: /* Attendee List */

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: 3D+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: [[2009 Project Week Breakout Session: XNAT]] (Dan M.)
** 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.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)
#Liver Ablation in Slicer (Haiying, Ziv)
#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 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)
#Skull Stripping (Xiaodong, Snehashis Roy)
#FastMarching for brain tumor segmentation (Fedorov, GeorgiaTech)
#Meningioma growth simulation for validation (Fedorov, Marcel, Ron)
#Automatic brain MRI processing pipeline (Marcel, Hans)
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)

===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)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# EM Segmenter (Sylvain, Nicolas)
# Plug-in 3D Viewer based on XIP (Lining)
# IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien Siebenthal)
# Fix [http://www.na-mic.org/Bug/view.php?id=416 bug 416] in registration (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)

== 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
#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
#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
#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
#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
#Sonia Pujol, BWH
#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

== 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]]

File:EMSegment TrainingTutorial.pdf

2009-02-06T19:13:26Z

Vidyaraj: uploaded a new version of "Image:EMSegment TrainingTutorial.pdf"

Tutorial for non-human primate segmentation using Slicer3

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2009-02-06T17:27:24Z

Vidyaraj: /* Meetings and Events Specific to this Collaboration */

Back to [[NA-MIC_External_Collaborations]]
==Abstract==
Alcohol abuse continues to be a major problem in the United States with an estimated 14 million adults
meeting the clinical criteria for a diagnosis of alcohol abuse or alcoholism at an estimated cost of $185
billion. Chronic alcohol exposure has been shown to impact structure and function of the brain. Since
most of what is known of alcohol's effects on the brain is based on studies of individuals who have
abused for a long time, it is unclear whether some of the effects might occur early in the abuse process.
Additionally, human studies are often complicated by many factors incuding polydrug abuse, poor
nutritional states and other medical conditions. Another complicating factor is the interaction of stress
and alcohol.

Using magnetic resonance imaging (MRI), we will examine the the effects of chronic alcohol self-
administration on brain structure and function in a group of monkeys that have been mother-reared or
nursery-reared. MRI scans will be acquired to determine whether there are differences in stucture or
functions as a result of alcohol exposure and whether rearing conditions play a role in these effects.
MRI techniques will also be used to examine how chronic alcohol consumption affects cerebral blood
flow, which is a measure of neuronal activity. Because we will conduct these measures both before
and after alcohol exposure in the same "young adult" animals, we will be able to track any changes that
might occur early in alcohol abuse which is something that cannot be accomplished in human studies.
Another goal is to adapt imaging tools and computer software that are used to measure the brains of
humans to the monkey brain. To accomplish this, we will collaborate with the National Alliance for
Medical Computing (NA-MIC), an existing NIH Center for Biomedical Computing.

We can control all variables associated with alcohol self-administration in these monkeys. They will be
monitored both before and after exposure to alcohol, thus, we will be able to monitor the progression of
any changes in structure or function that directly result from alcohol exposure. These studies will help
identify how exposure to long-term alcohol might affect how the brain works.

==Grant #==
1R01AA016748-01

==Key Personnel==
Wake Forest University: Jim Daunais, Bob Kraft

Virginia Tech: Chris Wyatt, Vidya Rajagopalan, Xiaojing Long

NAMIC: Kilian Pohl, Sandy Wells

==Projects==
Active projects in this collaboration are:

=== Tutorials on using EMSegmenter to segment nonhuman primate images ===
#Slicer3 based tutorial
##[http://www.na-mic.org/Wiki/index.php/Image:EMSegment_TrainingTutorial.pdf Tutorial Slide Handouts (PDF)]
##[http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Vervet Atlas]
##[http://www.na-mic.org/Wiki/images/c/c9/SlicerTutorialData_Vervet.tar.gz Example Data]
#[http://bsl.ece.vt.edu/download/NHP-EMSTut.zip older Slicer2.x based tutorial]

=== Nonhuman Primate Atlas Development ===
Vervet Probabalistic Atlas - Adult
# [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Vervet Probabilistic Atlas (VPA-10)]

Rhesus Probabalistic Atlas - Adult
#[[Rhesus_WMGM_Atlas|WM/GM Atlas]]
#[[Rhesus_Subcortical_Atlas|Subcortical Atlas]]

Rhesus Probabalistic Atlas - Juvenile
#[[Rhesus_Juvenile_WMGM_Atlas|WM/GM Atlas]]

Cyno Probabalistic Atlas - Adult
#[[Cyno_WMGM_Atlas|WM/GM Atlas]]

=== Segmentation ===
#[[Rhesus_ICV_Extraction | Rhesus ICV Extraction]]
#[[Rhesus_EM_Segmentation | Rhesus EM Segmentation]]

==Publications==
==Meetings and Events Specific to this Collaboration==
*[[2007_Programming/Project_Week_MIT|2007 Summer Programming/Project Week at MIT]]
*[[AHM_2008|2008 NA-MIC AHM]]
*[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction|2008 NA-MIC Summer Project Week Page]]
*2009 NA-MIC Winter Project Week Pages: [[2009_Winter_Project_Week_WFU1|Project 1]]

==Resource Links==

* [http://www.slicer.org slicer]
* [http://www.bsl.ece.vt.edu Bioimaging Systems Lab at VT]

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2009-02-06T17:26:13Z

Vidyaraj: /* Tutorials on using EMSegmenter to segment nonhuman primate images */

Back to [[NA-MIC_External_Collaborations]]
==Abstract==
Alcohol abuse continues to be a major problem in the United States with an estimated 14 million adults
meeting the clinical criteria for a diagnosis of alcohol abuse or alcoholism at an estimated cost of $185
billion. Chronic alcohol exposure has been shown to impact structure and function of the brain. Since
most of what is known of alcohol's effects on the brain is based on studies of individuals who have
abused for a long time, it is unclear whether some of the effects might occur early in the abuse process.
Additionally, human studies are often complicated by many factors incuding polydrug abuse, poor
nutritional states and other medical conditions. Another complicating factor is the interaction of stress
and alcohol.

Using magnetic resonance imaging (MRI), we will examine the the effects of chronic alcohol self-
administration on brain structure and function in a group of monkeys that have been mother-reared or
nursery-reared. MRI scans will be acquired to determine whether there are differences in stucture or
functions as a result of alcohol exposure and whether rearing conditions play a role in these effects.
MRI techniques will also be used to examine how chronic alcohol consumption affects cerebral blood
flow, which is a measure of neuronal activity. Because we will conduct these measures both before
and after alcohol exposure in the same "young adult" animals, we will be able to track any changes that
might occur early in alcohol abuse which is something that cannot be accomplished in human studies.
Another goal is to adapt imaging tools and computer software that are used to measure the brains of
humans to the monkey brain. To accomplish this, we will collaborate with the National Alliance for
Medical Computing (NA-MIC), an existing NIH Center for Biomedical Computing.

We can control all variables associated with alcohol self-administration in these monkeys. They will be
monitored both before and after exposure to alcohol, thus, we will be able to monitor the progression of
any changes in structure or function that directly result from alcohol exposure. These studies will help
identify how exposure to long-term alcohol might affect how the brain works.

==Grant #==
1R01AA016748-01

==Key Personnel==
Wake Forest University: Jim Daunais, Bob Kraft

Virginia Tech: Chris Wyatt, Vidya Rajagopalan, Xiaojing Long

NAMIC: Kilian Pohl, Sandy Wells

==Projects==
Active projects in this collaboration are:

=== Tutorials on using EMSegmenter to segment nonhuman primate images ===
#Slicer3 based tutorial
##[http://www.na-mic.org/Wiki/index.php/Image:EMSegment_TrainingTutorial.pdf Tutorial Slide Handouts (PDF)]
##[http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Vervet Atlas]
##[http://www.na-mic.org/Wiki/images/c/c9/SlicerTutorialData_Vervet.tar.gz Example Data]
#[http://bsl.ece.vt.edu/download/NHP-EMSTut.zip older Slicer2.x based tutorial]

=== Nonhuman Primate Atlas Development ===
Vervet Probabalistic Atlas - Adult
# [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Vervet Probabilistic Atlas (VPA-10)]

Rhesus Probabalistic Atlas - Adult
#[[Rhesus_WMGM_Atlas|WM/GM Atlas]]
#[[Rhesus_Subcortical_Atlas|Subcortical Atlas]]

Rhesus Probabalistic Atlas - Juvenile
#[[Rhesus_Juvenile_WMGM_Atlas|WM/GM Atlas]]

