NAMIC Wiki - User contributions [en]

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2010-09-22T13:19:25Z

Wyatt:

Back to [[NA-MIC_External_Collaborations|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#==
R01AA016748

==Key Personnel==
*Wake Forest University: Jim Daunais, Bob Kraft
*Virginia Tech: Chris Wyatt, Vidya Rajagopalan, Xiaoxing(Ginger) Li, Xiaojing Long
*NA-MIC: Kilian Pohl, Sandy Wells, Andriy Fedorov

==Funding Duration==
07/15/2009-03/31/2010

==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)], also [http://www.nitrc.org/projects/vervet_atlas on NITRC]

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 ===
# [[Atlas-to-subject registration with FSL and Diffeomorphic Demons, for EM segmentation.]]
# [http://wiki.na-mic.org/Wiki/index.php/Vervet_MRI_registration Atlas-to-subject registration with BRAINSFit]
# [[On the performance of Slicer 2 and Slicer3 EM segmentation modules]]
# [[Proposed revised atlas construction workflow]]
# [[Initial atlas construction workflow]] (initial workflow, obsolete)
# [[October_08_2009_Meeting:_VT-NAMIC_Revised_atlas_construction_workflow | Current vervet monkey atlas construction workflow]] (in progress)
# [[NA-MIC WFU VT Collaboration: Segmentation workflow and approaches | Considered segmentation approaches and workflow]] (in progress)
# [[Smoothing multi-label brain segmentations]]

==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_Winter_Project_Week_WFU1|2009 NA-MIC Winter Project Week Page]]
* [http://wiki.na-mic.org/Wiki/index.php/Measuring_Alcohol_Stress_Interaction 2009 Summer project week Boston]
* [http://wiki.na-mic.org/Wiki/index.php/Events:VT-NAMIC-NCBC-Collaboration-meeting-2009 2009 October 7-9 VT-NAMIC collaboration meeting]
* [[2010_Winter_Project_Week_VervetMRILongitudinalAnalysis|2010 NA-MIC Winter Project Week Page]]

==Resource Links==
* [http://www.slicer.org 3D Slicer]
* [http://www.bsl.ece.vt.edu Bioimaging Systems Lab at VT]
* [http://pin.primate.wisc.edu/factsheets/entry/vervet Primate Info Net: Vervet factsheet]

AHM 2010

2010-01-05T16:29:40Z

Wyatt: /* Agenda */

__NOTOC__
== Introduction ==
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2" align="left" | '''This is the home page for the 2010 NA-MIC all hands meeting (AHM).''' NA-MIC participants meet for a AHM once a year. The purpose of the AHM is to coordinate, discuss plans and report to NIH officers and the external advisory board (EAB). The external advisory board meets with the NA-MIC leadership immediately after the AHM. In parallel, NA-MIC is organizing a project week. These events, with the exception of the EAB meeting, are open to collaborators and potential collaborators.

For more information about the project weeks in general, click [[Engineering:Programming_Events|'''here''']].

For information about the January 2010 project week, see below or click [[2010_Winter_Project_Week|'''here''']].

For information about Utah as a travel destination click [http://www.utah.com '''here'''].
| style="background: #ebeced" align="center"| [[Image:SLC.jpg|center|350px|View of the City]]
|-
| style="background: #ebeced"|The 2010 AHM, EAB and Project Week will be held <br>'''January 4-8 2010''', in '''Salt Lake City''', Utah.
|}

== Agenda==

'''wireless connection: Select hotel wireless network - this gets you a non-secure line - Start your web browser, enter services.globalsuite.net in the address bar - Location is Capital Ball Room, group is Utah, passcode is Utah, both are case sensitive. If you have trouble, ask Deb or another attendee for help'''<br>

{| border="1" cellpadding="5"
|- style="background:#ebeced; color:black" align="left"
| style="width:4%" | '''Time'''
| style="width:12%" | '''Monday, January 4'''
| style="width:12%" | '''Tuesday, January 5'''
| style="width:12%" | '''Wednesday, January 6'''
| style="width:32%" | '''Thursday, January 7 '''
| style="width:12%" | '''Friday, January 8'''
|-
| style="background:#ffffdd; color:black"|
| style="background:#b4d597; color:#522200"| '''[[2010_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#b4d597; color:#522200"| '''[[2010_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#b4d597; color:#522200"| '''[[2010_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#fff6a6; color:#522200"| '''AHM''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/Capitol A-B], [[2010_EAB|'''EAB''']] in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus B]
'''[[2010_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus A]
| style="background:#b4d597; color:#522200"|'''[[2010_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
|-
| style="background:#ffffdd; color:black"|'''7:30-8:00'''
| style="background:#ebeced; color:black"|
| style="background:#b4d597; color:black"| Breakfast
| style="background:#b4d597; color:black"| Breakfast
| style="background:#fff6a6; color:black"| Breakfast
| style="background:#b4d597; color:black"| Breakfast
|-
| style="background:#ffffdd; color:black"|'''8:00-10:00'''
| style="background:#ebeced; color:black"|'''9:30''' Core 1 and 2 PI closed session in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol A]
| style="background:#b4d597; color:black"|Project Work <br> '''8:00-8:30''' [[AHM2010:NA-MIC Kit Update| NA-MIC Kit Update]] (Jim Miller, Steve Pieper)<br>
'''8:30-10:00''' [[AHM2010:QtTutorial#Qt_tutorial|Qt Tutorial]] (Julien Finet)
| style="background:#b4d597; color:black"|Project Work <br>'''8:00-9:00''' [[AHM2010:Tutorial Contest|Tutorial Contest]] [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
'''9:00-10:00''' [[AHM2010:AnnotationBreakout| Slicer Annotation Breakout (Kilian Pohl) ]] (Capital Ballroom A)
| style="background:#fff6a6; color:black"|'''8:00''' [[AHM 2010 Introduction|Introduction]], [http://www.spl.harvard.edu/~kikinis Ron Kikinis] <br>
'''8:05''' [[AHM 2010 NA-MIC Highlights|NA-MIC Highlights]] ([http://www.cs.utah.edu/~whitaker/ Ross Whitaker])<br>
'''8:20''' [[AHM 2010 NA-MIC Validation|Validation]] ([http://www.cs.unc.edu/~styner/ Martin Styner])<br>
'''Roadmap Projects'''<br>
'''8:35''': [[AHM2010:JHU|JHU/Queens]] ([http://research.cs.queensu.ca/~gabor/ Gabor Fichtinger])<br>
'''8:55''': [[AHM2010:UNC|UNC]] ([http://www.med.unc.edu/psych/directories/faculty/hazlett/ Heather Cody])<br>
'''9:15''': [[AHM2010:PNL|PNL]] ([http://pnl.bwh.harvard.edu/people/profiles/kubicki.html Marek Kubicki])<br>
'''9.35''': [[AHM2010:Mind|Mind Institute]] ([http://www.mrn.org/principle-investigators/h.-jeremy-bockholt.html Jeremy Bockolt])<br>
| style="background:#b4d597; color:black"|Project Work <br>
|-
| style="background:#ffffdd; color:black"|'''10:00-10:30'''
| style="background:#ebeced; color:black"| Core 1 and 2 PI closed session
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#fff6a6; color:black"| Coffee
| style="background:#b4d597; color:black"| '''10:00''' Project Review
|-
| style="background:#ffffdd; color:black"|'''10:30-12:00'''
| style="background:#ebeced; color:black"| Core 1 and 2 PI closed session
| style="background:#b4d597; color:black"|Project Work <br>
'''10:30-11:30'''[[2010_Winter_Project_Week_Slicer_Dashboard|Test We Must]] (Luis)
<br>
'''11:30-12:30'''[[AHM_2010_Tutorial_Polishing|Tutorial Polishing]] (Stuart Wallace, Sonia, Randy) <br>

| style="background:#b4d597; color:black"|Project Work <br>

'''10:30-11:30'''[[2010_Winter_Project_Week_DTI_Breakout_Session|DTI Breakout Session]] (Sonia Pujol, Lauren O'Donnell)
<br>

| style="background:#fff6a6; color:black"|
'''Collaborations'''<br>
'''10:30''': Iowa ([http://www.engineering.uiowa.edu/faculty-staff/profile-directory/bme/grosland_n.php Nicole Grosland])<br>
'''10:40''': [[Media:NAMIC External-Wyatt2010.ppt|Wake Forest]] ([http://www.ece.vt.edu/faculty/wyatt.html Chris Wyatt])<br>
'''10:50''': Georgetown ([http://www.isis.georgetown.edu/PORTALVBVS/DesktopDefault.aspx?tabindex=2&tabid=8 Kevin Cleary])<br>
'''11:00''': UNC ([http://www.med.unc.edu/~dgshen Dinggang Shen])<br>
'''11:10''': JHU ([http://iacl.ece.jhu.edu/~prince/ Jerry Prince])<br>
'''11:20''': MGH (Hiroyuki Yoshida)<br>
'''11:30''': JHU (Michael Miller) <br>
'''11:40''': Utah (Janet Lainhart) <br>
'''11:50''': BWH (Raul San Jose) <br>
| style="background:#b4d597; color:black"|Project Work
|-
| style="background:#ffffdd; color:black"|'''12:00-1:00'''
| style="background:#b4d597; color:black"| Lunch
| style="background:#b4d597; color:black"| Lunch <br>
| style="background:#b4d597; color:black"| Lunch<br>
| style="background:#fff6a6; color:black"| Lunch
| style="background:#b4d597; color:black"| Adjourn
|-
| style="background:#ffffdd; color:black"|'''1:00-3:00'''
| style="background:#b4d597; color:black"|[[2010_Winter_Project_Week|Begin Project Activities]]: '''2:00''' Introduce Projects and Participants
| style="background:#b4d597; color:black"|'''1:00-2:00''' [[AHM2010:RegistrationBreakout|Registration Breakout (Dominik, Casey)]] <br> in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/Amethyst Amethyst 1]
| style="background:#b4d597; color:black"|Project Work (Capital Ballroom A) <br> '''2:00-3:00''' Grid Wizard Tutorial (Marco Ruiz)
| style="background:#fff6a6; color:black"|
'''Tools and Tutorials''' <br>
'''1:00-1:20''' [[AHM2010:Slicer|Slicer]] ([http://www.spl.harvard.edu/~pieper Steve Pieper])<br>
'''1:20-1:40''' [[AHM2010:Plug-ins|Interfacing with Slicer]] ([http://wiki.na-mic.org/Wiki/index.php/User:Millerjv Jim Miller])<br>
'''1:40-2:00''' [[AHM2010:Non-interactive-tools|Non-interactive tools]] ([http://www.kitware.com/company/team/aylward.html Stephen Aylward])<br>
'''2:00-2:30''' Training Core & DTI Tractography Validation Update ([http://lmi.bwh.harvard.edu/~spujol/ Sonia Pujol]) <br>
'''2:30-3:00''' [[AHM2010:Tutorial-Contest-Winners|Tutorial Contest]]: Presentations by the winners ([http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=64 Randy Gollub])<br>
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''3:00-3:30'''
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#fff6a6; color:black"| Coffee
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''3:00-5:00'''
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|'''3:30-4:30''' [[AHM2010:QtTutorial#Qt_technical_workshop|Qt Workshop]] (Julien Finet) <br> Project Work <br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"|Project Work <br>'''3:00-5:00''' [[AHM2010:SlicerHandson|Slicer Hands-on with Ron]]<br>Breakout<br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#fff6a6; color:black"|[[2010_EAB|EAB]]<br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus B]<br>'''3:00-4:00''' Discussion with NA-MIC Leadership<br> '''4:00-5:00''' Closed Session
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''05:00-07:00'''
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|'''05:00-06:00''' Breakout(Capital Ballroom A)
| style="background:#fff6a6; color:black"|'''6:00''' Optional: [http://www.skisaltlake.com/murphys.htm Beer at Murphy's] (like last year)
| style="background:#ebeced; color:black"|
|}

Please note that there will be a Core 1&2 Site PI Retreat on the morning of Monday, January 4th. This is a closed session for Core 1&2 Site PIs, with no delegates. The topic is the competitive renewal.

== Dates Venue Registration ==
'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 7th'''.
* Project Activities will be held rest of the week between '''Monday, January 4th and Friday, January 8th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriott City Center, Salt Lake City, Utah] Marriott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. Please either call the hotel at +1-877-905-4491 (toll free) or book online at http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/?toDate=1/8/10&groupCode=NAMNAMA&fromDate=1/3/10&app=resvlink'''by December 14, 2009''' using the code NAMNAMA to get rooms at $139/night. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms. Please also note that the room rate without the code is ~$200/night and we will not be able to help you get a discount if you don't book in time.

'''Registration:''' We are charging a registration fee to all participants ($200 for AHM only, and $450 for AHM+). The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click http://www.sci.utah.edu/namic2010.html for online registration. This registration must be completed by December 12, 2009.<br>

'''Connectivity'''
We have three wireless access points at the AHM. Two of them are located in the capital ballroom. One is named capital-ballroom, the other is named capital-ballroom2. If one access point doesn't let you connect it is probably overloaded. In that case, please try connecting to the other one.