Cyno Probabalistic Atlas - Adult
#[[Cyno_WMGM_Atlas|WM/GM Atlas]]

=== Segmentation ===
#[[Rhesus_ICV_Extraction | Rhesus ICV Extraction]]
#[[Rhesus_EM_Segmentation | Rhesus EM Segmentation]]

==Publications==
==Meetings and Events Specific to this Collaboration==
*[[2007_Programming/Project_Week_MIT|2007 Summer Programming/Project Week at MIT]]
*[[AHM_2008|2008 NA-MIC AHM]]
*[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction|2008 NA-MIC Summer Project Week Page]]
*2009 NA-MIC Winter Project Week Pages: [[2009_Winter_Project_Week_WFU1|Project 1]], [[2009_Winter_Project_Week_WFU2|Project 2]]

==Resource Links==

* [http://www.slicer.org slicer]
* [http://www.bsl.ece.vt.edu Bioimaging Systems Lab at VT]

File:SlicerTutorialData Vervet.tar.gz

2009-02-06T17:25:17Z

Vidyaraj:

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2009-02-06T17:23:45Z

Vidyaraj: /* Tutorials on using EMSegmenter to segment nonhuman primate images */

Back to [[NA-MIC_External_Collaborations]]
==Abstract==
Alcohol abuse continues to be a major problem in the United States with an estimated 14 million adults
meeting the clinical criteria for a diagnosis of alcohol abuse or alcoholism at an estimated cost of $185
billion. Chronic alcohol exposure has been shown to impact structure and function of the brain. Since
most of what is known of alcohol's effects on the brain is based on studies of individuals who have
abused for a long time, it is unclear whether some of the effects might occur early in the abuse process.
Additionally, human studies are often complicated by many factors incuding polydrug abuse, poor
nutritional states and other medical conditions. Another complicating factor is the interaction of stress
and alcohol.

Using magnetic resonance imaging (MRI), we will examine the the effects of chronic alcohol self-
administration on brain structure and function in a group of monkeys that have been mother-reared or
nursery-reared. MRI scans will be acquired to determine whether there are differences in stucture or
functions as a result of alcohol exposure and whether rearing conditions play a role in these effects.
MRI techniques will also be used to examine how chronic alcohol consumption affects cerebral blood
flow, which is a measure of neuronal activity. Because we will conduct these measures both before
and after alcohol exposure in the same "young adult" animals, we will be able to track any changes that
might occur early in alcohol abuse which is something that cannot be accomplished in human studies.
Another goal is to adapt imaging tools and computer software that are used to measure the brains of
humans to the monkey brain. To accomplish this, we will collaborate with the National Alliance for
Medical Computing (NA-MIC), an existing NIH Center for Biomedical Computing.

We can control all variables associated with alcohol self-administration in these monkeys. They will be
monitored both before and after exposure to alcohol, thus, we will be able to monitor the progression of
any changes in structure or function that directly result from alcohol exposure. These studies will help
identify how exposure to long-term alcohol might affect how the brain works.

==Grant #==
1R01AA016748-01

==Key Personnel==
Wake Forest University: Jim Daunais, Bob Kraft

Virginia Tech: Chris Wyatt, Vidya Rajagopalan, Xiaojing Long

NAMIC: Kilian Pohl, Sandy Wells

==Projects==
Active projects in this collaboration are:

=== Tutorials on using EMSegmenter to segment nonhuman primate images ===
#Slicer3 based tutorial
##[http://www.na-mic.org/Wiki/index.php/Image:EMSegment_TrainingTutorial.pdf Tutorial Slide Handouts (PDF)]
##[http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Vervet Atlas]
#[http://bsl.ece.vt.edu/download/NHP-EMSTut.zip older Slicer2.x based tutorial]

=== Nonhuman Primate Atlas Development ===
Vervet Probabalistic Atlas - Adult
# [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Vervet Probabilistic Atlas (VPA-10)]

Rhesus Probabalistic Atlas - Adult
#[[Rhesus_WMGM_Atlas|WM/GM Atlas]]
#[[Rhesus_Subcortical_Atlas|Subcortical Atlas]]

Rhesus Probabalistic Atlas - Juvenile
#[[Rhesus_Juvenile_WMGM_Atlas|WM/GM Atlas]]

Cyno Probabalistic Atlas - Adult
#[[Cyno_WMGM_Atlas|WM/GM Atlas]]

=== Segmentation ===
#[[Rhesus_ICV_Extraction | Rhesus ICV Extraction]]
#[[Rhesus_EM_Segmentation | Rhesus EM Segmentation]]

==Publications==
==Meetings and Events Specific to this Collaboration==
*[[2007_Programming/Project_Week_MIT|2007 Summer Programming/Project Week at MIT]]
*[[AHM_2008|2008 NA-MIC AHM]]
*[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction|2008 NA-MIC Summer Project Week Page]]
*2009 NA-MIC Winter Project Week Pages: [[2009_Winter_Project_Week_WFU1|Project 1]], [[2009_Winter_Project_Week_WFU2|Project 2]]

==Resource Links==

* [http://www.slicer.org slicer]
* [http://www.bsl.ece.vt.edu Bioimaging Systems Lab at VT]

2009 Winter Project Week WFU1

2009-01-08T20:34:01Z

Vidyaraj: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:Rhesus_HpcCorScrnShot.jpg|thumb|220px|Subcortical Segmentation of Rhesus subject]]
|}

__NOTOC__

===Key Investigators===
* Virgina Tech: Chris Wyatt
* Virginia Tech: Vidya Rajagopalan
* TBD

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

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

<h1>Objective</h1>
We are developing methods for analysis of structural images from nonhuman primates for identifying regional differences in brain morphometry caused by interactions of stress and alcohol exposure. The current workflow for segmentation of the subject images involves a collection of tools that make it difficult to export to the neuroscience community. The goal of this project is to move our entire workflow into Slicer 3.

</div>

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

<h1>Approach, Plan</h1>

At the [[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction|2008 NA-MIC Summer Project Week]] we optimized EMSegmenter in slicer2 for segmentation of tissue classes and subcortical structures (above image). We have since moved to using the EMSegmenter module in Slicer3. Comparisons between the resulting segmentations show only small differences.

Our plan for the project week is to move our entire NHP segmentation workflow into Slicer3 so that it is easier for collaborators and others to use. This requires replacing our current registration procedure based on FSL-FLIRT and writing command-line modules for a few custom tools.
</div>

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

<h1>Progress</h1>
IN PROGRESS

* replace FLS-flirt with rigid and affine CLPs (working with Jim Miller)

COMPLETED

* write and test CLP module using our existing ITK-based deformable registration code
* write and test CLP module using our existing ITK-based brain extraction code
* write new tutorial using all-Slicer3 workflow
* develop a cleanup process using the Slicer3 editor

POSTPONED
* create XNAT delivery mechanism for NHP atlas and test subject data

</div>

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

</div>

===References===
[[NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction]]

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2009-01-06T15:09:26Z

Vidyaraj: /* Tutorials on using EMSegmenter to segment nonhuman primate images */

Back to [[NA-MIC_External_Collaborations]]
==Abstract==
Alcohol abuse continues to be a major problem in the United States with an estimated 14 million adults
meeting the clinical criteria for a diagnosis of alcohol abuse or alcoholism at an estimated cost of $185
billion. Chronic alcohol exposure has been shown to impact structure and function of the brain. Since
most of what is known of alcohol's effects on the brain is based on studies of individuals who have
abused for a long time, it is unclear whether some of the effects might occur early in the abuse process.
Additionally, human studies are often complicated by many factors incuding polydrug abuse, poor
nutritional states and other medical conditions. Another complicating factor is the interaction of stress
and alcohol.

Using magnetic resonance imaging (MRI), we will examine the the effects of chronic alcohol self-
administration on brain structure and function in a group of monkeys that have been mother-reared or
nursery-reared. MRI scans will be acquired to determine whether there are differences in stucture or
functions as a result of alcohol exposure and whether rearing conditions play a role in these effects.
MRI techniques will also be used to examine how chronic alcohol consumption affects cerebral blood
flow, which is a measure of neuronal activity. Because we will conduct these measures both before
and after alcohol exposure in the same "young adult" animals, we will be able to track any changes that
might occur early in alcohol abuse which is something that cannot be accomplished in human studies.
Another goal is to adapt imaging tools and computer software that are used to measure the brains of
humans to the monkey brain. To accomplish this, we will collaborate with the National Alliance for
Medical Computing (NA-MIC), an existing NIH Center for Biomedical Computing.

We can control all variables associated with alcohol self-administration in these monkeys. They will be
monitored both before and after exposure to alcohol, thus, we will be able to monitor the progression of
any changes in structure or function that directly result from alcohol exposure. These studies will help
identify how exposure to long-term alcohol might affect how the brain works.

==Grant #==
1R01AA016748-01

==Key Personnel==
Wake Forest University: Jim Daunais, Bob Kraft

Virginia Tech: Chris Wyatt, Vidya Rajagopalan, Xiaojing Long

NAMIC: Kilian Pohl, Sandy Wells

==Projects==
Active projects in this collaboration are:

=== Tutorials on using EMSegmenter to segment nonhuman primate images ===
#Slicer3 based tutorial
##[http://www.na-mic.org/Wiki/index.php/Image:EMSegment_TrainingTutorial.pdf Tutorial Slide Handouts (PDF)]
##[http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Example Data]
#[http://bsl.ece.vt.edu/download/NHP-EMSTut.zip older Slicer2.x based tutorial]

=== Nonhuman Primate Atlas Development ===
Vervet Probabalistic Atlas - Adult
# [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Vervet Probabilistic Atlas (VPA-10)]

Rhesus Probabalistic Atlas - Adult
#[[Rhesus_WMGM_Atlas|WM/GM Atlas]]
#[[Rhesus_Subcortical_Atlas|Subcortical Atlas]]

Rhesus Probabalistic Atlas - Juvenile
#[[Rhesus_Juvenile_WMGM_Atlas|WM/GM Atlas]]

Cyno Probabalistic Atlas - Adult
#[[Cyno_WMGM_Atlas|WM/GM Atlas]]

=== Segmentation ===
#[[Rhesus_ICV_Extraction | Rhesus ICV Extraction]]
#[[Rhesus_EM_Segmentation | Rhesus EM Segmentation]]

==Publications==
==Meetings and Events Specific to this Collaboration==
*[[2007_Programming/Project_Week_MIT|2007 Summer Programming/Project Week at MIT]]
*[[AHM_2008|2008 NA-MIC AHM]]
*[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction|2008 NA-MIC Summer Project Week Page]]
*2009 NA-MIC Winter Project Week Pages: [[2009_Winter_Project_Week_WFU1|Project 1]], [[2009_Winter_Project_Week_WFU2|Project 2]]

==Resource Links==

* [http://www.slicer.org slicer]
* [http://www.bsl.ece.vt.edu Bioimaging Systems Lab at VT]

Non-human Primates Segmentation Tutorial

2009-01-05T03:22:26Z

Vidyaraj: /* Tutorial */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:HPCSeg_V2.jpg|thumb|250pix|Subcortical Segmentation of Rhesus subject]]
|[[Image:Vervet_CorScrnShot.jpg|thumb|220px|Segmentation of major tissue classes in for vervet subject ]]
|}

__NOTOC__

===Key Investigators===
* Chris Wyatt
* Vidya Rajagopalan

===Tutorial===
* [http://www.na-mic.org/Wiki/index.php/Image:EMSegment_TrainingTutorial.pdf Tutorial Slide Handouts (PDF)]
* [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Example Data]

__NOTOC__
<div style="margin: 20px;">
<div style="width: 40%; float: left; padding-right: 3%;">
<h1>Objective</h1>
The objective of the tutorial is to enable users to segment non-human primate images
using Slicer3
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Approach, Plan</h1>
The tutorial provides step-by-step instructions to:
* skull strip subject image
* create subject specific tissue atlas from a generic atlas
* use EMSegmenter to segment the subject image.
</div>

<div style="width: 27%; float: left;">
<h1>Progress</h1>
A tutorial has been developed, segmentation atlas and data are available for tutorial
</div>

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

Non-human Primates Segmentation Tutorial

2009-01-05T03:20:43Z

Vidyaraj: New page: {| |Project Week Main Page ]] |Subcortical Segmentation of Rhesus subject |[[I...

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:HPCSeg_V2.jpg|thumb|250pix|Subcortical Segmentation of Rhesus subject]]
|[[Image:Vervet_CorScrnShot.jpg|thumb|220px|Segmentation of major tissue classes in for vervet subject ]]
|}

__NOTOC__

===Key Investigators===
* Chris Wyatt
* Vidya Rajagopalan

===Tutorial===
* [http://www.na-mic.org/Wiki/images/8/83/EMSegment_TrainingTutorial.pdf Tutorial Slide Handouts (PDF)]
* [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Example Data]

__NOTOC__
<div style="margin: 20px;">
<div style="width: 40%; float: left; padding-right: 3%;">
<h1>Objective</h1>
The objective of the tutorial is to enable users to segment non-human primate images
using Slicer3
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Approach, Plan</h1>
The tutorial provides step-by-step instructions to:
* skull strip subject image
* create subject specific tissue atlas from a generic atlas
* use EMSegmenter to segment the subject image.
</div>

<div style="width: 27%; float: left;">
<h1>Progress</h1>
A tutorial has been developed, segmentation atlas and data are available for tutorial
</div>

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

File:EMSegment TrainingTutorial.pdf

2009-01-05T03:07:22Z

Vidyaraj: Tutorial for non-human primate segmentation using Slicer3

Tutorial for non-human primate segmentation using Slicer3

Events:TutorialContestJan2009

2009-01-05T03:05:40Z

Vidyaraj: /* Entries */

[[Image:Munich2008-Seb.jpg |250px|thumb|right]]
=Background=

[http://www.slicer.org Slicer3] is now being used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and functionality available in Slicer. Examples for such existing tutorials are the level 1 and 2 courses in the [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training#Training_Compendium|NA-MIC training compendium].

<br>

=Tutorial Contest Goal=
The primary purpose of this contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe contestants will be motivated to participate to enhance the dissemination of their own algorithms that they have incorporated into the Slicer3 platform and/or to enhance training of Slicer3 functionality for their own laboratory groups.
<br>
There will be two categories:
#'''END TO END SOLUTION TUTORIAL:''' In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. Entries into this category will require at least:
#*materials about the scientific and application background and motivation,
#*step-by-step guides, and
#*sample data
#*Example: [[IGT:ToolKit/Neurosurgical-Planning|Neurosurgical Planning for Image Guided Therapy using Slicer3]]
#'''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data. Entries into this category will require at least:
#*materials about the scientific and application background of the algorithm(s) and their use in the Slicer environment
#*step-by-step guides, and
#*at least two different sample data sets from two different institutions
#*Example: [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|Automatic Segmentation Tutorial using Slicer3]]
<br>

=Template=
A basic template has been used for all of the tutorials. The same design should be used for the contest. It can be found here: [[Media:TrainingTutorialTemplate.ppt|Template]]
*Note: The examples above predate the template.

=Rules=
*Tutorial must be based on a snapshot or release of Slicer 3
*Tutorial must follow the guidelines specified above
*If applicable, provide clear directions for downloading and installing additional modules
*The tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]
*Applicants must agree to work with the NA-MIC Training and Dissemination Cores to curate their submission (we will test it on each of the available platforms and for usability and work with you to smooth any issues after the contest).
<br>

=Prizes=
Winning contestants from each category will receive a cash prize courtesy of Kitware Inc.
*1st: $250
*2nd: $150
*3rd: $100
<br>

=Dates=
*Submission: Tuesday, January 6th, Midnight, Utah time (MST) (there will be '''no extensions''')
*Review: Wednesday, January 7th
*Decisions announced: Thursday January 8th at NA-MIC All-Hands-Meeting
<br>

=Judges=
*Ron Kikinis
*Luis Ibanez
*Steve Pieper
*Randy Gollub
*Sonia Pujol
*Core 1 representative
<br>

=Questions=
Contact Training Core PI: Randy L. Gollub (rgollub at partners dot org)
<br>

=Entries=
#[[Iowa Meshing Tutorial]] - Demonstrates the new hexahedral meshing capabilities Slicer3 using a proximal phalanx bone
#[[Non-human Primates Segmentation Tutorial]] -Virginia Tech - Demonstrates how to use Slicer3 for skull stripping and automatically segmenting non-human primate MR images.