== Attendees ==

'''The registered attendee list will be posted here by the organizers. DO NOT add your name to this list yourself.'''
<br>
#Ron Kikinis, BWH
#Katie Mastrogiacomo, BWH
#Sonia Pujol, BWH
#Nicole Aucoin, BWH
#Katie Hayes, BWH
#Lauren O'Donnell, BWH
#Sandy Wells, BWH
#Andrew Rausch, PNL
#Alexander Zaitsev, BWH
#Andriy Fedorov, BWH
#Raul San Jose Estepar, BWH (AHM only)
#Wendy Plesniak, BWH
#Peter Savadjiev, BWH
#Petter Risholm, BWH
#Dominik Meier, BWH
#Junichi Tokuda, BWH
#Scott Hoge, BWH
#Ben Schwartz, BWH
#Marek Kubicki, BWH
#Sylvain Bouix, BWH
#James Malcolm, BWH
#James Ross, BWH (AHM only)
#Daniel Haehn, BWH
#Sandy Napel, EAB (AHM only)
#Bill Lorensen, EAB
#Fred Prior, EAB (AHM only)
#Chris Johnson, EAB
#Godfrey Pearlson, EAB (AHM only)
#Morry Blumenfeld, EAB (AHM only)
#Kevin Cleary, Georgetown (AHM only)
#Heather Hazlett, UNC (AHM only)
#Chris Wyatt, Virginia Tech (AHM only)
#Gabor Fichtinger, Queens (AHM only)
#Zohara Cohen, NIBIB (AHM only)
#Yi Gao, Georgia Tech
#Sylvain Jaume, MIT CSAIL
#Vandana Mohan, Georgia Tech
#Min Chen, Johns Hopkins
#Deepika Mahalingam, UNC-Chapel Hill
#SUN HYUNG KIM, UNC at Chapel Hill
#Clement Vachet, UNC Chapel Hill
#Will Schroeder, Kitware
#Casey Goodlett, Kitware
#Yang Zhang, The University of Western Australia M050
#Corentin Hamel, UNC
#Martin Styner, UNC
#Julien Finet, Kitware Inc.
#LUIS IBANEZ, KITWARE Inc.
#Stephen Aylward, Kitware, Inc.
#Garrett Larson, UNC
#Steve Pieper, Isomics, Inc.
#Daniel Marcus, Washington University
#Curtis Lisle, KnowledgeVis, LLC
#Andras Lasso, Queens University
#GOPALKRISHNA VENI, University of Utah
#Hans Johnson, University of IowaPsychiatry
#Julien Jomier, Kitware Inc.
#Adam Wittek, The University of Western Australia M050
#alexandre gouaillard, CoSMo Software
#Kilian Pohl, IBM
#German Cavelier, NIMHNIHDNBBS (AHM only)
#Jean-Christophe Fillion-Robin, Kitware Inc. (AHM only)
#Daniel Blezek
#Arnaud Gelas, Harvard Medical School
#Behnood Gholami, Georgia Tech
#Hans Johnson, University of Iowa Psychiatry
#Peter Karasev, Georgia Tech
#Ivan Kolesov, GaTech
#James Miller
#Timothy Olsen, Washington University STL
#John Paulett, Washington University
#Nicolas Rannou,Harvard Medical School
#Yundi Shi, UNC
#Lydie Souhait, Harvard Medical School
#Duygu Tosun, UCSFCIND
#Alexander Yarmarkovich, Isomics
#Linda Krigbaum, National Library of Medicine (AHM only)
#Dinggang Shen, UNC-Chapel Hill
#Jeremy Bockholt, The Mind Research Network
#Elvis Chen, Robarts Research Institute
#Michal Depa, MIT
#James Fishbaugh, SCI Institute
#Guido Gerig, SCI Institute
#Nicole Grosland, The University of Iowa, CCAD
#Nathan Hageman, UCLA School of Medicine
#Xiaoxing Li, Virginia Tech
#Mahnaz Maddah, General Electric Co.
#Vincent Magnotta, The University of Iowa, CCAD
#Harish Doddi, Stanford University
#bjoern menze, CSAIL MIT
#Saikat Pal, Stanford University
#Marcel Prastawa, SCI Institute
#Andrzej Przybyszewski, UMASS
#Marco Ruiz, UCSD
#Mark Scully, The Mind Research Network
#Anuja Sharma, SCI Institute
#Gregory Sharp, MGH
#Xiaodong Tao, General Electric Co.
#Guorong Wu, UNC-Chapel Hill
#Minjeong Kim, UNC Chapel Hill
#Josh Cates, SCI Institute
#Stuart Wallace, MGH
#Michael Ackerman, National Library of Medicine
#Yong Zhang
#Michael Miller, Johns Hopkins University
#Jerry Prince, Johns Hopkins University
#Ross Whitaker, SCI Institute

<br>
'''The registered attendee list will be posted here by the organizers. DO NOT add your name to this list yourself.'''

File:NAMIC External-Wyatt2010.ppt

2010-01-05T16:26:32Z

Wyatt:

October 07 2009 Meeting: VT-NAMIC Data review summary

2009-12-23T13:43:08Z

Wyatt:

== General comments ==

We made the following observations about the data at the first time point:

* In some sobjects the FOV is axis-aligned, while in others it is tilted. These directions were not preserved in the NIFTI data we were previously using.'''
* We have two SPGR scans of for each subject, but the scans are not perfectly aligned. Ron: possibly due to coil heating. We cannot right away use these images to average and get better SNR, need to check with imaging people. Not sure if discrepancy is the rigid one.
* Noticeable bias field in the atlas is observed by Ron.

Other observations with illustrations:

== Acquisition-related issues ==

{|
| '''Angio sequence (right name?) has apparently been used for some (7 out of 10) subjects''' CLW: This is normal T1w blood flow artifact, but it is pronounced, perhaps because of the small brain size.
{|
|
|<gallery perrow="3" heights="300px" widths="800px">
Image:calvin-angio.jpg|'''Calvin axial showing vessel and volume rendering of vasculature'''
</gallery>
|}
|}

{|
| '''Fat shift artifact significantly obstructs the cortex in the occipital lobe for all subjects'''
|
{|
|<gallery perrow="3" heights="200px" widths="300px">
Image:calvin-artefact1.jpg|'''Calvin occipital lobe'''
Image:calvin-artefact2.jpg|'''Calvin'''
Image:calvin-artefact3.jpg|'''Calvin'''
</gallery>
|}
|}

{|
| '''Ringing artifacts for some (few) subjects'''
|
{|
|<gallery perrow="3" heights="200px" widths="300px">
Image:calvin-ringing.jpg|'''Calvin ringing artifact'''
</gallery>
|}
|}

{|
| '''Zero filling artifact'''
|
{|
|<gallery perrow="3" heights="200px" widths="400px">
Image:calvin-zero_filling.jpg|'''Calvin time point 2'''
</gallery>
|}
|}

{|
| '''Susceptibility artifacts'''
|
{|
|<gallery perrow="3" heights="200px" widths="400px">
Image:calvin-susceptibility.jpg|'''Calvin time point 1'''
Image:gucci-susceptibility.jpg|'''Gucci time point 1'''
</gallery>
|}
|}

== Processing-related issues ==

{|
| '''The issue with noise in Tommy and Louis resolved: we do not know how the NIFTI images we used before for Tommy and Louis were obtained -- the DICOM data has much better noise characteristics'''
|
{|
|<gallery perrow="2" heights="200px" widths="300px">
Image:tommy-dicom.jpg|'''Tommy, DICOM'''
Image:louis-dicom.jpg|'''Louis, DICOM'''
</gallery>
|}

|}

{|
| '''Significant mis-alignment of some subjects with the template subject after FLIRT registration for some subjects is confirmed''' Should be fixed in the new analysis.
|
{|
|<gallery perrow="3" heights="200px" widths="300px">
Image:ralph-flirt.jpg|'''Ralph/atlas post-FLIRT checkerboard'''
Image:mark-flirt.jpg|'''Mark/atlas post-FLIRT overlay'''
</gallery>
|}
|}

== Biology-related issues ==

{|
| '''Valentino has structure not consistent with the normal anatomy''' ''Ron: this is likely a cyst.''
|
{|
|<gallery perrow="2" heights="200px" widths="300px">
Image:valentino-issue1.jpg|'''Valentino unknown structure, Fast marching segmentation'''
Image:valentino-issue2.jpg|''''''
Image:valentino-issue3.jpg|''''''
Image:valentino-issue4.jpg|'''Valentino unknown structure, surface model'''
</gallery>
|}
|}

Events:VT-NAMIC-NCBC-Collaboration-meeting-2009

2009-10-01T12:52:42Z

Wyatt: /* Goals */

== Logistics ==

* Andriy Fedorov and Ginger Li: work on pre-meeting agenda Wed-Thu October 7-8, 2009
* All participants meeting: Friday, '''October 9, 2009, 9am-4pm''' (time is tentative, but room has been reserved, confirmed with Katie Mastrogiacomo)
* Wednesday and Thursday location: [http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street. 1249 Boylston Street]
* Friday meeting location: [http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street. 1249 Boylston Street], 2nd floor conference room

== Goals ==

* To be completed or partially completed prior to the meeting by Andriy Fedorov and Ginger Li (Oct 7-8):
** Provide necessary user- and developer-level Slicer training for Ginger
** Understand the currently used processing workflow
** Confirm reproducibility of the processing steps between VT and SPL
** Document the processing steps as precisely as necessary for reproducibility and cross-validation of the results (wiki page)
* To be completed during the meeting
** Review and confirm the correctness of the workflow based on the wiki documentation (Chris, Ron and Sandy)
** Review the available data and current segmentation results
** Discuss action timeline for the remaining part of the funded project period
*** Potential for segmentation validation using cryo-histology (Chris can show some results of reconstructed 3D cryo-histo volumes)
*** Potential for cortical thickness measures / integration with Caret or freesurfer
** Discuss publication plans

== Agenda ==

*Review, discuss and finalize the processing workflow (to be discussed and documented by Andriy Fedorov and Ginger Li prior to the meeting Oct 7-8)
**atlas construction
**image pre-processing
**registration
**segmentation
*Review currents results
* Identify Slicer components of the workflow that are ... working, broken, missing

== Attendance ==

Open to all interested parties:

#Chris Wyatt
#Ginger Li
#Ron Kikinis
#Sandy Wells
#Andriy Fedorov

== References ==
* Measuring alcohol and stress interaction [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction NCBC Collaboration page]
* [http://wiki.na-mic.org/Wiki/index.php/Atlas-to-subject_registration_with_FSL_and_Diffeomorphic_Demons,_for_EM_segmentation Atlas construction workflow], put together by Ginger prior to the meeting
* [http://wiki.na-mic.org/Wiki/index.php/On_the_performance_of_Slicer_2_and_Slicer3_EM_segmentation_modules Slicer 2 vs. Slicer 3 EM Segmentation performance qualitative comparison], completed by Ginger prior to the meeting
* [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Atlas construction workflow] off BSL web site
* [http://www.na-mic.org/Wiki/index.php/Vervet_MRI_registration Evaluation of BRAINSFit performance on atlas-to-subject vervet registration], completed by Andrey prior to the meeting
* 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 [http://www.google.com/url?sa=t&source=web&ct=res&cd=1&url=http%3A%2F%2Fwww.cs.unc.edu%2F~styner%2Fpublic%2FMyPapers%2Fpapers%2FMedical%2520Imaging%25202007%2520Image%2520Processing%25202007%2520Styner-1.pdf&ei=DubDSt3AAciwlAfJp5TwBA&usg=AFQjCNGojUvBkh6TwbS0vJ9X7OEFLDFxqQ&sig2=wHgXTrdAXzUC5DuL_C7CCQ pdf]

AHM2009:ExternalWFU

2009-01-08T14:36:35Z

Wyatt: /* Methods */

[[AHM_2009#Agenda|Back to AHM 2009 Agenda]]

__NOTOC__
==External Collaboration: Measuring Alcohol and Stress Interactions with Structural and Perfusion MRI==

[[media:NAMIC_External-Wyatt09.ppt|Wake Forest Collaboration Update (ppt)]]

{|
|[[Image:MonkeyProject09Slicer.png|thumb|170px|Segmentation of Vervet Subcortical Structures]]
|}

==Introduction==
Our goal is to use MRI to examine 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.

[[NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction|Main Project Page]]

[[Image:MonkeyProjectOverview.png‎|thumb|170px|Project Overview]]

==Team==
* Jim Daunais (WFUHS PI)
* Bob Kraft (WFUHS MR Physicist)
* Chris Wyatt (VT Engineering)
* Vidya Rajagopalan (VT Engineering)
* Killian Pohl (NA-MIC Core 1)

==Goals for 2008==
* Acquisition of baseline vervet images for atlas development (completed)
* Vervet atlas completed (completed)
* Animal Training and Induction 3-4 months (completed)

==Methods==
The first stage of atlas construction was based on a method by
Styner et al [1]. A template image was chosen randomly from the
training images. This image was manually skull-stripped and a
skull-strip mask determined. All other training images were histogram
matched and then affinely registered to this template using FSL FLIRT
[2] and skull-stripped using the skull-strip mask after dilation by
one voxel. The images of only the Extra Cranial Content (ECC) are
averaged to form the ECC template.

The Intra Cranial Content (ICC) images of the various subjects are
again affinely registered to the ICC image of the chosen template
using FSL FLIRT [2]. The affinely registered images were deformably
registered to the same target using the diffeomorphic demons
registration method. The registered images were then averaged. The ICC
average was now combined with the ECC template to form the template
image for the whole head.

This high-CNR template image was then segmented into gray matter,
white matter, and CSF tissue classes using initial k-means clustering
and manual correction. Subcortical structures were then manually
traced on the high-CNR template. The tissue and structure
segmentations were smoothed using a Gaussian kernel to obtain the
initial spatial probability maps.

The second stage of the construction used the initial spatial
probability maps from stage 1 with the expectation-maximization
segmentation (EMSegmenter) method by Pohl et al. [3]. Using the initial
spatial probabilities the EMS algorithm, the initial spatial
probability maps were combined with manually estimated structure
intensity distributions for each structure to produce the final
segmentation for the template image. This segmentation was then
manually corrected for errors and then was smoothed using a guassian
kernel of variance 1.

[1] 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.

[2] M. Jenkinson and S.M. Smith. A global optimisation method for robust affine registration of brain images. Medical Image Analysis, 5(2):143-156, June 2001.

[3] Pohl KM, Fisher J, Levitt JJ, Shenton ME, Kikinis R, Grimson WEL, Wells WM. A unifying approach to registration, segmentation, and intensity correction. Medical Image Computing And Computer-Assisted Intervention - MICCAI 2005; PT 1 Lecture Notes In Computer Science 3749: 310-318.

==Products==
* [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Vervet template, tissue, and subcortical atlas]
* [http://www.bsl.ece.vt.edu/tutorials.php Tutorial: Using Slicer3 to segment vervet images]

==Future Work==
* Animal ad-lib access to alcohol for 12 months
* Final structural scans ~August 2009

AHM2009:ExternalWFU

2009-01-08T14:34:50Z

Wyatt: New page: Back to AHM 2009 Agenda __NOTOC__ ==External Collaboration: Measuring Alcohol and Stress Interactions with Structural and Perfusion MRI== [[media:NAMIC_External-Wyatt...

[[AHM_2009#Agenda|Back to AHM 2009 Agenda]]

__NOTOC__
==External Collaboration: Measuring Alcohol and Stress Interactions with Structural and Perfusion MRI==

[[media:NAMIC_External-Wyatt09.ppt|Wake Forest Collaboration Update (ppt)]]

{|
|[[Image:MonkeyProject09Slicer.png|thumb|170px|Segmentation of Vervet Subcortical Structures]]
|}

==Introduction==
Our goal is to use MRI to examine 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.