Events:TutorialContestJan2009

2009-01-05T03:00:57Z

Vidyaraj: /* Entries */

Events:TutorialContestJan2009

2009-01-05T02:59:54Z

Vidyaraj: /* Entries */

[[Image:Munich2008-Seb.jpg |250px|thumb|right]]
=Background=

[http://www.slicer.org Slicer3] is now being used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and functionality available in Slicer. Examples for such existing tutorials are the level 1 and 2 courses in the [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training#Training_Compendium|NA-MIC training compendium].

<br>

=Tutorial Contest Goal=
The primary purpose of this contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe contestants will be motivated to participate to enhance the dissemination of their own algorithms that they have incorporated into the Slicer3 platform and/or to enhance training of Slicer3 functionality for their own laboratory groups.
<br>
There will be two categories:
#'''END TO END SOLUTION TUTORIAL:''' In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. Entries into this category will require at least:
#*materials about the scientific and application background and motivation,
#*step-by-step guides, and
#*sample data
#*Example: [[IGT:ToolKit/Neurosurgical-Planning|Neurosurgical Planning for Image Guided Therapy using Slicer3]]
#'''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data. Entries into this category will require at least:
#*materials about the scientific and application background of the algorithm(s) and their use in the Slicer environment
#*step-by-step guides, and
#*at least two different sample data sets from two different institutions
#*Example: [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|Automatic Segmentation Tutorial using Slicer3]]
<br>

=Template=
A basic template has been used for all of the tutorials. The same design should be used for the contest. It can be found here: [[Media:TrainingTutorialTemplate.ppt|Template]]
*Note: The examples above predate the template.

=Rules=
*Tutorial must be based on a snapshot or release of Slicer 3
*Tutorial must follow the guidelines specified above
*If applicable, provide clear directions for downloading and installing additional modules
*The tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]
*Applicants must agree to work with the NA-MIC Training and Dissemination Cores to curate their submission (we will test it on each of the available platforms and for usability and work with you to smooth any issues after the contest).
<br>

=Prizes=
Winning contestants from each category will receive a cash prize courtesy of Kitware Inc.
*1st: $250
*2nd: $150
*3rd: $100
<br>

=Dates=
*Submission: Tuesday, January 6th, Midnight, Utah time (MST) (there will be '''no extensions''')
*Review: Wednesday, January 7th
*Decisions announced: Thursday January 8th at NA-MIC All-Hands-Meeting
<br>

=Judges=
*Ron Kikinis
*Luis Ibanez
*Steve Pieper
*Randy Gollub
*Sonia Pujol
*Core 1 representative
<br>

=Questions=
Contact Training Core PI: Randy L. Gollub (rgollub at partners dot org)
<br>

=Entries=
#[[Iowa Meshing Tutorial]] - Demonstrates the new hexahedral meshing capabilities Slicer3 using a proximal phalanx bone

#[[Non-human Primates Segmentation Tutorial]] - Demonstrates how to use Slicer3 for skull stripping and automatically segmenting non-human primate MR images.

2009 Winter Project Week WFU1

2009-01-02T19:08:45Z

Vidyaraj: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:Rhesus_HpcCorScrnShot.jpg|thumb|220px|Subcortical Segmentation of Rhesus subject]]
|}

__NOTOC__

===Key Investigators===
* Virgina Tech: Chris Wyatt
* Virginia Tech: Vidya Rajagopalan
* TBD

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

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

<h1>Objective</h1>
We are developing methods for analysis of structural images from nonhuman primates for identifying regional differences in brain morphometry caused by interactions of stress and alcohol exposure. The current workflow for segmentation of the subject images involves a collection of tools that make it difficult to export to the neuroscience community. The goal of this project is to move our entire workflow into Slicer 3.

</div>

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

<h1>Approach, Plan</h1>

At the [[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction|2008 NA-MIC Summer Project Week]] we optimized EMSegmenter in slicer2 for segmentation of tissue classes and subcortical structures (above image). We have since moved to using the EMSegmenter module in Slicer3. Comparisons between the resulting segmentations show only small differences.

Our plan for the project week is to move our entire NHP segmentation workflow into Slicer3 so that it is easier for collaborators and others to use. This requires replacing our current registration procedure based on FSL-FLIRT and writing command-line modules for a few custom tools.
</div>

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

<h1>Progress</h1>
TO-DO:
* replace FLS-flirt with rigid and affine CLPs
* develop a cleanup process using the Slicer3 editor
* create XNAT delivery mechanism for NHP atlas and test subject data

COMPLETED

* write and test CLP module using our existing ITK-based deformable registration code
* write and test CLP module using our existing ITK-based brain extraction code
* write new tutorial using all-Slicer3 workflow

</div>

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

</div>

===References===
[[NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction]]

NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction

2008-06-26T22:02:33Z

Vidyaraj:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]

|}

__NOTOC__

===Key Investigators===

* BWH: Kilian Pohl
* Virginia Tech: Chris Wyatt, Vidya Rajagopalan
* Kitware: Luis Ibanez

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

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

<h1>Objective</h1>

The objectives of this project are to:
* Optimize the EM Brain Classifier in Slicer on MRI images of vervets.
* Segment data from N subjects.
* Optimize GM/WM/CSF segmentation so that calculation of GM/WM volume and ratios between the two states can be automated.
* Optimize hippocampus, putamen and caudate segmentation so that volume comparison between states can be performed.

</div>

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

<h1>Approach, Plan</h1>
We will use the current implementation of the EM Segmenter in Slicer. Using a manual segmentation as an estimate of ground truth in a single subject, we will optimize the EM segmenter parameters over the classification error and running time.
</div>

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

<h1>Progress</h1>
Prior to the project week:
* Study data on 8 subjects at two time points (alcohol naive and post-induction) organized
* GM/WM/CSF atlas will be constructed for the study data.

During Project Week

* Optimized segmentation parameters for vervet data
* Improved accuracy of subcortical segmentation in rhesus data set

{|
|[[Image:Vervet_CorScrnShot.jpg|thumb|220px|Segmentation of major tissue classes in for vervet subject ]]
|[[Image:Rhesus_HpcCorScrnShot.jpg|thumb|220px|Subcortical Segmentation of Rhesus subject]]
|}

* Developed an ITK utility for multiresolution demons registration. (Source code available for download from the NAMIC sandbox)
{|
|[[Image:CheckerB4Reg_Screenshot.jpg |thumb|220px|Checker Image of source and target before registration ]]
|[[Image:CheckerAfterreg_Screenshot.png|thumb|220px|Checker Image of source and target after registration]]
|}

</div>

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

</div>

===References===
*

NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction

2008-06-26T22:01:06Z

Vidyaraj:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]

|}

__NOTOC__

===Key Investigators===

* Wake Forest: Bob Kraft, Jim Daunais
* BWH: Kilian Pohl
* Virginia Tech: Chris Wyatt, Vidya Rajagopalan
* Kitware: Luis Ibanez

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

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

<h1>Objective</h1>

The objectives of this project are to:
* Optimize the EM Brain Classifier in Slicer on MRI images of vervets.
* Segment data from N subjects.
* Optimize GM/WM/CSF segmentation so that calculation of GM/WM volume and ratios between the two states can be automated.
* Optimize hippocampus, putamen and caudate segmentation so that volume comparison between states can be performed.

</div>

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

<h1>Approach, Plan</h1>
We will use the current implementation of the EM Segmenter in Slicer. Using a manual segmentation as an estimate of ground truth in a single subject, we will optimize the EM segmenter parameters over the classification error and running time.
</div>

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

<h1>Progress</h1>
Prior to the project week:
* Study data on 8 subjects at two time points (alcohol naive and post-induction) organized
* GM/WM/CSF atlas will be constructed for the study data.

During Project Week

* Optimized segmentation parameters for vervet data
* Improved accuracy of subcortical segmentation in rhesus data set

{|
|[[Image:Vervet_CorScrnShot.jpg|thumb|220px|Segmentation of major tissue classes in for vervet subject ]]
|[[Image:Rhesus_HpcCorScrnShot.jpg|thumb|220px|Subcortical Segmentation of Rhesus subject]]
|}

* Developed an ITK utility for multiresolution demons registration. (Source code available for download from the NAMIC sandbox)
{|
|[[Image:CheckerB4Reg_Screenshot.jpg |thumb|220px|Checker Image of source and target before registration ]]
|[[Image:CheckerAfterreg_Screenshot.png|thumb|220px|Checker Image of source and target after registration]]
|}

</div>

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

</div>

===References===
*

NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction

2008-06-26T21:55:28Z

Vidyaraj:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]

|}

__NOTOC__

===Key Investigators===

* Wake Forest: Bob Kraft, Jim Daunais
* BWH: Kilian Pohl
* Virginia Tech: Chris Wyatt, Vidya Rajagopalan
* Kitware: Luis Ibanez

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

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

<h1>Objective</h1>

The objectives of this project are to:
* Optimize the EM Brain Classifier in Slicer on MRI images of vervets.
* Segment data from N subjects.
* Optimize GM/WM/CSF segmentation so that calculation of GM/WM volume and ratios between the two states can be automated.
* Optimize hippocampus, putamen and caudate segmentation so that volume comparison between states can be performed.

</div>

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

<h1>Approach, Plan</h1>
We will use the current implementation of the EM Segmenter in Slicer. Using a manual segmentation as an estimate of ground truth in a single subject, we will optimize the EM segmenter parameters over the classification error and running time.
</div>

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

<h1>Progress</h1>
Prior to the project week:
* Study data on 8 subjects at two time points (alcohol naive and post-induction) organized
* GM/WM/CSF atlas will be constructed for the study data.

During Project Week

* Optimized segmentation parameters for vervet data
* Improved accuracy of subcortical segmentation in rhesus data set

{|
|[[Image:Vervet_CorScrnShot.jpg|thumb|320px|Segmentation of major tissue classes in for vervet subject ]]
|[[Image:Rhesus_HpcCorScrnShot.jpg|thumb|320px|Subcortical Segmentation of Rhesus subject]]
|}

* Developed an ITK utility for multiresolution demons registration. (Source code available for download from the NAMIC sandbox)
{|
|[[Image:CheckerB4Reg_Screenshot.jpg |thumb|320px|Checker Image of source and target before registration ]]
|[[Image:CheckerAfterreg_Screenshot.png|thumb|320px|Checker Image of source and target after registration]]
|}

</div>

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

</div>

===References===
*

NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction

2008-06-26T21:54:37Z

Vidyaraj:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]

|}

__NOTOC__

===Key Investigators===

* Wake Forest: Bob Kraft, Jim Daunais
* BWH: Kilian Pohl
* Virginia Tech: Chris Wyatt, Vidya Rajagopalan
* Kitware: Luis Ibanez

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

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

<h1>Objective</h1>

The objectives of this project are to:
# Optimize the EM Brain Classifier in Slicer on MRI images of vervets.
# Segment data from N subjects.
# Optimize GM/WM/CSF segmentation so that calculation of GM/WM volume and ratios between the two states can be automated.
# Optimize hippocampus, putamen and caudate segmentation so that volume comparison between states can be performed.

</div>

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

<h1>Approach, Plan</h1>
We will use the current implementation of the EM Segmenter in Slicer. Using a manual segmentation as an estimate of ground truth in a single subject, we will optimize the EM segmenter parameters over the classification error and running time.
</div>

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

<h1>Progress</h1>
Prior to the project week:
* Study data on 8 subjects at two time points (alcohol naive and post-induction) organized
* GM/WM/CSF atlas will be constructed for the study data.

During Project Week

* Optimized segmentation parameters for vervet data
* Improved accuracy of subcortical segmentation in rhesus data set

{|
|[[Image:Vervet_CorScrnShot.jpg|thumb|320px|Segmentation of major tissue classes in for vervet subject ]]
|[[Image:Rhesus_HpcCorScrnShot.jpg|thumb|320px|Subcortical Segmentation of Rhesus subject]]
|}

* Developed an ITK utility for multiresolution demons registration. (Source code available for download from the NAMIC sandbox)
{|
|[[Image:CheckerB4Reg_Screenshot.jpg |thumb|320px|Checker Image of source and target before registration ]]
|[[Image:CheckerAfterreg_Screenshot.png|thumb|320px|Checker Image of source and target after registration]]
|}

</div>

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

</div>

===References===
*

NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction

2008-06-26T21:51:27Z

Vidyaraj:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]

|}

__NOTOC__

===Key Investigators===

* Wake Forest: Bob Kraft, Jim Daunais
* BWH: Kilian Pohl
* Virginia Tech: Chris Wyatt, Vidya Rajagopalan
* Kitware: Luis Ibanez

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

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

<h1>Objective</h1>

The objectives of this project are to:
# Optimize the EM Brain Classifier in Slicer on MRI images of vervets.
# Segment data from N subjects.
# Optimize GM/WM/CSF segmentation so that calculation of GM/WM volume and ratios between the two states can be automated.
# Optimize hippocampus, putamen and caudate segmentation so that volume comparison between states can be performed.

</div>

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

<h1>Approach, Plan</h1>
We will use the current implementation of the EM Segmenter in Slicer. Using a manual segmentation as an estimate of ground truth in a single subject, we will optimize the EM segmenter parameters over the classification error and running time.
</div>

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

<h1>Progress</h1>
Prior to the project week:
# Study data on 8 subjects at two time points (alcohol naive and post-induction) organized
# GM/WM/CSF atlas will be constructed for the study data.

During Project Week

1 Optimized segmentation parameters for vervet data
2 Improved accuracy of subcortical segmentation in rhesus data set

{|
|[[Image:Vervet_CorScrnShot.jpg|thumb|320px|Segmentation of major tissue classes in for vervet subject ]]
|[[Image:Rhesus_HpcCorScrnShot.jpg|thumb|320px|Subcortical Segmentation of Rhesus subject]]
|}

3 Developed an ITK utility for multiresolution demons registration. (Source code available for download from the NAMIC sandbox)
{|
|[[Image:CheckerB4Reg_Screenshot.jpg |thumb|320px|Checker Image of source and target before registration ]]
|[[Image:CheckerAfterreg_Screenshot.png|thumb|320px|Checker Image of source and target after registration]]
|}

</div>

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

</div>

===References===
*

File:CheckerAfterreg Screenshot.png

2008-06-26T21:38:33Z

Vidyaraj:

File:CheckerB4Reg Screenshot.jpg

2008-06-26T21:38:15Z

Vidyaraj:

File:Rhesus HpcCorScrnShot.jpg

2008-06-26T21:37:54Z

Vidyaraj:

File:Vervet CorScrnShot.jpg

2008-06-26T21:37:21Z

Vidyaraj:

NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction

2008-06-02T13:56:17Z

Vidyaraj:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:HPCSeg_V2.jpg|thumb|320px|Subcortical Segmentation of Rhesus subject]]
|}

__NOTOC__

===Key Investigators===

* Wake Forest: Bob Kraft, Jim Daunais
* BWH: Kilian Pohl
* Virginia Tech: Chris Wyatt, Vidya Rajagopalan

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

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

<h1>Objective</h1>

The objectives of this project are to:
# Optimize the EM Brain Classifier in Slicer on MRI images of vervets.
# Segment data from N subjects.
# Optimize GM/WM/CSF segmentation so that calculation of GM/WM volume and ratios between the two states can be automated.
# Optimize hippocampus, putamen and caudate segmentation so that volume comparison between states can be performed.

</div>

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

<h1>Approach, Plan</h1>
We will use the current implementation of the EM Segmenter in Slicer. Using a manual segmentation as an estimate of ground truth in a single subject, we will optimize the EM segmenter parameters over the classification error and running time.
</div>

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

<h1>Progress</h1>
Prior to the project week:
# Study data on 8 subjects at two time points (alcohol naive and post-induction) organized
# GM/WM/CSF atlas will be constructed for the study data.
# An atlas for subcortical structures will be constructed and integrated into the GM/WM/CSF atlas.

</div>

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

</div>

===References===
*

NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction

2008-06-02T13:25:12Z

Vidyaraj:

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2008-06-02T13:23:29Z

Vidyaraj: /* Meetings and Events Specific to this Collaboration */

Back to [[NA-MIC_External_Collaborations]]
==Abstract==
Alcohol abuse continues to be a major problem in the United States with an estimated 14 million adults
meeting the clinical criteria for a diagnosis of alcohol abuse or alcoholism at an estimated cost of $185
billion. Chronic alcohol exposure has been shown to impact structure and function of the brain. Since
most of what is known of alcohol's effects on the brain is based on studies of individuals who have
abused for a long time, it is unclear whether some of the effects might occur early in the abuse process.
Additionally, human studies are often complicated by many factors incuding polydrug abuse, poor
nutritional states and other medical conditions. Another complicating factor is the interaction of stress
and alcohol.