[[NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction|Main Project Page]]

[[Image:MonkeyProjectOverview.png‎|thumb|170px|Project Overview]]

==Team==
* Jim Daunais (WFUHS PI)
* Bob Kraft (WFUHS MR Physicist)
* Chris Wyatt (VT Engineering)
* Vidya Rajagopalan (VT Engineering)
* Killian Pohl (NA-MIC Core 1)

==Goals for 2008==
* Acquisition of baseline vervet images for atlas development (completed)
* Vervet atlas completed (completed)
* Animal Training and Induction 3-4 months (completed)

==Methods==
The first stage of atlas construction was based on a method by
Styner et al [1]. A template image was chosen randomly from the
training images. This image was manually skull-stripped and a
skull-strip mask determined. All other training images were histogram
matched and then affinely registered to this template using FSL FLIRT
[2] and skull-stripped using the skull-strip mask after dilation by
one voxel. The images of only the Extra Cranial Content (ECC) are
averaged to form the ECC template.

The Intra Cranial Content (ICC) images of the various subjects are
again affinely registered to the ICC image of the chosen template
using FSL FLIRT [2]. The affinely registered images were deformably
registered to the same target using the diffeomorphic demons
registration method. The registered images were then averaged. The ICC
average was now combined with the ECC template to form the template
image for the whole head.

This high-CNR template image was then segmented into gray matter,
white matter, and CSF tissue classes using initial k-means clustering
and manual correction. Subcortical structures were then manually
traced on the high-CNR template. The tissue and structure
segmentations were smoothed using a Gaussian kernel to obtain the
initial spatial probability maps.

The second stage of the construction used the initial spatial
probability maps from stage 1 with the expectation-maximization
segmentation (EMS) method by Pohl et al. [4]. Using the initial
spatial probabilities the EMS algorithm, the initial spatial
probability maps were combined with manually estimated structure
intensity distributions for each structure to produce the final
segmentation for the template image. This segmentation was then
manually corrected for errors and then was smoothed using a guassian
kernel of variance 1.

[1] 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.

[2] M. Jenkinson and S.M. Smith. A global optimisation method for robust affine registration of brain images. Medical Image Analysis, 5(2):143-156, June 2001.

[3] Balci, Serdar K.; Golland, Polina; Wells, William M. Non-rigid Groupwise Registration using B-Spline Deformation Model, ISC/NA-MIC Workshop on Open Science at MICCAI 2007.

[4] Pohl KM, Fisher J, Levitt JJ, Shenton ME, Kikinis R, Grimson WEL, Wells WM. A unifying approach to registration, segmentation, and intensity correction. Medical Image Computing And Computer-Assisted Intervention - MICCAI 2005; PT 1 Lecture Notes In Computer Science 3749: 310-318.

==Products==
* [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Vervet template, tissue, and subcortical atlas]
* [http://www.bsl.ece.vt.edu/tutorials.php Tutorial: Using Slicer3 to segment vervet images]

==Future Work==
* Animal ad-lib access to alcohol for 12 months
* Final structural scans ~August 2009

File:MonkeyProject09Slicer.png

2009-01-08T14:20:35Z

Wyatt:

File:MonkeyProjectOverview.png

2009-01-08T14:20:09Z

Wyatt:

AHM 2009

2009-01-08T14:15:52Z

Wyatt: /* Agenda */

__NOTOC__
== Introduction ==
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2"| '''This is the home page for the 2009 NA-MIC all hands meeting (AHM).''' NA-MIC participants meet for a AHM once a year. The purpose of the AHM is to coordinate, discuss plans and report to NIH officers and the external advisory board (EAB). The external advisory board meets with the NA-MIC leadership immediately after the AHM. In parallel, NA-MIC is organizing a project week. These events, with the exception of the EAB meeting, are open to collaborators and potential collaborators.

For more information about the project weeks in general, click [[Engineering:Programming_Events|'''here''']].

For information about the January 2009 project week, see below or click [[2009_Winter_Project_Week|'''here''']].

For information about Utah as a travel destination click [http://www.utah.com '''here'''].
| style="background: #ebeced" align="center"| [[Image:SLC.jpg|center|350px|View of the City]]
|-
| style="background: #ebeced"|The 2009 AHM, EAB and Project Week will be held <br>'''January 5-9 2009''', in '''Salt Lake City''', Utah.
|}

== Agenda==

'''wireless connection: capital-ballroom, namic-ballroomB, namic-amethyst'''<br>

{| border="1" cellpadding="5"
|- style="background:#ebeced; color:black" align="left"
| style="width:4%" | '''Time'''
| style="width:12%" | '''Monday, January 5'''
| style="width:12%" | '''Tuesday, January 6'''
| style="width:12%" | '''Wednesday, January 7'''
| style="width:32%" | '''Thursday, January 8 '''
| style="width:12%" | '''Friday, January 9'''
|-
| style="background:#ffffdd; color:black"|
| style="background:#b4d597; color:#522200"| '''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#b4d597; color:#522200"| '''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#b4d597; color:#522200"| '''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#fff6a6; color:#522200"| '''AHM''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/Capitol A-B], [[2009_EAB|'''EAB''']] in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus B]
'''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus A]
| style="background:#b4d597; color:#522200"|'''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
|-
| style="background:#ffffdd; color:black"|'''7:30-8:00'''
| style="background:#ebeced; color:black"|
| style="background:#b4d597; color:black"| Breakfast
| style="background:#b4d597; color:black"| Breakfast
| style="background:#fff6a6; color:black"| Breakfast
| style="background:#b4d597; color:black"| Breakfast
|-
| style="background:#ffffdd; color:black"|'''8:00-10:00'''
| style="background:#ebeced; color:black"|'''9:30''' Core 1 and 2 PI closed session in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol A]
| style="background:#b4d597; color:black"|Project Work <br> '''8:00-9:00''' [[AHM2009:NITRC and Slicer|How to use NITRC and slicer]] (Steve, Terry)<br>
'''9:00-10:00''' [[AHM2009:Batchmake and XNAT|Using Batchmake and XNAT to process large studies]] (Stephen Aylward and Dan Marcus) in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"|Project Work <br>'''8:00-9:00''' [[AHM2009:Tutorial Review and Judging|Tutorial Review and Judging]] [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
'''9:00-10:00''' Particle Correspondence Breakout (Capital Ballroom A)
| style="background:#fff6a6; color:black"|'''8:00''' [[AHM 2009 Introduction|Introduction]], [http://www.spl.harvard.edu/~kikinis Ron Kikinis] <br>
'''8:05''' [[AHM 2009 NA-MIC Highlights|NA-MIC Highlights]] ([http://www.cs.utah.edu/~whitaker/ Ross Whitaker])<br>
'''Roadmap Projects'''<br>
'''8:35''': [[AHM2009:JHU|JHU/Queens]] ([http://research.cs.queensu.ca/~gabor/ Gabor Fichtinger])<br>
'''8:55''': [[AHM2009:UNC|UNC]] ([http://www.med.unc.edu/psych/directories/hazlett.htm Heather Cody])<br>
'''9:15''': [[AHM2009:PNL|PNL]] ([http://pnl.bwh.harvard.edu/people/profiles/kubicki.html Marek Kubicki])<br>
'''9.35''': [[AHM2009:Mind|Mind Institute]] ([http://www.mrn.org/principle-investigators/h.-jeremy-bockholt.html Jeremy Bockolt])<br>
| style="background:#b4d597; color:black"|Project Work <br>
|-
| style="background:#ffffdd; color:black"|'''10:00-10:30'''
| style="background:#ebeced; color:black"| Core 1 and 2 PI closed session
| style="background:#b4d597; color:black"| '''10:30-11:30'''[[AHM2009:GUI Testing|Automated GUI Testing for Slicer]] (Sebastien) [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"| Coffee
| style="background:#fff6a6; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
|-
| style="background:#ffffdd; color:black"|'''10:30-12:00'''
| style="background:#ebeced; color:black"| Core 1 and 2 PI closed session
| style="background:#b4d597; color:black"|Project Work
| style="background:#b4d597; color:black"|Project Work <br>

| style="background:#fff6a6; color:black"|
'''Collaborations'''<br>
'''10:30''': [[media:NA-MIC_Mesh_Collaboration_2009.ppt|Iowa collaboration]] ([http://www.engineering.uiowa.edu/faculty-staff/profile-directory/bme/grosland_n.php Nicole Grosland])<br>
'''10:45''': [[AHM2009:ExternalWFU|Wake Forest collaboration]] ([http://www.ece.vt.edu/faculty/wyatt.html Chris Wyatt])<br>
'''11:00''': [[media:NA-MIC_Cleary_RF_Ablation_Georgetown_Jan_2009.ppt|Georgetown U. collaboration]] ([http://www.isis.georgetown.edu/PORTALVBVS/DesktopDefault.aspx?tabindex=2&tabid=8 Kevin Cleary])<br>
'''11:15''': [[media:HAMMER.ppt | UNC collaboration]] ([http://www.med.unc.edu/~dgshen Dinggang Shen])<br>
'''11:30''': Mario Negri Collaboration ([http://villacamozzi.marionegri.it/~luca/ Luca Antiga])<br>
'''11:45''': Discussion<br>
| style="background:#b4d597; color:black"|Project Work
|-
| style="background:#ffffdd; color:black"|'''12:00-1:00'''
| style="background:#b4d597; color:black"| Lunch
| style="background:#b4d597; color:black"| Lunch <br>
| style="background:#b4d597; color:black"| Lunch<br>
| style="background:#fff6a6; color:black"| Lunch
| style="background:#b4d597; color:black"| Adjourn
|-
| style="background:#ffffdd; color:black"|'''1:00-3:00'''
| style="background:#b4d597; color:black"|[[2009_Winter_Project_Week|Begin Project Activities]]: Introduce Projects and Participants
| style="background:#b4d597; color:black"|[[AHM 2009:DTI Breakout|DTI Discussion]] (Sonia, Randy, Others) [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/Amethyst 1]
| style="background:#b4d597; color:black"|Project Work (Capital Ballroom A) <br> '''1:00-2:00''' [[AHM2009:Python Modules|Python Modules]] (Luca Antiga) <br> '''2:00-3:00''' [[AHM2009:VTKWidgets | VTK Widgets]] (Will Schroeder)
| style="background:#fff6a6; color:black"|
'''Tools and Tutorials''' (coordinator) <br>
'''1:00-1:20''' [[AHM2009:Slicer|Slicer]] ([http://www.spl.harvard.edu/~pieper Steve Pieper])<br>
'''1:20-1:40''' [[AHM2009:Plug-ins|Plug-ins for Slicer]] ([http://wiki.na-mic.org/Wiki/index.php/User:Millerjv Jim Miller])<br>
'''1:40-2:00''' [[AHM2009:Non-interactive-tools|Non-interactive tools]] ([http://www.kitware.com/company/team/aylward.html Stephen Aylward])<br>
'''2:00-3:00''' [[AHM2009:Tutorial-Contest-Winners|Tutorial Contest]]: Presentations by the winners ([http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=64 Randy Gollub])<br>
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''3:00-3:30'''
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#fff6a6; color:black"| Coffee
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''3:00-5:00'''
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|'''3:30-4:30''' [[AHM2009:Cell Segmentation|Cell Segmentation]] (Alex G) <br> Project Work <br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"|Project Work <br>'''3:00-5:00''' Meshing Tutorial (Nicole Grosland, Vincent Magnotta)<br>[[Iowa_Meshing_Tutorial]]<br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#fff6a6; color:black"|[[2008 EAB|EAB]]<br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus B]<br>'''3:00-4:00''' Discussion with NA-MIC Leadership<br> '''4:00-5:00''' Closed Session
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''05:00-07:00'''
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|'''05:00-06:00''' [[AHM2009:Meshing Breakout | Meshing Breakout]] (Capital Ballroom A)
| style="background:#fff6a6; color:black"|'''6:00''' Optional: [http://www.skisaltlake.com/murphys.htm Beer at Murphy's] (like last year)
| style="background:#ebeced; color:black"|
|}

Please note that there will be a Core 1&2 Site PI Retreat on the morning of Monday, January 5th. This is a closed session for Core 1&2 Site PIs, with no delegates. The topic is the competitive renewal.

== Dates. Venue. Registration ==
'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 8th'''.
* Project Activities will be held rest of the week between '''Monday, January 5th and Friday, January 9th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. Please either call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) or book online '''by December 4, 2008''' using the code SCISCIA to get rooms at $139/night. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

'''Registration:''' We are charging a registration fee to all participants ($200 for AHM only, and $450 for AHM+). The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click http://www.sci.utah.edu/namic2009/registration.html for online registration. This registration must be completed by December 12, 2008.<br>

'''Connectivity'''
We have three wireless access points at the AHM. Two of them are located in the capital ballroom. One is named capital-ballroom, the other is named capital-ballroom2. If one access point doesn't let you connect it is probably overloaded. In that case, please try connecting to the other one.