Using magnetic resonance imaging (MRI), we will examine the the effects of chronic alcohol self-
administration on brain structure and function in a group of monkeys that have been mother-reared or
nursery-reared. MRI scans will be acquired to determine whether there are differences in stucture or
functions as a result of alcohol exposure and whether rearing conditions play a role in these effects.
MRI techniques will also be used to examine how chronic alcohol consumption affects cerebral blood
flow, which is a measure of neuronal activity. Because we will conduct these measures both before
and after alcohol exposure in the same "young adult" animals, we will be able to track any changes that
might occur early in alcohol abuse which is something that cannot be accomplished in human studies.
Another goal is to adapt imaging tools and computer software that are used to measure the brains of
humans to the monkey brain. To accomplish this, we will collaborate with the National Alliance for
Medical Computing (NA-MIC), an existing NIH Center for Biomedical Computing.

We can control all variables associated with alcohol self-administration in these monkeys. They will be
monitored both before and after exposure to alcohol, thus, we will be able to monitor the progression of
any changes in structure or function that directly result from alcohol exposure. These studies will help
identify how exposure to long-term alcohol might affect how the brain works.

==Grant #==
1R01AA016748-01

==Key Personnel==
Wake Forest University: Jim Daunais, Bob Kraft

Virginia Tech: Chris Wyatt, Vidya Rajagopalan, Xiaojing Long

NAMIC: Kilian Pohl, Sandy Wells

==Projects==
Active projects in this collaboration are:

=== Tutorial on using EMSegment in Slicer 2.x to segment NHP images (New!) ===
We now have a tutorial demonstrating how to apply EMSegment to non-human primate data. We hope this tutorial will assist others in the primate imaging community to segment their structural images. The tutorial includes our Adult Rhesus template and GM/WM/CSF atlas, but works as well with the young rhesus and cyno atlas as well (see the atlas descriptions below). The tutorial and the accompanying images are available [http://bsl.ece.vt.edu/download/NHP-EMSTut.zip here]. Any comments or questions can be directed to bsl@vt.edu.

=== Rhesus Probabalistic Atlas - Adult ===
#[[Rhesus_WMGM_Atlas|WM/GM Atlas]]
#[[Rhesus_Subcortical_Atlas|Subcortical Atlas]]

=== Rhesus Probabalistic Atlas - Juvenile ===
#[[Rhesus_Juvenile_WMGM_Atlas|WM/GM Atlas]]

=== Cyno Probabalistic Atlas - Adult ===
#[[Cyno_WMGM_Atlas|WM/GM Atlas]]

=== Segmentation ===
#[[Rhesus_ICV_Extraction | Rhesus ICV Extraction]]
#[[Rhesus_EM_Segmentation | Rhesus EM Segmentation]]

==Publications==
==Meetings and Events Specific to this Collaboration==
*[[2007_Programming/Project_Week_MIT|2007 Summer Programming/Project Week at MIT]]
*[[AHM_2008|2008 NA-MIC AHM]]
*[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction|2008 NA-MIC Summer Project Week Page]]

==Resource Links==

* [http://www.slicer.org slicer]
* [http://www.bsl.ece.vt.edu Bioimaging Systems Lab at VT]

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2008-06-02T13:19:08Z

Vidyaraj: /* Meetings and Events Specific to this Collaboration */

Back to [[NA-MIC_External_Collaborations]]
==Abstract==
Alcohol abuse continues to be a major problem in the United States with an estimated 14 million adults
meeting the clinical criteria for a diagnosis of alcohol abuse or alcoholism at an estimated cost of $185
billion. Chronic alcohol exposure has been shown to impact structure and function of the brain. Since
most of what is known of alcohol's effects on the brain is based on studies of individuals who have
abused for a long time, it is unclear whether some of the effects might occur early in the abuse process.
Additionally, human studies are often complicated by many factors incuding polydrug abuse, poor
nutritional states and other medical conditions. Another complicating factor is the interaction of stress
and alcohol.

Using magnetic resonance imaging (MRI), we will examine the the effects of chronic alcohol self-
administration on brain structure and function in a group of monkeys that have been mother-reared or
nursery-reared. MRI scans will be acquired to determine whether there are differences in stucture or
functions as a result of alcohol exposure and whether rearing conditions play a role in these effects.
MRI techniques will also be used to examine how chronic alcohol consumption affects cerebral blood
flow, which is a measure of neuronal activity. Because we will conduct these measures both before
and after alcohol exposure in the same "young adult" animals, we will be able to track any changes that
might occur early in alcohol abuse which is something that cannot be accomplished in human studies.
Another goal is to adapt imaging tools and computer software that are used to measure the brains of
humans to the monkey brain. To accomplish this, we will collaborate with the National Alliance for
Medical Computing (NA-MIC), an existing NIH Center for Biomedical Computing.

We can control all variables associated with alcohol self-administration in these monkeys. They will be
monitored both before and after exposure to alcohol, thus, we will be able to monitor the progression of
any changes in structure or function that directly result from alcohol exposure. These studies will help
identify how exposure to long-term alcohol might affect how the brain works.

==Grant #==
1R01AA016748-01

==Key Personnel==
Wake Forest University: Jim Daunais, Bob Kraft

Virginia Tech: Chris Wyatt, Vidya Rajagopalan, Xiaojing Long

NAMIC: Kilian Pohl, Sandy Wells

==Projects==
Active projects in this collaboration are:

=== Tutorial on using EMSegment in Slicer 2.x to segment NHP images (New!) ===
We now have a tutorial demonstrating how to apply EMSegment to non-human primate data. We hope this tutorial will assist others in the primate imaging community to segment their structural images. The tutorial includes our Adult Rhesus template and GM/WM/CSF atlas, but works as well with the young rhesus and cyno atlas as well (see the atlas descriptions below). The tutorial and the accompanying images are available [http://bsl.ece.vt.edu/download/NHP-EMSTut.zip here]. Any comments or questions can be directed to bsl@vt.edu.

=== Rhesus Probabalistic Atlas - Adult ===
#[[Rhesus_WMGM_Atlas|WM/GM Atlas]]
#[[Rhesus_Subcortical_Atlas|Subcortical Atlas]]

=== Rhesus Probabalistic Atlas - Juvenile ===
#[[Rhesus_Juvenile_WMGM_Atlas|WM/GM Atlas]]

=== Cyno Probabalistic Atlas - Adult ===
#[[Cyno_WMGM_Atlas|WM/GM Atlas]]

=== Segmentation ===
#[[Rhesus_ICV_Extraction | Rhesus ICV Extraction]]
#[[Rhesus_EM_Segmentation | Rhesus EM Segmentation]]

==Publications==
==Meetings and Events Specific to this Collaboration==
*[[2007_Programming/Project_Week_MIT|2007 Summer Programming/Project Week at MIT]]
*[[AHM_2008|2008 NA-MIC AHM]]
*2008 NA-MIC Summer Project Week Page [[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction link]]

==Resource Links==

* [http://www.slicer.org slicer]
* [http://www.bsl.ece.vt.edu Bioimaging Systems Lab at VT]

NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction

2008-06-02T13:17:32Z

Vidyaraj: New page: '''Objective:''' * Develop an atlas of subcortical structures from normal subject images. '''Progress:''' * We are currently developing a subcortical atlas following the methods outline...

'''Objective:'''

* Develop an atlas of subcortical structures from normal subject images.

'''Progress:'''

* We are currently developing a subcortical atlas following the methods outlined in
M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. Proc SPIE Medical Imaging Conference, Proc SPIE Vol 6512 Medical Imaging 2007, pp 65122L-1 - 65122L-8.

* Below is a snap shot of subcortical segmention of one of the subjects. The hippocampus, caudate and putamen are clearly visible (marked in blue, yellow and indigo) amidst the gray matter(marked in red) and WM (marked in green).
[[Image:HPCSeg_V2.jpg|thumb|250pix|Subcortical Segmentation of Rhesus subject]]

'''Key Investigators:'''

* Wake Forest: Bob Kraft, Jim Daunais
* Virginia Tech: Chris Wyatt, Vidya Rajagopalan

'''Links:'''

2008 Summer Project Week

2008-06-02T13:17:08Z

Vidyaraj: /* External Collaborations */

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)
##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)
##[[Projects:ProstateSegmentation|Prostate Segmentation and Registration (Yi Gao GATech, Gabor Fichtinger JHU)]]

===Structural Analysis===

===Diffusion Image Analysis===
#[[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)

===Calibration/Validation===

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

===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]]

===Non-Medical Collaborations===

==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 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
# 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

==Pictures==

2008 NA-MIC Summer Project Week Page

2008-06-02T13:14:07Z

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2008-06-02T13:13:28Z

Vidyaraj: /* Meetings and Events Specific to this Collaboration */

Back to [[NA-MIC_External_Collaborations]]
==Abstract==
Alcohol abuse continues to be a major problem in the United States with an estimated 14 million adults
meeting the clinical criteria for a diagnosis of alcohol abuse or alcoholism at an estimated cost of $185
billion. Chronic alcohol exposure has been shown to impact structure and function of the brain. Since
most of what is known of alcohol's effects on the brain is based on studies of individuals who have
abused for a long time, it is unclear whether some of the effects might occur early in the abuse process.
Additionally, human studies are often complicated by many factors incuding polydrug abuse, poor
nutritional states and other medical conditions. Another complicating factor is the interaction of stress
and alcohol.

Using magnetic resonance imaging (MRI), we will examine the the effects of chronic alcohol self-
administration on brain structure and function in a group of monkeys that have been mother-reared or
nursery-reared. MRI scans will be acquired to determine whether there are differences in stucture or
functions as a result of alcohol exposure and whether rearing conditions play a role in these effects.
MRI techniques will also be used to examine how chronic alcohol consumption affects cerebral blood
flow, which is a measure of neuronal activity. Because we will conduct these measures both before
and after alcohol exposure in the same "young adult" animals, we will be able to track any changes that
might occur early in alcohol abuse which is something that cannot be accomplished in human studies.
Another goal is to adapt imaging tools and computer software that are used to measure the brains of
humans to the monkey brain. To accomplish this, we will collaborate with the National Alliance for
Medical Computing (NA-MIC), an existing NIH Center for Biomedical Computing.

We can control all variables associated with alcohol self-administration in these monkeys. They will be
monitored both before and after exposure to alcohol, thus, we will be able to monitor the progression of
any changes in structure or function that directly result from alcohol exposure. These studies will help
identify how exposure to long-term alcohol might affect how the brain works.

==Grant #==
1R01AA016748-01

==Key Personnel==
Wake Forest University: Jim Daunais, Bob Kraft

Virginia Tech: Chris Wyatt, Vidya Rajagopalan, Xiaojing Long

NAMIC: Kilian Pohl, Sandy Wells

==Projects==
Active projects in this collaboration are:

=== Tutorial on using EMSegment in Slicer 2.x to segment NHP images (New!) ===
We now have a tutorial demonstrating how to apply EMSegment to non-human primate data. We hope this tutorial will assist others in the primate imaging community to segment their structural images. The tutorial includes our Adult Rhesus template and GM/WM/CSF atlas, but works as well with the young rhesus and cyno atlas as well (see the atlas descriptions below). The tutorial and the accompanying images are available [http://bsl.ece.vt.edu/download/NHP-EMSTut.zip here]. Any comments or questions can be directed to bsl@vt.edu.

=== Rhesus Probabalistic Atlas - Adult ===
#[[Rhesus_WMGM_Atlas|WM/GM Atlas]]
#[[Rhesus_Subcortical_Atlas|Subcortical Atlas]]

=== Rhesus Probabalistic Atlas - Juvenile ===
#[[Rhesus_Juvenile_WMGM_Atlas|WM/GM Atlas]]

=== Cyno Probabalistic Atlas - Adult ===
#[[Cyno_WMGM_Atlas|WM/GM Atlas]]

=== Segmentation ===
#[[Rhesus_ICV_Extraction | Rhesus ICV Extraction]]
#[[Rhesus_EM_Segmentation | Rhesus EM Segmentation]]

==Publications==
==Meetings and Events Specific to this Collaboration==
*[[2007_Programming/Project_Week_MIT|2007 Summer Programming/Project Week at MIT]]
*[[AHM_2008|2008 NA-MIC AHM]]
*[[2008 NA-MIC Summer Project Week Page]]

==Resource Links==

* [http://www.slicer.org slicer]
* [http://www.bsl.ece.vt.edu Bioimaging Systems Lab at VT]

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2008-06-02T13:12:06Z

Vidyaraj: /* Meetings and Events Specific to this Collaboration */

Back to [[NA-MIC_External_Collaborations]]
==Abstract==
Alcohol abuse continues to be a major problem in the United States with an estimated 14 million adults
meeting the clinical criteria for a diagnosis of alcohol abuse or alcoholism at an estimated cost of $185
billion. Chronic alcohol exposure has been shown to impact structure and function of the brain. Since
most of what is known of alcohol's effects on the brain is based on studies of individuals who have
abused for a long time, it is unclear whether some of the effects might occur early in the abuse process.
Additionally, human studies are often complicated by many factors incuding polydrug abuse, poor
nutritional states and other medical conditions. Another complicating factor is the interaction of stress
and alcohol.

Using magnetic resonance imaging (MRI), we will examine the the effects of chronic alcohol self-
administration on brain structure and function in a group of monkeys that have been mother-reared or
nursery-reared. MRI scans will be acquired to determine whether there are differences in stucture or
functions as a result of alcohol exposure and whether rearing conditions play a role in these effects.
MRI techniques will also be used to examine how chronic alcohol consumption affects cerebral blood
flow, which is a measure of neuronal activity. Because we will conduct these measures both before
and after alcohol exposure in the same "young adult" animals, we will be able to track any changes that
might occur early in alcohol abuse which is something that cannot be accomplished in human studies.
Another goal is to adapt imaging tools and computer software that are used to measure the brains of
humans to the monkey brain. To accomplish this, we will collaborate with the National Alliance for
Medical Computing (NA-MIC), an existing NIH Center for Biomedical Computing.

We can control all variables associated with alcohol self-administration in these monkeys. They will be
monitored both before and after exposure to alcohol, thus, we will be able to monitor the progression of
any changes in structure or function that directly result from alcohol exposure. These studies will help
identify how exposure to long-term alcohol might affect how the brain works.

==Grant #==
1R01AA016748-01

==Key Personnel==
Wake Forest University: Jim Daunais, Bob Kraft

Virginia Tech: Chris Wyatt, Vidya Rajagopalan, Xiaojing Long

NAMIC: Kilian Pohl, Sandy Wells

==Projects==
Active projects in this collaboration are:

=== Tutorial on using EMSegment in Slicer 2.x to segment NHP images (New!) ===
We now have a tutorial demonstrating how to apply EMSegment to non-human primate data. We hope this tutorial will assist others in the primate imaging community to segment their structural images. The tutorial includes our Adult Rhesus template and GM/WM/CSF atlas, but works as well with the young rhesus and cyno atlas as well (see the atlas descriptions below). The tutorial and the accompanying images are available [http://bsl.ece.vt.edu/download/NHP-EMSTut.zip here]. Any comments or questions can be directed to bsl@vt.edu.

=== Rhesus Probabalistic Atlas - Adult ===
#[[Rhesus_WMGM_Atlas|WM/GM Atlas]]
#[[Rhesus_Subcortical_Atlas|Subcortical Atlas]]

=== Rhesus Probabalistic Atlas - Juvenile ===
#[[Rhesus_Juvenile_WMGM_Atlas|WM/GM Atlas]]

=== Cyno Probabalistic Atlas - Adult ===
#[[Cyno_WMGM_Atlas|WM/GM Atlas]]

=== Segmentation ===
#[[Rhesus_ICV_Extraction | Rhesus ICV Extraction]]
#[[Rhesus_EM_Segmentation | Rhesus EM Segmentation]]

==Publications==
==Meetings and Events Specific to this Collaboration==
*[[2007_Programming/Project_Week_MIT|2007 Summer Programming/Project Week at MIT]]
*[[AHM_2008|2008 NA-MIC AHM]]
*[[2008 NA-MIC Summer Project Week| Measuring Alcohol Stress Interaction]]

==Resource Links==

* [http://www.slicer.org slicer]
* [http://www.bsl.ece.vt.edu Bioimaging Systems Lab at VT]

2008 Summer Project Week

2008-06-02T13:09:40Z

Vidyaraj: /* External Collaborations */

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)
##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)
##[[Projects:ProstateSegmentation|Prostate Segmentation and Registration (Yi Gao GATech, Gabor Fichtinger JHU)]]

===Structural Analysis===

===Diffusion Image Analysis===
#[[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)

===Calibration/Validation===

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

===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 [2008 NA-MIC Summer Project Week link]

===Non-Medical Collaborations===

==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 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
# 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

==Pictures==

2008 NA-MIC Summer Project Week

2008-06-02T13:03:35Z

Vidyaraj: New page: {| |Project Week Main Page ]] |[[Image:HPCSeg_V2.jpg|thumb|320px|Subcortical Segmentation of Rhesus subject]...