== Attendees ==

Please follow http://www.sci.utah.edu/namic2009/registration.html to complete your online registration. The organizers will periodically publish the list of registered attendees in the space below. Attendees should '''NOT''' add their names in this section. This list is a snapshop as of 01:46, 23 December 2008 (UTC)

# Michael Ackerman NA-MIC All Hands Meeting National Library of Medicine at NIH
# Luca Antiga NA-MIC All Hands Meeting and Project Week 2009 Mario Negri Institute
# Kevin Archie NA-MIC All Hands Meeting and Project Week 2009 Washington University
# Nicole Aucoin NA-MIC All Hands Meeting and Project Week 2009 BWH
# Stephen Aylward NA-MIC All Hands Meeting and Project Week 2009 Kitware
# Sebastien Barre NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Morry Blumenfeld NA-MIC All Hands Meeting EAB
# H Jeremy Bockholt NA-MIC All Hands Meeting and Project Week 2009 The Mind Research Network
# Sylvain Bouix NA-MIC All Hands Meeting and Project Week 2009 PNL
# Josh Cates NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# German Cavelier NA-MIC All Hands Meeting NIH-NIMH
# Kiyoyuki Chinzei NA-MIC All Hands Meeting and Project Week 2009 AIST
# Kevin Cleary NA-MIC All Hands Meeting Georgetown University
# Manasi Datar NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Michal Depa NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Harish Doddi NA-MIC All Hands Meeting and Project Week 2009 Stanford University
# Andriy Fedorov NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Gabor Fichtinger NA-MIC All Hands Meeting Queens Univ
# Yi Gao NA-MIC All Hands Meeting and Project Week 2009
# Arnaud Gelas NA-MIC All Hands Meeting and Project Week 2009 Harvard Medical School
# Guido Gerig NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Polina Golland NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Randy L. Gollub NA-MIC All Hands Meeting and Project Week 2009 MGH
# Casey Goodlett NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Alexandre Gouaillard NA-MIC All Hands Meeting and Project Week 2009 Harvard Medical School
# Sylvain Gouttard NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Jeffrey Grethe NA-MIC All Hands Meeting and Project Week 2009 UC San Diego
# Nicole Grosland NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Daniel Haehn NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Nathan Hageman NA-MIC All Hands Meeting and Project Week 2009 UCLA
# Nobuhiko Hata NA-MIC All Hands Meeting and Project Week 2009 Brigham and Womens Hospital
# Kathryn Hayes NA-MIC All Hands Meeting and Project Week 2009 Brigham and Womens Hospital
# Heather Cody Hazlett NA-MIC All Hands Meeting University of North Carolina
# Jaesung Hong NA-MIC All Hands Meeting and Project Week 2009 Kyushu University
# Luis Ibanez NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Chris Johnson NA-MIC All Hands Meeting and Project Week 2009 EAB
# Ron Kikinis NA-MIC All Hands Meeting and Project Week 2009 SPL - BWH
# Ivan Kolesov NA-MIC All Hands Meeting and Project Week 2009 Georgia Tech
# Karthik Krishnan NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Marek Kubicki NA-MIC All Hands Meeting and Project Week 2009 PNL_BWH
# Curtis Lisle NA-MIC All Hands Meeting and Project Week 2009 KnowledgeVis, LLC
# Yanling Liu NA-MIC All Hands Meeting and Project Week 2009 SAIC-Frederick, Inc.
# Zhexing Liu NA-MIC All Hands Meeting and Project Week 2009 NIRAL, UNC
# Terry Lorber NA-MIC All Hands Meeting and Project Week 2009 Isomics, Inc
# Bill Lorensen NA-MIC All Hands Meeting and Project Week 2009 EAB
# Vincent Magnotta NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Daniel Marcus NA-MIC All Hands Meeting and Project Week 2009 Washington University
# Katie Mastrogiacomo NA-MIC All Hands Meeting and Project Week 2009 SPL - BWH
# Cedric Mathieu NA-MIC All Hands Meeting and Project Week 2009 UNC
# Bjoern Menze NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Mikhail Milchenko NA-MIC All Hands Meeting Washington University in St Louis
# James Miller NA-MIC All Hands Meeting and Project Week 2009
# Vandana Mohan NA-MIC All Hands Meeting and Project Week 2009 Georgia Inst of Technology
# kishore mosaliganti NA-MIC All Hands Meeting and Project Week 2009 Harvard Medical School
# Sandy Napel NA-MIC All Hands Meeting EAB
# Marc Niethammer NA-MIC All Hands Meeting and Project Week 2009 UNC Chapel Hill
# Guy Nir NA-MIC All Hands Meeting and Project Week 2009 Technion
# Ipek Oguz NA-MIC All Hands Meeting and Project Week 2009 UNC
# Saikat Pal NA-MIC All Hands Meeting and Project Week 2009 Stanford University
# Steve Pieper NA-MIC All Hands Meeting and Project Week 2009 Isomics, Inc.
# Marcel Prastawa NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Fred Prior NA-MIC All Hands Meeting EAB
# Sonia Pujol NA-MIC All Hands Meeting and Project Week 2009 Surgical Planning Lab, Brigham Womens Hosp
# Vidya Rajagopalan NA-MIC All Hands Meeting and Project Week 2009 Virginia Tech
# Austin Ramme NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Petter Risholm NA-MIC All Hands Meeting and Project Week 2009 Brigham Womens Hospital
# James Ross NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Marco Ruiz NA-MIC All Hands Meeting and Project Week 2009 UCSD
# Raul San Jose NA-MIC All Hands Meeting and Project Week 2009 LMI-BWH
# Peter Savadjiev NA-MIC All Hands Meeting and Project Week 2009 Brigham Womens Hospital
# William Schroeder NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Mark Scully NA-MIC All Hands Meeting and Project Week 2009 The Mind Research Network
# Madeleine Seeland NA-MIC All Hands Meeting and Project Week 2009 LMI
# Gregory Sharp NA-MIC All Hands Meeting and Project Week 2009 MGH
# Dinggang Shen NA-MIC All Hands Meeting UNC-Chapel Hill
# Kiran Shivanna NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Shantanu Singh NA-MIC All Hands Meeting and Project Week 2009 The Ohio State University
# Martin Styner NA-MIC All Hands Meeting and Project Week 2009 University of North Carolina
# Allen Tannenbaum NA-MIC All Hands Meeting and Project Week 2009 Georgia Tech
# Xiaodong Tao NA-MIC All Hands Meeting and Project Week 2009 GE Global Research
# Doug Terry NA-MIC All Hands Meeting and Project Week 2009 Psychiatry Neuroimaging Lab
# Clement Vachet NA-MIC All Hands Meeting and Project Week 2009 UNC
# Koen Van Leemput NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Archana Venkataraman NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Siddharth Vikal NA-MIC All Hands Meeting and Project Week 2009 Queens University
# William Wells NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Carl-Fredrik Westin NA-MIC All Hands Meeting and Project Week 2009 Brigham and Womens Hospital
# Ross Whitaker NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Nathan Wilson NA-MIC All Hands Meeting Cardiovascular Simulation, Inc.
# Chris Wyatt NA-MIC All Hands Meeting
# Alexander Yarmarkovich NA-MIC All Hands Meeting and Project Week 2009 ISOMIC
# Dr. Terry S Yoo NA-MIC All Hands Meeting DHHSNIHNLM

AHM 2009

2009-01-08T13:46:52Z

Wyatt: /* Agenda */

__NOTOC__
== Introduction ==
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2"| '''This is the home page for the 2009 NA-MIC all hands meeting (AHM).''' NA-MIC participants meet for a AHM once a year. The purpose of the AHM is to coordinate, discuss plans and report to NIH officers and the external advisory board (EAB). The external advisory board meets with the NA-MIC leadership immediately after the AHM. In parallel, NA-MIC is organizing a project week. These events, with the exception of the EAB meeting, are open to collaborators and potential collaborators.

For more information about the project weeks in general, click [[Engineering:Programming_Events|'''here''']].

For information about the January 2009 project week, see below or click [[2009_Winter_Project_Week|'''here''']].

For information about Utah as a travel destination click [http://www.utah.com '''here'''].
| style="background: #ebeced" align="center"| [[Image:SLC.jpg|center|350px|View of the City]]
|-
| style="background: #ebeced"|The 2009 AHM, EAB and Project Week will be held <br>'''January 5-9 2009''', in '''Salt Lake City''', Utah.
|}

== Agenda==

'''wireless connection: capital-ballroom, namic-ballroomB, namic-amethyst'''<br>

{| border="1" cellpadding="5"
|- style="background:#ebeced; color:black" align="left"
| style="width:4%" | '''Time'''
| style="width:12%" | '''Monday, January 5'''
| style="width:12%" | '''Tuesday, January 6'''
| style="width:12%" | '''Wednesday, January 7'''
| style="width:32%" | '''Thursday, January 8 '''
| style="width:12%" | '''Friday, January 9'''
|-
| style="background:#ffffdd; color:black"|
| style="background:#b4d597; color:#522200"| '''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#b4d597; color:#522200"| '''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#b4d597; color:#522200"| '''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#fff6a6; color:#522200"| '''AHM''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/Capitol A-B], [[2009_EAB|'''EAB''']] in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus B]
'''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus A]
| style="background:#b4d597; color:#522200"|'''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
|-
| style="background:#ffffdd; color:black"|'''7:30-8:00'''
| style="background:#ebeced; color:black"|
| style="background:#b4d597; color:black"| Breakfast
| style="background:#b4d597; color:black"| Breakfast
| style="background:#fff6a6; color:black"| Breakfast
| style="background:#b4d597; color:black"| Breakfast
|-
| style="background:#ffffdd; color:black"|'''8:00-10:00'''
| style="background:#ebeced; color:black"|'''9:30''' Core 1 and 2 PI closed session in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol A]
| style="background:#b4d597; color:black"|Project Work <br> '''8:00-9:00''' [[AHM2009:NITRC and Slicer|How to use NITRC and slicer]] (Steve, Terry)<br>
'''9:00-10:00''' [[AHM2009:Batchmake and XNAT|Using Batchmake and XNAT to process large studies]] (Stephen Aylward and Dan Marcus) in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"|Project Work <br>'''8:00-9:00''' [[AHM2009:Tutorial Review and Judging|Tutorial Review and Judging]] [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
'''9:00-10:00''' Particle Correspondence Breakout (Capital Ballroom A)
| style="background:#fff6a6; color:black"|'''8:00''' [[AHM 2009 Introduction|Introduction]], [http://www.spl.harvard.edu/~kikinis Ron Kikinis] <br>
'''8:05''' [[AHM 2009 NA-MIC Highlights|NA-MIC Highlights]] ([http://www.cs.utah.edu/~whitaker/ Ross Whitaker])<br>
'''Roadmap Projects'''<br>
'''8:35''': [[AHM2009:JHU|JHU/Queens]] ([http://research.cs.queensu.ca/~gabor/ Gabor Fichtinger])<br>
'''8:55''': [[AHM2009:UNC|UNC]] ([http://www.med.unc.edu/psych/directories/hazlett.htm Heather Cody])<br>
'''9:15''': [[AHM2009:PNL|PNL]] ([http://pnl.bwh.harvard.edu/people/profiles/kubicki.html Marek Kubicki])<br>
'''9.35''': [[AHM2009:Mind|Mind Institute]] ([http://www.mrn.org/principle-investigators/h.-jeremy-bockholt.html Jeremy Bockolt])<br>
| style="background:#b4d597; color:black"|Project Work <br>
|-
| style="background:#ffffdd; color:black"|'''10:00-10:30'''
| style="background:#ebeced; color:black"| Core 1 and 2 PI closed session
| style="background:#b4d597; color:black"| '''10:30-11:30'''[[AHM2009:GUI Testing|Automated GUI Testing for Slicer]] (Sebastien) [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"| Coffee
| style="background:#fff6a6; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
|-
| style="background:#ffffdd; color:black"|'''10:30-12:00'''
| style="background:#ebeced; color:black"| Core 1 and 2 PI closed session
| style="background:#b4d597; color:black"|Project Work
| style="background:#b4d597; color:black"|Project Work <br>

| style="background:#fff6a6; color:black"|
'''Collaborations'''<br>
'''10:30''': [[media:NA-MIC_Mesh_Collaboration_2009.ppt|Iowa collaboration]] ([http://www.engineering.uiowa.edu/faculty-staff/profile-directory/bme/grosland_n.php Nicole Grosland])<br>
'''10:45''': [[media:NAMIC_External-Wyatt09.ppt|Wake Forest collaboration]] ([http://www.ece.vt.edu/faculty/wyatt.html Chris Wyatt])<br>
'''11:00''': [[media:NA-MIC_Cleary_RF_Ablation_Georgetown_Jan_2009.ppt|Georgetown U. collaboration]] ([http://www.isis.georgetown.edu/PORTALVBVS/DesktopDefault.aspx?tabindex=2&tabid=8 Kevin Cleary])<br>
'''11:15''': [[media:HAMMER.ppt | UNC collaboration]] ([http://www.med.unc.edu/~dgshen Dinggang Shen])<br>
'''11:30''': Mario Negri Collaboration ([http://villacamozzi.marionegri.it/~luca/ Luca Antiga])<br>
'''11:45''': Discussion<br>
| style="background:#b4d597; color:black"|Project Work
|-
| style="background:#ffffdd; color:black"|'''12:00-1:00'''
| style="background:#b4d597; color:black"| Lunch
| style="background:#b4d597; color:black"| Lunch <br>
| style="background:#b4d597; color:black"| Lunch<br>
| style="background:#fff6a6; color:black"| Lunch
| style="background:#b4d597; color:black"| Adjourn
|-
| style="background:#ffffdd; color:black"|'''1:00-3:00'''
| style="background:#b4d597; color:black"|[[2009_Winter_Project_Week|Begin Project Activities]]: Introduce Projects and Participants
| style="background:#b4d597; color:black"|[[AHM 2009:DTI Breakout|DTI Discussion]] (Sonia, Randy, Others) [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/Amethyst 1]
| style="background:#b4d597; color:black"|Project Work (Capital Ballroom A) <br> '''1:00-2:00''' [[AHM2009:Python Modules|Python Modules]] (Luca Antiga) <br> '''2:00-3:00''' [[AHM2009:VTKWidgets | VTK Widgets]] (Will Schroeder)
| style="background:#fff6a6; color:black"|
'''Tools and Tutorials''' (coordinator) <br>
'''1:00-1:20''' [[AHM2009:Slicer|Slicer]] ([http://www.spl.harvard.edu/~pieper Steve Pieper])<br>
'''1:20-1:40''' [[AHM2009:Plug-ins|Plug-ins for Slicer]] ([http://wiki.na-mic.org/Wiki/index.php/User:Millerjv Jim Miller])<br>
'''1:40-2:00''' [[AHM2009:Non-interactive-tools|Non-interactive tools]] ([http://www.kitware.com/company/team/aylward.html Stephen Aylward])<br>
'''2:00-3:00''' [[AHM2009:Tutorial-Contest-Winners|Tutorial Contest]]: Presentations by the winners ([http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=64 Randy Gollub])<br>
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''3:00-3:30'''
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#fff6a6; color:black"| Coffee
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''3:00-5:00'''
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|'''3:30-4:30''' [[AHM2009:Cell Segmentation|Cell Segmentation]] (Alex G) <br> Project Work <br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"|Project Work <br>'''3:00-5:00''' Meshing Tutorial (Nicole Grosland, Vincent Magnotta)<br>[[Iowa_Meshing_Tutorial]]<br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#fff6a6; color:black"|[[2008 EAB|EAB]]<br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus B]<br>'''3:00-4:00''' Discussion with NA-MIC Leadership<br> '''4:00-5:00''' Closed Session
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''05:00-07:00'''
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|'''05:00-06:00''' [[AHM2009:Meshing Breakout | Meshing Breakout]] (Capital Ballroom A)
| style="background:#fff6a6; color:black"|'''6:00''' Optional: [http://www.skisaltlake.com/murphys.htm Beer at Murphy's] (like last year)
| style="background:#ebeced; color:black"|
|}

Please note that there will be a Core 1&2 Site PI Retreat on the morning of Monday, January 5th. This is a closed session for Core 1&2 Site PIs, with no delegates. The topic is the competitive renewal.

== Dates. Venue. Registration ==
'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 8th'''.
* Project Activities will be held rest of the week between '''Monday, January 5th and Friday, January 9th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. Please either call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) or book online '''by December 4, 2008''' using the code SCISCIA to get rooms at $139/night. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

'''Registration:''' We are charging a registration fee to all participants ($200 for AHM only, and $450 for AHM+). The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click http://www.sci.utah.edu/namic2009/registration.html for online registration. This registration must be completed by December 12, 2008.<br>

'''Connectivity'''
We have three wireless access points at the AHM. Two of them are located in the capital ballroom. One is named capital-ballroom, the other is named capital-ballroom2. If one access point doesn't let you connect it is probably overloaded. In that case, please try connecting to the other one.

== Attendees ==

Please follow http://www.sci.utah.edu/namic2009/registration.html to complete your online registration. The organizers will periodically publish the list of registered attendees in the space below. Attendees should '''NOT''' add their names in this section. This list is a snapshop as of 01:46, 23 December 2008 (UTC)

# Michael Ackerman NA-MIC All Hands Meeting National Library of Medicine at NIH
# Luca Antiga NA-MIC All Hands Meeting and Project Week 2009 Mario Negri Institute
# Kevin Archie NA-MIC All Hands Meeting and Project Week 2009 Washington University
# Nicole Aucoin NA-MIC All Hands Meeting and Project Week 2009 BWH
# Stephen Aylward NA-MIC All Hands Meeting and Project Week 2009 Kitware
# Sebastien Barre NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Morry Blumenfeld NA-MIC All Hands Meeting EAB
# H Jeremy Bockholt NA-MIC All Hands Meeting and Project Week 2009 The Mind Research Network
# Sylvain Bouix NA-MIC All Hands Meeting and Project Week 2009 PNL
# Josh Cates NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# German Cavelier NA-MIC All Hands Meeting NIH-NIMH
# Kiyoyuki Chinzei NA-MIC All Hands Meeting and Project Week 2009 AIST
# Kevin Cleary NA-MIC All Hands Meeting Georgetown University
# Manasi Datar NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Michal Depa NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Harish Doddi NA-MIC All Hands Meeting and Project Week 2009 Stanford University
# Andriy Fedorov NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Gabor Fichtinger NA-MIC All Hands Meeting Queens Univ
# Yi Gao NA-MIC All Hands Meeting and Project Week 2009
# Arnaud Gelas NA-MIC All Hands Meeting and Project Week 2009 Harvard Medical School
# Guido Gerig NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Polina Golland NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Randy L. Gollub NA-MIC All Hands Meeting and Project Week 2009 MGH
# Casey Goodlett NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Alexandre Gouaillard NA-MIC All Hands Meeting and Project Week 2009 Harvard Medical School
# Sylvain Gouttard NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Jeffrey Grethe NA-MIC All Hands Meeting and Project Week 2009 UC San Diego
# Nicole Grosland NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Daniel Haehn NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Nathan Hageman NA-MIC All Hands Meeting and Project Week 2009 UCLA
# Nobuhiko Hata NA-MIC All Hands Meeting and Project Week 2009 Brigham and Womens Hospital
# Kathryn Hayes NA-MIC All Hands Meeting and Project Week 2009 Brigham and Womens Hospital
# Heather Cody Hazlett NA-MIC All Hands Meeting University of North Carolina
# Jaesung Hong NA-MIC All Hands Meeting and Project Week 2009 Kyushu University
# Luis Ibanez NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Chris Johnson NA-MIC All Hands Meeting and Project Week 2009 EAB
# Ron Kikinis NA-MIC All Hands Meeting and Project Week 2009 SPL - BWH
# Ivan Kolesov NA-MIC All Hands Meeting and Project Week 2009 Georgia Tech
# Karthik Krishnan NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Marek Kubicki NA-MIC All Hands Meeting and Project Week 2009 PNL_BWH
# Curtis Lisle NA-MIC All Hands Meeting and Project Week 2009 KnowledgeVis, LLC
# Yanling Liu NA-MIC All Hands Meeting and Project Week 2009 SAIC-Frederick, Inc.
# Zhexing Liu NA-MIC All Hands Meeting and Project Week 2009 NIRAL, UNC
# Terry Lorber NA-MIC All Hands Meeting and Project Week 2009 Isomics, Inc
# Bill Lorensen NA-MIC All Hands Meeting and Project Week 2009 EAB
# Vincent Magnotta NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Daniel Marcus NA-MIC All Hands Meeting and Project Week 2009 Washington University
# Katie Mastrogiacomo NA-MIC All Hands Meeting and Project Week 2009 SPL - BWH
# Cedric Mathieu NA-MIC All Hands Meeting and Project Week 2009 UNC
# Bjoern Menze NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Mikhail Milchenko NA-MIC All Hands Meeting Washington University in St Louis
# James Miller NA-MIC All Hands Meeting and Project Week 2009
# Vandana Mohan NA-MIC All Hands Meeting and Project Week 2009 Georgia Inst of Technology
# kishore mosaliganti NA-MIC All Hands Meeting and Project Week 2009 Harvard Medical School
# Sandy Napel NA-MIC All Hands Meeting EAB
# Marc Niethammer NA-MIC All Hands Meeting and Project Week 2009 UNC Chapel Hill
# Guy Nir NA-MIC All Hands Meeting and Project Week 2009 Technion
# Ipek Oguz NA-MIC All Hands Meeting and Project Week 2009 UNC
# Saikat Pal NA-MIC All Hands Meeting and Project Week 2009 Stanford University
# Steve Pieper NA-MIC All Hands Meeting and Project Week 2009 Isomics, Inc.
# Marcel Prastawa NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Fred Prior NA-MIC All Hands Meeting EAB
# Sonia Pujol NA-MIC All Hands Meeting and Project Week 2009 Surgical Planning Lab, Brigham Womens Hosp
# Vidya Rajagopalan NA-MIC All Hands Meeting and Project Week 2009 Virginia Tech
# Austin Ramme NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Petter Risholm NA-MIC All Hands Meeting and Project Week 2009 Brigham Womens Hospital
# James Ross NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Marco Ruiz NA-MIC All Hands Meeting and Project Week 2009 UCSD
# Raul San Jose NA-MIC All Hands Meeting and Project Week 2009 LMI-BWH
# Peter Savadjiev NA-MIC All Hands Meeting and Project Week 2009 Brigham Womens Hospital
# William Schroeder NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Mark Scully NA-MIC All Hands Meeting and Project Week 2009 The Mind Research Network
# Madeleine Seeland NA-MIC All Hands Meeting and Project Week 2009 LMI
# Gregory Sharp NA-MIC All Hands Meeting and Project Week 2009 MGH
# Dinggang Shen NA-MIC All Hands Meeting UNC-Chapel Hill
# Kiran Shivanna NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Shantanu Singh NA-MIC All Hands Meeting and Project Week 2009 The Ohio State University
# Martin Styner NA-MIC All Hands Meeting and Project Week 2009 University of North Carolina
# Allen Tannenbaum NA-MIC All Hands Meeting and Project Week 2009 Georgia Tech
# Xiaodong Tao NA-MIC All Hands Meeting and Project Week 2009 GE Global Research
# Doug Terry NA-MIC All Hands Meeting and Project Week 2009 Psychiatry Neuroimaging Lab
# Clement Vachet NA-MIC All Hands Meeting and Project Week 2009 UNC
# Koen Van Leemput NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Archana Venkataraman NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Siddharth Vikal NA-MIC All Hands Meeting and Project Week 2009 Queens University
# William Wells NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Carl-Fredrik Westin NA-MIC All Hands Meeting and Project Week 2009 Brigham and Womens Hospital
# Ross Whitaker NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Nathan Wilson NA-MIC All Hands Meeting Cardiovascular Simulation, Inc.
# Chris Wyatt NA-MIC All Hands Meeting
# Alexander Yarmarkovich NA-MIC All Hands Meeting and Project Week 2009 ISOMIC
# Dr. Terry S Yoo NA-MIC All Hands Meeting DHHSNIHNLM

File:NAMIC External-Wyatt09.ppt

2009-01-08T00:28:42Z

Wyatt: uploaded a new version of "Image:NAMIC External-Wyatt09.ppt"

AHM 2009

2009-01-08T00:25:00Z

Wyatt: /* Agenda */

__NOTOC__
== Introduction ==
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2"| '''This is the home page for the 2009 NA-MIC all hands meeting (AHM).''' NA-MIC participants meet for a AHM once a year. The purpose of the AHM is to coordinate, discuss plans and report to NIH officers and the external advisory board (EAB). The external advisory board meets with the NA-MIC leadership immediately after the AHM. In parallel, NA-MIC is organizing a project week. These events, with the exception of the EAB meeting, are open to collaborators and potential collaborators.

For more information about the project weeks in general, click [[Engineering:Programming_Events|'''here''']].

For information about the January 2009 project week, see below or click [[2009_Winter_Project_Week|'''here''']].

For information about Utah as a travel destination click [http://www.utah.com '''here'''].
| style="background: #ebeced" align="center"| [[Image:SLC.jpg|center|350px|View of the City]]
|-
| style="background: #ebeced"|The 2009 AHM, EAB and Project Week will be held <br>'''January 5-9 2009''', in '''Salt Lake City''', Utah.
|}

== Agenda==

'''wireless connection: capital-ballroom, namic-ballroomB, namic-amethyst'''<br>

{| border="1" cellpadding="5"
|- style="background:#ebeced; color:black" align="left"
| style="width:4%" | '''Time'''
| style="width:12%" | '''Monday, January 5'''
| style="width:12%" | '''Tuesday, January 6'''
| style="width:12%" | '''Wednesday, January 7'''
| style="width:32%" | '''Thursday, January 8 '''
| style="width:12%" | '''Friday, January 9'''
|-
| style="background:#ffffdd; color:black"|
| style="background:#b4d597; color:#522200"| '''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#b4d597; color:#522200"| '''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#b4d597; color:#522200"| '''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#fff6a6; color:#522200"| '''AHM''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/Capitol A-B], [[2009_EAB|'''EAB''']] in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus B]
'''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus A]
| style="background:#b4d597; color:#522200"|'''[[2009_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
|-
| style="background:#ffffdd; color:black"|'''7:30-8:00'''
| style="background:#ebeced; color:black"|
| style="background:#b4d597; color:black"| Breakfast
| style="background:#b4d597; color:black"| Breakfast
| style="background:#fff6a6; color:black"| Breakfast
| style="background:#b4d597; color:black"| Breakfast
|-
| style="background:#ffffdd; color:black"|'''8:00-10:00'''
| style="background:#ebeced; color:black"|'''9:30''' Core 1 and 2 PI closed session in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol A]
| style="background:#b4d597; color:black"|Project Work <br> '''8:00-9:00''' [[AHM2009:NITRC and Slicer|How to use NITRC and slicer]] (Steve, Terry)<br>
'''9:00-10:00''' [[AHM2009:Batchmake and XNAT|Using Batchmake and XNAT to process large studies]] (Stephen Aylward and Dan Marcus) in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"|Project Work <br>'''8:00-9:00''' [[AHM2009:Tutorial Review and Judging|Tutorial Review and Judging]] [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
'''9:00-10:00''' Particle Correspondence Breakout (Capital Ballroom A)
| style="background:#fff6a6; color:black"|'''8:00''' [[AHM 2009 Introduction|Introduction]], [http://www.spl.harvard.edu/~kikinis Ron Kikinis] <br>
'''8:05''' [[AHM 2009 NA-MIC Highlights|NA-MIC Highlights]] ([http://www.cs.utah.edu/~whitaker/ Ross Whitaker])<br>
'''Roadmap Projects'''<br>
'''8:35''': [[AHM2009:JHU|JHU/Queens]] ([http://research.cs.queensu.ca/~gabor/ Gabor Fichtinger])<br>
'''8:55''': [[AHM2009:UNC|UNC]] ([http://www.med.unc.edu/psych/directories/hazlett.htm Heather Cody])<br>
'''9:15''': [[AHM2009:PNL|PNL]] ([http://pnl.bwh.harvard.edu/people/profiles/kubicki.html Marek Kubicki])<br>
'''9.35''': [[AHM2009:Mind|Mind Institute]] ([http://www.mrn.org/principle-investigators/h.-jeremy-bockholt.html Jeremy Bockolt])<br>
| style="background:#b4d597; color:black"|Project Work <br>
|-
| style="background:#ffffdd; color:black"|'''10:00-10:30'''
| style="background:#ebeced; color:black"| Core 1 and 2 PI closed session
| style="background:#b4d597; color:black"| '''10:30-11:30'''[[AHM2009:GUI Testing|Automated GUI Testing for Slicer]] (Sebastien) [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"| Coffee
| style="background:#fff6a6; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
|-
| style="background:#ffffdd; color:black"|'''10:30-12:00'''
| style="background:#ebeced; color:black"| Core 1 and 2 PI closed session
| style="background:#b4d597; color:black"|Project Work
| style="background:#b4d597; color:black"|Project Work <br>

| style="background:#fff6a6; color:black"|
'''Collaborations'''<br>
'''10:30''': Iowa collaboration ([http://www.engineering.uiowa.edu/faculty-staff/profile-directory/bme/grosland_n.php Nicole Grosland])<br>
'''10:45''': [http://www.na-mic.org/Wiki/images/1/1b/NAMIC_External-Wyatt09.ppt Wake Forest collaboration] ([http://www.ece.vt.edu/faculty/wyatt.html Chris Wyatt])<br>
'''11:00''': Georgetown U. collaboration ([http://www.isis.georgetown.edu/PORTALVBVS/DesktopDefault.aspx?tabindex=2&tabid=8 Kevin Cleary])<br>
'''11:15''': [[media:HAMMER.ppt | UNC collaboration]] ([http://www.med.unc.edu/~dgshen Dinggang Shen])<br>
'''11:30''': Mario Negri Collaboration ([http://villacamozzi.marionegri.it/~luca/ Luca Antiga])<br>
'''11:45''': Discussion<br>
| style="background:#b4d597; color:black"|Project Work
|-
| style="background:#ffffdd; color:black"|'''12:00-1:00'''
| style="background:#b4d597; color:black"| Lunch
| style="background:#b4d597; color:black"| Lunch <br>
| style="background:#b4d597; color:black"| Lunch<br>
| style="background:#fff6a6; color:black"| Lunch
| style="background:#b4d597; color:black"| Adjourn
|-
| style="background:#ffffdd; color:black"|'''1:00-3:00'''
| style="background:#b4d597; color:black"|[[2009_Winter_Project_Week|Begin Project Activities]]: Introduce Projects and Participants
| style="background:#b4d597; color:black"|[[AHM 2009:DTI Breakout|DTI Discussion]] (Sonia, Randy, Others) [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/Amethyst 1]
| style="background:#b4d597; color:black"|Project Work (Capital Ballroom A) <br> '''1:00-2:00''' [[AHM2009:Python Modules|Python Modules]] (Luca Antiga) <br> '''2:00-3:00''' [[AHM2009:VTKWidgets | VTK Widgets]] (Will Schroeder)
| style="background:#fff6a6; color:black"|
'''Tools and Tutorials''' (coordinator) <br>
'''1:00-1:20''' [[AHM2009:Slicer|Slicer]] ([http://www.spl.harvard.edu/~pieper Steve Pieper])<br>
'''1:20-1:40''' [[AHM2009:Plug-ins|Plug-ins for Slicer]] ([http://wiki.na-mic.org/Wiki/index.php/User:Millerjv Jim Miller])<br>
'''1:40-2:00''' [[AHM2009:Non-interactive-tools|Non-interactive tools]] ([http://www.kitware.com/company/team/aylward.html Stephen Aylward])<br>
'''2:00-3:00''' [[AHM2009:Tutorial-Contest-Winners|Tutorial Contest]]: Presentations by the winners ([http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=64 Randy Gollub])<br>
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''3:00-3:30'''
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#fff6a6; color:black"| Coffee
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''3:00-5:00'''
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|'''3:30-4:30''' [[AHM2009:Cell Segmentation|Cell Segmentation]] (Alex G) <br> Project Work <br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"|Project Work <br>'''3:00-5:00''' Meshing Tutorial (Nicole Grosland, Vincent Magnotta)<br>[[Iowa_Meshing_Tutorial]]<br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#fff6a6; color:black"|[[2008 EAB|EAB]]<br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus B]<br>'''3:00-4:00''' Discussion with NA-MIC Leadership<br> '''4:00-5:00''' Closed Session
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''05:00-07:00'''
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|'''05:00-06:00''' [[AHM2009:Meshing Breakout | Meshing Breakout]] (Capital Ballroom A)
| style="background:#fff6a6; color:black"|'''6:00''' Optional: [http://www.skisaltlake.com/murphys.htm Beer at Murphy's] (like last year)
| style="background:#ebeced; color:black"|
|}

Please note that there will be a Core 1&2 Site PI Retreat on the morning of Monday, January 5th. This is a closed session for Core 1&2 Site PIs, with no delegates. The topic is the competitive renewal.