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2008-06-02T12:46:56Z

Vidyaraj: /* Meetings and Events Specific to this Collaboration */

Back to [[NA-MIC_External_Collaborations]]
==Abstract==
Alcohol abuse continues to be a major problem in the United States with an estimated 14 million adults
meeting the clinical criteria for a diagnosis of alcohol abuse or alcoholism at an estimated cost of $185
billion. Chronic alcohol exposure has been shown to impact structure and function of the brain. Since
most of what is known of alcohol's effects on the brain is based on studies of individuals who have
abused for a long time, it is unclear whether some of the effects might occur early in the abuse process.
Additionally, human studies are often complicated by many factors incuding polydrug abuse, poor
nutritional states and other medical conditions. Another complicating factor is the interaction of stress
and alcohol.

Using magnetic resonance imaging (MRI), we will examine the the effects of chronic alcohol self-
administration on brain structure and function in a group of monkeys that have been mother-reared or
nursery-reared. MRI scans will be acquired to determine whether there are differences in stucture or
functions as a result of alcohol exposure and whether rearing conditions play a role in these effects.
MRI techniques will also be used to examine how chronic alcohol consumption affects cerebral blood
flow, which is a measure of neuronal activity. Because we will conduct these measures both before
and after alcohol exposure in the same "young adult" animals, we will be able to track any changes that
might occur early in alcohol abuse which is something that cannot be accomplished in human studies.
Another goal is to adapt imaging tools and computer software that are used to measure the brains of
humans to the monkey brain. To accomplish this, we will collaborate with the National Alliance for
Medical Computing (NA-MIC), an existing NIH Center for Biomedical Computing.

We can control all variables associated with alcohol self-administration in these monkeys. They will be
monitored both before and after exposure to alcohol, thus, we will be able to monitor the progression of
any changes in structure or function that directly result from alcohol exposure. These studies will help
identify how exposure to long-term alcohol might affect how the brain works.

==Grant #==
1R01AA016748-01

==Key Personnel==
Wake Forest University: Jim Daunais, Bob Kraft

Virginia Tech: Chris Wyatt, Vidya Rajagopalan, Xiaojing Long

NAMIC: Kilian Pohl, Sandy Wells

==Projects==
Active projects in this collaboration are:

=== Tutorial on using EMSegment in Slicer 2.x to segment NHP images (New!) ===
We now have a tutorial demonstrating how to apply EMSegment to non-human primate data. We hope this tutorial will assist others in the primate imaging community to segment their structural images. The tutorial includes our Adult Rhesus template and GM/WM/CSF atlas, but works as well with the young rhesus and cyno atlas as well (see the atlas descriptions below). The tutorial and the accompanying images are available [http://bsl.ece.vt.edu/download/NHP-EMSTut.zip here]. Any comments or questions can be directed to bsl@vt.edu.

=== Rhesus Probabalistic Atlas - Adult ===
#[[Rhesus_WMGM_Atlas|WM/GM Atlas]]
#[[Rhesus_Subcortical_Atlas|Subcortical Atlas]]

=== Rhesus Probabalistic Atlas - Juvenile ===
#[[Rhesus_Juvenile_WMGM_Atlas|WM/GM Atlas]]

=== Cyno Probabalistic Atlas - Adult ===
#[[Cyno_WMGM_Atlas|WM/GM Atlas]]

=== Segmentation ===
#[[Rhesus_ICV_Extraction | Rhesus ICV Extraction]]
#[[Rhesus_EM_Segmentation | Rhesus EM Segmentation]]

==Publications==
==Meetings and Events Specific to this Collaboration==
*[[2007_Programming/Project_Week_MIT|2007 Summer Programming/Project Week at MIT]]
*[[AHM_2008|2008 NA-MIC AHM]]
*[[2008 NA-MIC Summer Project Week]]

==Resource Links==

* [http://www.slicer.org slicer]
* [http://www.bsl.ece.vt.edu Bioimaging Systems Lab at VT]

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2008-06-02T12:45:27Z

Vidyaraj: /* Meetings and Events Specific to this Collaboration */

Back to [[NA-MIC_External_Collaborations]]
==Abstract==
Alcohol abuse continues to be a major problem in the United States with an estimated 14 million adults
meeting the clinical criteria for a diagnosis of alcohol abuse or alcoholism at an estimated cost of $185
billion. Chronic alcohol exposure has been shown to impact structure and function of the brain. Since
most of what is known of alcohol's effects on the brain is based on studies of individuals who have
abused for a long time, it is unclear whether some of the effects might occur early in the abuse process.
Additionally, human studies are often complicated by many factors incuding polydrug abuse, poor
nutritional states and other medical conditions. Another complicating factor is the interaction of stress
and alcohol.

Using magnetic resonance imaging (MRI), we will examine the the effects of chronic alcohol self-
administration on brain structure and function in a group of monkeys that have been mother-reared or
nursery-reared. MRI scans will be acquired to determine whether there are differences in stucture or
functions as a result of alcohol exposure and whether rearing conditions play a role in these effects.
MRI techniques will also be used to examine how chronic alcohol consumption affects cerebral blood
flow, which is a measure of neuronal activity. Because we will conduct these measures both before
and after alcohol exposure in the same "young adult" animals, we will be able to track any changes that
might occur early in alcohol abuse which is something that cannot be accomplished in human studies.
Another goal is to adapt imaging tools and computer software that are used to measure the brains of
humans to the monkey brain. To accomplish this, we will collaborate with the National Alliance for
Medical Computing (NA-MIC), an existing NIH Center for Biomedical Computing.

We can control all variables associated with alcohol self-administration in these monkeys. They will be
monitored both before and after exposure to alcohol, thus, we will be able to monitor the progression of
any changes in structure or function that directly result from alcohol exposure. These studies will help
identify how exposure to long-term alcohol might affect how the brain works.

==Grant #==
1R01AA016748-01

==Key Personnel==
Wake Forest University: Jim Daunais, Bob Kraft

Virginia Tech: Chris Wyatt, Vidya Rajagopalan, Xiaojing Long

NAMIC: Kilian Pohl, Sandy Wells

==Projects==
Active projects in this collaboration are:

=== Tutorial on using EMSegment in Slicer 2.x to segment NHP images (New!) ===
We now have a tutorial demonstrating how to apply EMSegment to non-human primate data. We hope this tutorial will assist others in the primate imaging community to segment their structural images. The tutorial includes our Adult Rhesus template and GM/WM/CSF atlas, but works as well with the young rhesus and cyno atlas as well (see the atlas descriptions below). The tutorial and the accompanying images are available [http://bsl.ece.vt.edu/download/NHP-EMSTut.zip here]. Any comments or questions can be directed to bsl@vt.edu.

=== Rhesus Probabalistic Atlas - Adult ===
#[[Rhesus_WMGM_Atlas|WM/GM Atlas]]
#[[Rhesus_Subcortical_Atlas|Subcortical Atlas]]

=== Rhesus Probabalistic Atlas - Juvenile ===
#[[Rhesus_Juvenile_WMGM_Atlas|WM/GM Atlas]]

=== Cyno Probabalistic Atlas - Adult ===
#[[Cyno_WMGM_Atlas|WM/GM Atlas]]

=== Segmentation ===
#[[Rhesus_ICV_Extraction | Rhesus ICV Extraction]]
#[[Rhesus_EM_Segmentation | Rhesus EM Segmentation]]

==Publications==
==Meetings and Events Specific to this Collaboration==
*[[2007_Programming/Project_Week_MIT|2007 Summer Programming/Project Week at MIT]]
*[[AHM_2008|2008 NA-MIC AHM]]
*[[2008 Summer Project Week]]

==Resource Links==

* [http://www.slicer.org slicer]
* [http://www.bsl.ece.vt.edu Bioimaging Systems Lab at VT]

2008 Summer Project Week

2008-06-02T12:32:22Z

Vidyaraj: /* External Collaborations */

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)
##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)
##[[Projects:ProstateSegmentation|Prostate Segmentation and Registration (Yi Gao GATech, Gabor Fichtinger JHU)]]

===Structural Analysis===

===Diffusion Image Analysis===
#[[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)

===Calibration/Validation===

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

===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_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction

===Non-Medical Collaborations===

==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 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
# 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

==Pictures==