== Dates. Venue. Registration ==
'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 8th'''.
* Project Activities will be held rest of the week between '''Monday, January 5th and Friday, January 9th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. Please either call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) or book online '''by December 4, 2008''' using the code SCISCIA to get rooms at $139/night. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

'''Registration:''' We are charging a registration fee to all participants ($200 for AHM only, and $450 for AHM+). The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click http://www.sci.utah.edu/namic2009/registration.html for online registration. This registration must be completed by December 12, 2008.<br>

'''Connectivity'''
We have three wireless access points at the AHM. Two of them are located in the capital ballroom. One is named capital-ballroom, the other is named capital-ballroom2. If one access point doesn't let you connect it is probably overloaded. In that case, please try connecting to the other one.

== Attendees ==

Please follow http://www.sci.utah.edu/namic2009/registration.html to complete your online registration. The organizers will periodically publish the list of registered attendees in the space below. Attendees should '''NOT''' add their names in this section. This list is a snapshop as of 01:46, 23 December 2008 (UTC)

# Michael Ackerman NA-MIC All Hands Meeting National Library of Medicine at NIH
# Luca Antiga NA-MIC All Hands Meeting and Project Week 2009 Mario Negri Institute
# Kevin Archie NA-MIC All Hands Meeting and Project Week 2009 Washington University
# Nicole Aucoin NA-MIC All Hands Meeting and Project Week 2009 BWH
# Stephen Aylward NA-MIC All Hands Meeting and Project Week 2009 Kitware
# Sebastien Barre NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Morry Blumenfeld NA-MIC All Hands Meeting EAB
# H Jeremy Bockholt NA-MIC All Hands Meeting and Project Week 2009 The Mind Research Network
# Sylvain Bouix NA-MIC All Hands Meeting and Project Week 2009 PNL
# Josh Cates NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# German Cavelier NA-MIC All Hands Meeting NIH-NIMH
# Kiyoyuki Chinzei NA-MIC All Hands Meeting and Project Week 2009 AIST
# Kevin Cleary NA-MIC All Hands Meeting Georgetown University
# Manasi Datar NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Michal Depa NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Harish Doddi NA-MIC All Hands Meeting and Project Week 2009 Stanford University
# Andriy Fedorov NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Gabor Fichtinger NA-MIC All Hands Meeting Queens Univ
# Yi Gao NA-MIC All Hands Meeting and Project Week 2009
# Arnaud Gelas NA-MIC All Hands Meeting and Project Week 2009 Harvard Medical School
# Guido Gerig NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Polina Golland NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Randy L. Gollub NA-MIC All Hands Meeting and Project Week 2009 MGH
# Casey Goodlett NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Alexandre Gouaillard NA-MIC All Hands Meeting and Project Week 2009 Harvard Medical School
# Sylvain Gouttard NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Jeffrey Grethe NA-MIC All Hands Meeting and Project Week 2009 UC San Diego
# Nicole Grosland NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Daniel Haehn NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Nathan Hageman NA-MIC All Hands Meeting and Project Week 2009 UCLA
# Nobuhiko Hata NA-MIC All Hands Meeting and Project Week 2009 Brigham and Womens Hospital
# Kathryn Hayes NA-MIC All Hands Meeting and Project Week 2009 Brigham and Womens Hospital
# Heather Cody Hazlett NA-MIC All Hands Meeting University of North Carolina
# Jaesung Hong NA-MIC All Hands Meeting and Project Week 2009 Kyushu University
# Luis Ibanez NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Chris Johnson NA-MIC All Hands Meeting and Project Week 2009 EAB
# Ron Kikinis NA-MIC All Hands Meeting and Project Week 2009 SPL - BWH
# Ivan Kolesov NA-MIC All Hands Meeting and Project Week 2009 Georgia Tech
# Karthik Krishnan NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Marek Kubicki NA-MIC All Hands Meeting and Project Week 2009 PNL_BWH
# Curtis Lisle NA-MIC All Hands Meeting and Project Week 2009 KnowledgeVis, LLC
# Yanling Liu NA-MIC All Hands Meeting and Project Week 2009 SAIC-Frederick, Inc.
# Zhexing Liu NA-MIC All Hands Meeting and Project Week 2009 NIRAL, UNC
# Terry Lorber NA-MIC All Hands Meeting and Project Week 2009 Isomics, Inc
# Bill Lorensen NA-MIC All Hands Meeting and Project Week 2009 EAB
# Vincent Magnotta NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Daniel Marcus NA-MIC All Hands Meeting and Project Week 2009 Washington University
# Katie Mastrogiacomo NA-MIC All Hands Meeting and Project Week 2009 SPL - BWH
# Cedric Mathieu NA-MIC All Hands Meeting and Project Week 2009 UNC
# Bjoern Menze NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Mikhail Milchenko NA-MIC All Hands Meeting Washington University in St Louis
# James Miller NA-MIC All Hands Meeting and Project Week 2009
# Vandana Mohan NA-MIC All Hands Meeting and Project Week 2009 Georgia Inst of Technology
# kishore mosaliganti NA-MIC All Hands Meeting and Project Week 2009 Harvard Medical School
# Sandy Napel NA-MIC All Hands Meeting EAB
# Marc Niethammer NA-MIC All Hands Meeting and Project Week 2009 UNC Chapel Hill
# Guy Nir NA-MIC All Hands Meeting and Project Week 2009 Technion
# Ipek Oguz NA-MIC All Hands Meeting and Project Week 2009 UNC
# Saikat Pal NA-MIC All Hands Meeting and Project Week 2009 Stanford University
# Steve Pieper NA-MIC All Hands Meeting and Project Week 2009 Isomics, Inc.
# Marcel Prastawa NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Fred Prior NA-MIC All Hands Meeting EAB
# Sonia Pujol NA-MIC All Hands Meeting and Project Week 2009 Surgical Planning Lab, Brigham Womens Hosp
# Vidya Rajagopalan NA-MIC All Hands Meeting and Project Week 2009 Virginia Tech
# Austin Ramme NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Petter Risholm NA-MIC All Hands Meeting and Project Week 2009 Brigham Womens Hospital
# James Ross NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Marco Ruiz NA-MIC All Hands Meeting and Project Week 2009 UCSD
# Raul San Jose NA-MIC All Hands Meeting and Project Week 2009 LMI-BWH
# Peter Savadjiev NA-MIC All Hands Meeting and Project Week 2009 Brigham Womens Hospital
# William Schroeder NA-MIC All Hands Meeting and Project Week 2009 Kitware, Inc.
# Mark Scully NA-MIC All Hands Meeting and Project Week 2009 The Mind Research Network
# Madeleine Seeland NA-MIC All Hands Meeting and Project Week 2009 LMI
# Gregory Sharp NA-MIC All Hands Meeting and Project Week 2009 MGH
# Dinggang Shen NA-MIC All Hands Meeting UNC-Chapel Hill
# Kiran Shivanna NA-MIC All Hands Meeting and Project Week 2009 The University of Iowa
# Shantanu Singh NA-MIC All Hands Meeting and Project Week 2009 The Ohio State University
# Martin Styner NA-MIC All Hands Meeting and Project Week 2009 University of North Carolina
# Allen Tannenbaum NA-MIC All Hands Meeting and Project Week 2009 Georgia Tech
# Xiaodong Tao NA-MIC All Hands Meeting and Project Week 2009 GE Global Research
# Doug Terry NA-MIC All Hands Meeting and Project Week 2009 Psychiatry Neuroimaging Lab
# Clement Vachet NA-MIC All Hands Meeting and Project Week 2009 UNC
# Koen Van Leemput NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Archana Venkataraman NA-MIC All Hands Meeting and Project Week 2009 MIT CSAIL
# Siddharth Vikal NA-MIC All Hands Meeting and Project Week 2009 Queens University
# William Wells NA-MIC All Hands Meeting and Project Week 2009 SPL-BWH
# Carl-Fredrik Westin NA-MIC All Hands Meeting and Project Week 2009 Brigham and Womens Hospital
# Ross Whitaker NA-MIC All Hands Meeting and Project Week 2009 SCI Institute
# Nathan Wilson NA-MIC All Hands Meeting Cardiovascular Simulation, Inc.
# Chris Wyatt NA-MIC All Hands Meeting
# Alexander Yarmarkovich NA-MIC All Hands Meeting and Project Week 2009 ISOMIC
# Dr. Terry S Yoo NA-MIC All Hands Meeting DHHSNIHNLM

File:NAMIC External-Wyatt09.ppt

2009-01-08T00:18:56Z

Wyatt:

2009 Winter Project Week

2008-12-29T13:31:16Z

Wyatt: /* External Collaborations */

Back to [[Project Events]], [[AHM_2009]], [[Events]]

==Introduction to NA-MIC Project Week==

Please read an introduction about these events [[Project_Events#Introduction|here]].

== Dates.Venue.Registration ==

Please [[AHM_2009#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2009#Agenda|click here for the agenda for AHM 2009 and Project Week]].

==Projects==
Please note:
*Please use the [[2009_Winter_Project_Week_Template|'''2009 Project Week Template''']] to create a page for your project(s)
*[[2008_Summer_Project_Week#Projects|Last Event'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]]
*Next Project Week is at MIT -- June 22-26, 2009
The following is a list of all projects that will be pursued at this meeting.

===NA-MIC DBP Roadmap Projects===
Please note that these projects correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.

#[[DBP2:Harvard:Brain_Segmentation_Roadmap|Harvard Roadmap Project: Stochastic Tractography for VCFS]]
##[[2009_Winter_Project_Week:GT_TubularSurfaceSeg|Tubular Surface Segmentation for fiber bundle extraction]] (Vandana Mohan GATech, Allen Tannenbaum GATech, Marek Kubicki BWH, Stephen Aylward Kitware)
##[[2009_Winter_Project_Week_StochasticTractography |Stochastic Tractograhy Tool for Slicer]] (Marek Kubicki BWH, Julien de Siebenthal BWH, Steve Pieper Isomics)
##[[2009_Winter_Project_Week_Slicer3Functioning |Evaluation of basic Slicer 3.0 Functionality from a User Perspective]] (Doug Terry BWH, Marek Kubicki BWH, Sylvain Bouix BWH, Steve Pieper, Wendy Plesniak, Nicole Aucoin)
##[[2009_Winter_Project_Week:DTIGroupAnalysis |Group analysis of DTI fiber bundles]] (Casey Goodlett, Guido Gerig, Marek Kubicki, Sylvain Bouix)
#[[DBP2:UNC:Cortical_Thickness_Roadmap|UNC Roadmap Project: Cortical Thickness Measurement for Autism]]
##[[2009_Winter_Project_Week:LocalCorticalThicknessPipeline|Local Cortical Thickness Pipeline]] (Clement Vachet, Martin Styner, Heather Cody Hazlett, Marc Niethammer, Ipek Oguz)
##[[2009_Winter_Project_Week:RegionalCorticalThicknessPipeline|Regional Cortical Thickness Pipeline]] (Cedric Mathieu, Clement Vachet, Martin Styner, Heather Cody Hazlett)
#[[DBP2:MIND:Roadmap|MIND Roadmap Project: Brain Lesion Analysis in Lupus]]
##[[2009_Winter_Project_Week:HighLevelWizard|Slicer High Level Wizard Project]](Steve Pieper, Mark Scully, Jeremy Bockholt)
##[[2009_Winter_Project_Week:LesionAlgorithms|Review of Lesion Algorithms]](Ross Whitaker, Vincent Magnotta, Marcel Prastawa, Mark Scully, Jeremy Bockholt)
##[[2009_Winter_Project_Week:LongitudinalLesions|Determine Requirements of Longitudinal Lesion Analyses]](Jeremy Bockholt, Marcel Prastawa, Mark Scully, Andriy Fedorov)
#[[DBP2:JHU:Roadmap|JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]
##[[prostateSegmentationAHM2009|Prostate segmentation module for Slicer3]] (Siddharth Vikal, Gabor Fichtinger, Queens University, Katie Hayes, Brigham and Women's Hospital, Yi Gao, Allen Tannenbaum, Georgia Tech)

===Other NA-MIC Projects===
#[[2009_Winter_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA, Steve Pieper and Alex Yarmarkovich Isomics)
#[[2009_Winter_Project_Week_Hageman_UCLANSBrainLab | UCLA BrainLab/Slicer Neurosurgery Preoperative Tumor Planning]] Using Slicer and its link to BrainLab to investigate whether different tractography methods aid in preoperative planning of tumor resection.(Nathan Hageman UCLA)
#[[2009_Winter_Project_Week_Hageman_FEMSolverLib | Development of FEM / FVM solver library in ITK/VTK]] (and/or Python?) (Nathan Hageman UCLA, Vince, Nicole Grosland, Luca, Steve)
#[[2009_Winter_Project_Week_Transform_Management | Transform Management]](Jim Miller)
#[[2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 | Interactive 3D Widgets - Introduce new interactors into Slicer; extensions to current widgets to support Slicer]] (Karthik, Will Schroeder, Nicole Aucoin)
#[[2009_Winter_Project_Week_vtkITK_Pipeline | Using ITK in VTK Pipelines]] (Jim, Steve)
#[[2009_Winter_Project_Week_SlicerLayouts | User Interface Flexible Layouts]] (Wendy, Jim, Steve, Sebastien, Ron)
#[[2009_Winter_Project_Week_Python | Python interface completion and packaging - Fortran and openssl problems]] (Luca, Steve, Demian)
#[[Two-tensor tractography in Slicer using Python and Teem]] (Madeleine Seeland, C-F Westin, Xiaodong Tao)
#[[2009_Winter_Project_Week_Rotation_Tangents | Diffusion Tensor Invariant gradients and rotation tangents in Python and Teem]] (Peter Savadjiev, C-F Westin, Luis Ibanez)
#[[2009_Winter_Project_Week_Automated_GUI_Testing | KWWidgets and Slicer automated GUI testing ]](Sebastien, Yumin, Interested User: Vince)
#[[2009_Winter_Project_Week_ColorModule | Slicer Colors Module update ]](Nicole)
# [[2009_Winter_Project_Week_MRSI | MRSI Module for Slicer ]] (Bjoern Menze)
#[[Volume Rendering]] (Alex, Curt, Nicholas)
#[[2009_Winter_Project_Week_XND | XNAT Desktop BatchMake integration & Slicer interface]] (Dan Marcus, Stephen Aylward, Wendy Plesniak, Curt Lisle)
#[[2009_Winter_Project_Week_Cortical_Correspondence | Cortical correspondence using DTI]] (Ipek, Martin, Xiaodong)
#[[2009_Winter_Project_Week_Command_Line_Program_Testing |Command Line Program Testing]] (Lorensen, Ron)
#[[2009_Winter_Project_Week_Slicer_VMTK |Vessel Segmentation in Slicer using VMTK]] ([[User:haehn|Daniel Haehn]], [[User:lantiga| Luca Antiga]])
#[[2009_Winter_Project_Week_fMRI_Clustering |Exploring Functional Connectivity in fMRI via Clustering]] (Archana Venkataraman, Marek Kubicki, Polina Golland)
#[[2009_Winter_Project_Week_Compiler_Warnings:Slicer3_Graffiti |Compiler Warnings:Slicer3's Graffiti]] (Lorensen, NA-MIC)
#[[2009_Winter_Project_Week_ChangeTracker |Measuring dynamics of tumor growth in Slicer3 with ChangeTracker]] (Andriy Fedorov)
#[[2009_Winter_Project_Week_GWE_Catalogs |GWE integration with catalog files]] (Marco)
#[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti)
#[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard)
#[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas)
#[[2009_Winter_Project_Week_UtahPlugins | Integration of Utah registration and segmentation methods as Slicer plugins]] (Marcel Prastawa)
#[[2009_Winter_Project_Week_OMTRegistration | DWI to MRI Registration Using Optimat Mass Transport]] (Sylvain Bouix, Ivan Kolesov GATech)
#[[2009_Winter_Project_Week_Event_Broker |Propagating Event Broker through Slicer code base]] (Jim, Steve)
#[[2009_Winter_Project_Week_LungImagingPlatform | Lung Imaging Platform]] (James Ross, Raul San Jose)
#[[2009_Winter_Project_Week_SegmentationAtlases | Brain Atlases for Segmentation]] (Michal Depa, Koen Van Leemput, Mert Rory Sabuncu, Polina Golland)
#[[2009_Winter_Project_Week_ShapePipeline | Particle-based Shape Analysis Pipeline]] (Manasi Datar, Josh Cates, Ross Whitaker)
#[[2009_Winter_Project_Week_EPI_Correction | EPI Geometric Distortion Correction
]] (Ran Tao, Tom Fletcher, Ross Whitaker)

===External Collaborations===
# [[Iowa Meshing Project 2009]]
##[[Iowa Meshing Tutorial]]
#Wake Forest - Virginia Tech: [[2009_Winter_Project_Week_WFU1 | Move to All Slicer3 Workflow]]
#Georgetown U: [[2009_Winter_Project_Week_NAVRFA | Prototype RF Lesion Ablation Workflow prototyped in Slicer]]
#UNC: [[2009_UNC_HAMMER_WML | MR-image registration and white matter lesion segmentation algorithms to be extended and added to namic kit]]
#[[Stanford SIMBIOS: Whole Body Segmentation for Simulation]]
#[[NCI Evaluating NA-MIC Tools for Image Analysis]]

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# Starting Thursday, October 16th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 16: Engineering Infrastructure Projects
#*October 23: Funded External Collaboration Projects
#*November 6: DPB Projects
#*November 20: New Collaborations
#*December 4: Other Projects
#*December 18: Loose Ends
#By December 17, 2008: [[2009_Winter_Project_Week_Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By December 17, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# FINAL TCON: December 18th 3pm ET to tie loose ends
# 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...

== Previous Project Events ==

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

2009 Winter Project Week

2008-12-29T13:30:53Z

Wyatt: /* External Collaborations */

Back to [[Project Events]], [[AHM_2009]], [[Events]]

==Introduction to NA-MIC Project Week==

Please read an introduction about these events [[Project_Events#Introduction|here]].

== Dates.Venue.Registration ==

Please [[AHM_2009#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2009#Agenda|click here for the agenda for AHM 2009 and Project Week]].

==Projects==
Please note:
*Please use the [[2009_Winter_Project_Week_Template|'''2009 Project Week Template''']] to create a page for your project(s)
*[[2008_Summer_Project_Week#Projects|Last Event'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]]
*Next Project Week is at MIT -- June 22-26, 2009
The following is a list of all projects that will be pursued at this meeting.

===NA-MIC DBP Roadmap Projects===
Please note that these projects correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.

#[[DBP2:Harvard:Brain_Segmentation_Roadmap|Harvard Roadmap Project: Stochastic Tractography for VCFS]]
##[[2009_Winter_Project_Week:GT_TubularSurfaceSeg|Tubular Surface Segmentation for fiber bundle extraction]] (Vandana Mohan GATech, Allen Tannenbaum GATech, Marek Kubicki BWH, Stephen Aylward Kitware)
##[[2009_Winter_Project_Week_StochasticTractography |Stochastic Tractograhy Tool for Slicer]] (Marek Kubicki BWH, Julien de Siebenthal BWH, Steve Pieper Isomics)
##[[2009_Winter_Project_Week_Slicer3Functioning |Evaluation of basic Slicer 3.0 Functionality from a User Perspective]] (Doug Terry BWH, Marek Kubicki BWH, Sylvain Bouix BWH, Steve Pieper, Wendy Plesniak, Nicole Aucoin)
##[[2009_Winter_Project_Week:DTIGroupAnalysis |Group analysis of DTI fiber bundles]] (Casey Goodlett, Guido Gerig, Marek Kubicki, Sylvain Bouix)
#[[DBP2:UNC:Cortical_Thickness_Roadmap|UNC Roadmap Project: Cortical Thickness Measurement for Autism]]
##[[2009_Winter_Project_Week:LocalCorticalThicknessPipeline|Local Cortical Thickness Pipeline]] (Clement Vachet, Martin Styner, Heather Cody Hazlett, Marc Niethammer, Ipek Oguz)
##[[2009_Winter_Project_Week:RegionalCorticalThicknessPipeline|Regional Cortical Thickness Pipeline]] (Cedric Mathieu, Clement Vachet, Martin Styner, Heather Cody Hazlett)
#[[DBP2:MIND:Roadmap|MIND Roadmap Project: Brain Lesion Analysis in Lupus]]
##[[2009_Winter_Project_Week:HighLevelWizard|Slicer High Level Wizard Project]](Steve Pieper, Mark Scully, Jeremy Bockholt)
##[[2009_Winter_Project_Week:LesionAlgorithms|Review of Lesion Algorithms]](Ross Whitaker, Vincent Magnotta, Marcel Prastawa, Mark Scully, Jeremy Bockholt)
##[[2009_Winter_Project_Week:LongitudinalLesions|Determine Requirements of Longitudinal Lesion Analyses]](Jeremy Bockholt, Marcel Prastawa, Mark Scully, Andriy Fedorov)
#[[DBP2:JHU:Roadmap|JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]
##[[prostateSegmentationAHM2009|Prostate segmentation module for Slicer3]] (Siddharth Vikal, Gabor Fichtinger, Queens University, Katie Hayes, Brigham and Women's Hospital, Yi Gao, Allen Tannenbaum, Georgia Tech)

===Other NA-MIC Projects===
#[[2009_Winter_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA, Steve Pieper and Alex Yarmarkovich Isomics)
#[[2009_Winter_Project_Week_Hageman_UCLANSBrainLab | UCLA BrainLab/Slicer Neurosurgery Preoperative Tumor Planning]] Using Slicer and its link to BrainLab to investigate whether different tractography methods aid in preoperative planning of tumor resection.(Nathan Hageman UCLA)
#[[2009_Winter_Project_Week_Hageman_FEMSolverLib | Development of FEM / FVM solver library in ITK/VTK]] (and/or Python?) (Nathan Hageman UCLA, Vince, Nicole Grosland, Luca, Steve)
#[[2009_Winter_Project_Week_Transform_Management | Transform Management]](Jim Miller)
#[[2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 | Interactive 3D Widgets - Introduce new interactors into Slicer; extensions to current widgets to support Slicer]] (Karthik, Will Schroeder, Nicole Aucoin)
#[[2009_Winter_Project_Week_vtkITK_Pipeline | Using ITK in VTK Pipelines]] (Jim, Steve)
#[[2009_Winter_Project_Week_SlicerLayouts | User Interface Flexible Layouts]] (Wendy, Jim, Steve, Sebastien, Ron)
#[[2009_Winter_Project_Week_Python | Python interface completion and packaging - Fortran and openssl problems]] (Luca, Steve, Demian)
#[[Two-tensor tractography in Slicer using Python and Teem]] (Madeleine Seeland, C-F Westin, Xiaodong Tao)
#[[2009_Winter_Project_Week_Rotation_Tangents | Diffusion Tensor Invariant gradients and rotation tangents in Python and Teem]] (Peter Savadjiev, C-F Westin, Luis Ibanez)
#[[2009_Winter_Project_Week_Automated_GUI_Testing | KWWidgets and Slicer automated GUI testing ]](Sebastien, Yumin, Interested User: Vince)
#[[2009_Winter_Project_Week_ColorModule | Slicer Colors Module update ]](Nicole)
# [[2009_Winter_Project_Week_MRSI | MRSI Module for Slicer ]] (Bjoern Menze)
#[[Volume Rendering]] (Alex, Curt, Nicholas)
#[[2009_Winter_Project_Week_XND | XNAT Desktop BatchMake integration & Slicer interface]] (Dan Marcus, Stephen Aylward, Wendy Plesniak, Curt Lisle)
#[[2009_Winter_Project_Week_Cortical_Correspondence | Cortical correspondence using DTI]] (Ipek, Martin, Xiaodong)
#[[2009_Winter_Project_Week_Command_Line_Program_Testing |Command Line Program Testing]] (Lorensen, Ron)
#[[2009_Winter_Project_Week_Slicer_VMTK |Vessel Segmentation in Slicer using VMTK]] ([[User:haehn|Daniel Haehn]], [[User:lantiga| Luca Antiga]])
#[[2009_Winter_Project_Week_fMRI_Clustering |Exploring Functional Connectivity in fMRI via Clustering]] (Archana Venkataraman, Marek Kubicki, Polina Golland)
#[[2009_Winter_Project_Week_Compiler_Warnings:Slicer3_Graffiti |Compiler Warnings:Slicer3's Graffiti]] (Lorensen, NA-MIC)
#[[2009_Winter_Project_Week_ChangeTracker |Measuring dynamics of tumor growth in Slicer3 with ChangeTracker]] (Andriy Fedorov)
#[[2009_Winter_Project_Week_GWE_Catalogs |GWE integration with catalog files]] (Marco)
#[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti)
#[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard)
#[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas)
#[[2009_Winter_Project_Week_UtahPlugins | Integration of Utah registration and segmentation methods as Slicer plugins]] (Marcel Prastawa)
#[[2009_Winter_Project_Week_OMTRegistration | DWI to MRI Registration Using Optimat Mass Transport]] (Sylvain Bouix, Ivan Kolesov GATech)
#[[2009_Winter_Project_Week_Event_Broker |Propagating Event Broker through Slicer code base]] (Jim, Steve)
#[[2009_Winter_Project_Week_LungImagingPlatform | Lung Imaging Platform]] (James Ross, Raul San Jose)
#[[2009_Winter_Project_Week_SegmentationAtlases | Brain Atlases for Segmentation]] (Michal Depa, Koen Van Leemput, Mert Rory Sabuncu, Polina Golland)
#[[2009_Winter_Project_Week_ShapePipeline | Particle-based Shape Analysis Pipeline]] (Manasi Datar, Josh Cates, Ross Whitaker)
#[[2009_Winter_Project_Week_EPI_Correction | EPI Geometric Distortion Correction
]] (Ran Tao, Tom Fletcher, Ross Whitaker)

===External Collaborations===
# [[Iowa Meshing Project 2009]]
##[[Iowa Meshing Tutorial]]
#Wake Forest - Virginia Tech
## [[2009_Winter_Project_Week_WFU1 | Move to All Slicer3 Workflow]]
#Georgetown U: [[2009_Winter_Project_Week_NAVRFA | Prototype RF Lesion Ablation Workflow prototyped in Slicer]]
#UNC: [[2009_UNC_HAMMER_WML | MR-image registration and white matter lesion segmentation algorithms to be extended and added to namic kit]]
#[[Stanford SIMBIOS: Whole Body Segmentation for Simulation]]
#[[NCI Evaluating NA-MIC Tools for Image Analysis]]

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# Starting Thursday, October 16th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 16: Engineering Infrastructure Projects
#*October 23: Funded External Collaboration Projects
#*November 6: DPB Projects
#*November 20: New Collaborations
#*December 4: Other Projects
#*December 18: Loose Ends
#By December 17, 2008: [[2009_Winter_Project_Week_Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By December 17, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# FINAL TCON: December 18th 3pm ET to tie loose ends
# 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...

== Previous Project Events ==

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

2009 Winter Project Week WFU1

2008-12-29T13:28:05Z

Wyatt: /* References */

{|
|[[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
* 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
* develop a cleanup process using the Slicer3 editor
* create XNAT delivery mechanism for NHP atlas and test subject data
* 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 NCBC Collaboration:Measuring Alcohol and Stress Interaction

2008-12-10T14:39:21Z

Wyatt: /* Nonhuman Primate Atlas Development */

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 (coming soon)
#[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]

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2008-11-05T12:41:46Z

Wyatt: /* Nonhuman Primate Atlas Development */

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 (coming soon)
#[http://bsl.ece.vt.edu/download/NHP-EMSTut.zip older Slicer2.x based tutorial]

=== Nonhuman Primate Atlas Development ===
Vervet Probabalistic Atlas - Adult
# coming soon

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]

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2008-11-05T12:38:06Z

Wyatt: /* Projects */

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 (coming soon)
#[http://bsl.ece.vt.edu/download/NHP-EMSTut.zip older Slicer2.x based tutorial]

=== Nonhuman Primate Atlas Development ===
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]

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2008-11-05T12:30:46Z

Wyatt: /* 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]]
*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 WFU2

2008-10-23T13:25:41Z

Wyatt: /* References */

2009 Winter Project Week WFU2

2008-10-23T13:22:01Z

Wyatt: New page: {| |Project Week Main Page ]] |} __NOTOC__ ===Key Investigators=== * Virginia Tech: Chris Wyatt * Virgina Tech:...

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|}

__NOTOC__

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

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

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

<h1>Objective</h1>
We have developed a deformation based morphometry approach that combines multiple registration methods, using the log-Euclidean framework, to help remove bias in DBM based studies. The goal of this project is to interface this code with slicer using CLP modules.

</div>

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

<h1>Approach, Plan</h1>

The existing code is an ITK-based command line program that operates on vector fields and produces Jacobians averaged over the registation algorithm. We have another command line program that does permutation testing of hypothesized group differences.

</div>

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

<h1>Progress</h1>
TODO:
* develop CLP module for existing ITK-based code
* develop means to do permutation testing within slicer (list of files in groups?)

</div>

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

</div>

===References===
*Peters DC, Wylie JV, Hauser TH, Kissinger KV, Botnar RM, Essebag V, Josephson ME, Manning WJ. Detection of pulmonary vein and left atrial scar after catheter ablation with three-dimensional navigator-gated delayed enhancement MR imaging: initial experience. Radiology 2007; 243:690-695.
* Taclas JE, Wylie JV, Hauser TH, Manning WJ, Josephson ME, Peters, DC. Correlation and Visualization of Left Atrial Scar due to Pulmonary Vein Ablation with Recorded Ablation Sites. Proceedings of the 16th scientific meeting of the International Society for Magnetic Resonance in Medicine (2008), Toronto, CA, p. 1042.
*Malchano ZJ, Neuzil P, Cury RC, Holmvang G, Weichet J, Schmidt EJ, Ruskin JN, Reddy VY. Integration of cardiac CT/MR imaging with three-dimensional electroanatomical mapping to guide catheter manipulation in the left atrium: implications for catheter ablation of atrial fibrillation. J Cardiovasc Electrophysiol 2006; 17:1221-1229.

2009 Winter Project Week

2008-10-23T13:10:46Z

Wyatt: /* External Collaborations */

Back to [[Project Events]], [[AHM_2009]], [[Events]]
__NOTOC__

==Introduction to NA-MIC Project Week==

Please read an introduction about these events [[Project_Events#Introduction|here]].

== Dates.Venue.Registration ==

Please [[AHM_2009#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2009#Agenda|click here for the agenda for AHM 2009 and Project Week]].

==Projects==
Please note:
*Please use the [[2009_Winter_Project_Week_Template|'''2009 Project Week Template''']] to create a page for your project(s)
*[[2008_Summer_Project_Week#Projects|Last Event'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]]
*Next Project Week is at MIT -- June 22-26, 2009
The following is a list of all projects that will be pursued at this meeting.

===NA-MIC DBP Roadmap Projects===
Please note that these projects correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.

#[[DBP2:Harvard:Brain_Segmentation_Roadmap|Harvard Roadmap Project: Stochastic Tractography for VCFS]]
#[[DBP2:UNC:Cortical_Thickness_Roadmap|UNC Roadmap Project: Cortical Thickness Measurement for Autism]]
#[[DBP2:MIND:Roadmap|MIND Roadmap Project: Brain Lesion Analysis in Lupus]]
#[[DBP2:JHU:Roadmap|JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]

===Other NA-MIC Projects===
'''Preliminary List of Projects'''

#Fluid mechanics tractography and visualization (Nathan Hageman UCLA)
#UCLA BrainLab/Slicer Neurosurgery Preoperative Tumor Planning - using Slicer and its link to BrainLab to investigate whether different tractography methods aid in preoperative planning of tumor resection.(Nathan Hageman UCLA)
#Development of FEM / FVM solver library in ITK/VTK (and/or Python?) (Nathan Hageman UCLA, Vince, Luca, Steve)
#Transform Management(Jim Miller)
#Interactive 3D Widgets - Introduce new interactors into Slicer (Karthik)
#vtkITK Pipeline (Jim, Steve)
#User Interface Flexible Layouts (Wendy, Jim, Steve)
#Packaging Python Interface - Fortran and openssl problems(Luca, Steve)
#xnat and batchmake integration (Julien, Dan Marcus)
#Automated GUI testing (Sebastien)
#Slicer Colors Module update (Nicole)
#Volume Rendering (Alex, Curt)
#XNAT Dekstop & File Repository prototypes (Dan Marcus)

===External Collaborations===
*Iowa
*Wake Forest - Virginia Tech
** [[2009_Winter_Project_Week_WFU1 | Move to All Slicer3 Workflow]]
** [[2009_Winter_Project_Week_WFU2 | Development of deformation based morphometry module]]
*Georgetown U.
*UNC
*Mario Negri

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# Starting Thursday, October 16th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 16: Engineering Infrastructure Projects
#*October 23: Funded External Collaboration Projects
#*October 30: DPB Projects (2)
#*November 6: DPB Projects (2)
#*November 13: New Collaborations
#*November 20: New Collaborations
#*December 4: Other Projects
#*December 18: Loose Ends
#By December 17, 2008: [[2009_Winter_Project_Week_Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By December 17, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# FINAL TCON: December 18th 3pm ET to tie loose ends
# 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...

== Previous Project Events ==

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

2009 Winter Project Week WFU1

2008-10-23T13:05:21Z

Wyatt: New page: {| |Project Week Main Page ]] |[[Image:Rhesus_HpcCorScrnShot.jpg|thumb|220px|Subcortical Segmentation of Rhesus sub...

Engineering:TCON 2008

2008-05-29T15:46:39Z

Wyatt:

Back to [[TCON:Main|TCON:Main]]
__NOTOC__
== Slicer 3 Dartboard ==
Link to the Slicer 3 Dartboard [http://www.na-mic.org/Dart/Slicer3/Dashboard/ here]

==2008-06-19==
*Agenda: Project Week Prep Loose Ends

==2008-06-12==
Agenda: Discuss NEW EXTERNAL Collaboration projects for project week
*3:00-3:15pm Rutgers (Jinghao)
*3:15-3:45pm UIowa (Gary Christensen)
*3:45-4:00pm regular NAMIC engr business

==2008-06-05==
Agenda: Discuss FUNDED EXTERNAL Collaboration projects for project week
*3:00-3:15pm Meshing Collaboration (Iowa)
*3:15-3:30pm RF Ablation Liver Collaboration (Georgetown)
*3:30-3:45pm Vervet EM Segmentation Collaboration (WFU/VT)
*3:45-4:00pm regular NAMIC engr business

==2008-05-29==
Agenda: Discuss ALGORITHM CORE lead projects for project week
*3:00-3:15pm
*3:15-3:30pm
*3:30-3:45pm
*3:45-4:00pm
* Status of Slicer 3.2: Steve Pieper et al.
** Status
** Bug squashing

==2008-05-22==
[[Image:Slicer3Dashboard-5-20.png||thumb|right|Dashboard]]
Agenda:
* <big>'''A round of applause for Sebastian, Steve and all the code freezers'''</big>
*http://www.slicer.org/slicerWiki/index.php/Announcements:Slicer3.2 documentation assignments and schedule for the 3.2 release:
**Outstanding issues in release
***EM Segment Wizard - Button Issues
***EM Segment Command line is in the wrong directory - should be put in bin
***EM Segment Template Builders
****First, second and 3rd steps do not work correctly - pull down list
****Possible issue with MRML manager changes
***Feature Request
****Can not changes the name of the parameters because it references the node ID and not the name
****EM Segment simple - images are specified by XML type file and not image - requires reloading and does not use images loaded within Slicer3
****Loading parameter set - Add a hierarchy of the nodes for better visualization of parameters
**registration,
**loadable modules,
**interactive editor,
**volume rendering
*New Slice Control Widget added by Wendy - last GUI based change
*Issues with Resize of Slicer and 3D Widgets
*Discuss Engineering Core Projects for the Project Week
*Discuss Jeremy's request to add Support Vector Machine library to NA-MIC Kit. http://www.csie.ntu.edu.tw/~cjlin/libsvm/

Highlights:
*Attendees: Will, Sebastien, katie, tina, brad, steve, xiadong, vince, jim, nicole, dan marcus, Ron, Sonia.

==2008-05-15==
Agenda:
*DBP II update and plans for project week. 2 DBPs and engr+algo core liaisons should attend.
**3-3:20 Harvard. Marek, Brad, Polina confirmed.
**3:20-3:40 UNC. Heather confirmed. Jim, Martin, Heather, Clement held offline mtg already.
**3:40-4pm regular NAMIC engr business
***Slicer code freeze and release
***Focus during the upcoming months on "ruggedizing" Slicer

Attendees: Tina, Katie, Nicole, Vince, Will, Marek, Sylvain, Polina, Clement, Brad, Ron, Alex, Sebastien

Highlights:
*Harvard DBP projects for Project Week
*#Probabilistic Tractography - on hold since Tri left
*#Slicer3 - Need bug fix for why Slicer 3 can't load and run UNC data that Martin tried
*#EPI Distortion correction (Sylvain, Tauseef GATech)
*#Eddy CUrrent distortion correction (Sylvain, Ran Tao Utah)
*# Parcellation - need help parametrization (Sylvain, Brad)
*# fmri - apply polina's algorithm to Marek's data (Marek, Bryce Kim)
*# Finsler method (John Melonakos, Eric Melonakos)
*# Group Analysis on DTI (Casey Goodlett, Marek)
*Code Freeze: scheduled for tomorrow
*RSNA Demo
*#editor, lightbox, data fusion
*#Sonia is developing the curriculum for course
*UNC DBP Projects
*#Cortical thickness pipeline
*#workflow module
*#NITRC - need to talk to Steve pieper
*#batchmake pipeline in Slicer
*#use Bspline module in ITK

==2008-05-08==
Agenda:
*DBP II update and plans for project week. 2 DBPs and engr+algo core liaisons should attend.
**3:00-3:20 MIND. Jeremy, Ross, Steve Confirmed.
*** Testing lots of methods. None working well.
*** Bayesian labeling seems to be working the best.
*** Close the look on itkEMS method
**3:20-3:40 JHU. David G, Allen T., Katie H. confirmed.
*** Prostate really difficult task
*** Delphine's work was originally on prostate.
*** Optimal mass transport registration project at project week
**3:40-4pm: regular na-mic engr core business
*** Short update on UNC DBP needs: registration, module chaining
*** Discussion on plans for chaining. Prototype for project week?

==2008-05-01==

Attendees: Steve, Jim, Will, Tina, Xiaodong, Katie, Danielle, Sebastian, Sonia,

* Slicer 3 stable release schedule planning (Slicer 3.2)
** We would like a stable version before the [[Events:June-Germany | Mid-June German training event]] that includes all the latest namic technology (CMake 2.6, ITK 3.6, VTK 5.2, Tcl/Tk 8.5, KWWidgets...). Some problems were fixed this week for ITK3.6 and VTK 5.2; Slicer3 was successfully built using CMake 2.6 against VTK 5.2, ITK 3.6, and Tcl/TK on Linux, Windows, and Mac (by Sebastien). Need more coverage on Slicer. TODOs: Developing tutorial material for the new Slicer release. Testing, automated part plus user interaction part.
** [[2008_Summer_Project_Week | Project Week]] projects can go into the trunk after the release is branched. GUI changes to show "axial", "sagittal", "coronal" slices in the acquisition orientation.
** Proposed schedule:
*** May 16: Feature Freeze of the trunk followed by group debugging/testing
*** May 23: Create Release Branch for Slicer 3.2
*Danielle Pace @ Robarts Inst. joined NCIGT/SNR to develop [[LEGO_IGT_and_Medical_Robotics_Tutorial | Slicer IGT Tutorial]].

==2008-04-24==

Attendees: Steve, Katie, Nicole, Tina, Nathan, Jim, Vince, Brad, Louis, Marco

Agenda
* Slicer3D Wikipedia page discussion. Check it out [http://en.wikipedia.org/wiki/Slicer here].
** Need to tone it down a little so it sounds less like ad copy.
** Needs more pawprints on it from unique editors/authors for Wikipedia to keep it online.

* Nathan
** Helical phantom available to LONI web service.
** Should we make the link available through Slicer or not?

* Project pages need to be updated.
** Deadline: May 15th for NA-MIC, a week earlier is preferred
** [[2008_Annual_Scientific_Report | Progress report link]]
** Project week pages need to be linked off the progress report (indirectly)

* Waiting for CMake and ITK releases to be finalized
** Probably will be cut tomorrow

* Set up special T-con time for Oz

* What's the deal with the CMake Policy Change warnings?
** Copy three lines before CMAKE_MINIMAL_REQUIRED
** Ask the CMake list

==2008-04-17==

Attendees: Jim, Dan Marcus, Xiaodong, Nicole, Tina, Steve, Katie, Jeff, Sebastien, Vince

Topics:

*[[2008_Annual_Scientific_Report]]
*[[2008_Summer_Project_Week]]
*VTK (5.2) and CMake (2.6) release schedules
**VTK Plan on branching next week
**CMake is on RC8, guessing will branch in 1-2 weeks
*VTK (5.2) performance issues when rendering
**In the meshing project we have seen a significant reduction in the rendering of a large number of vtkSphereSource and vtkPointWidgets in 5.2 as compared to 5.0
***100x performance hit in debug mode on Linux
***Jeff added code to make sure the check doesn't happen more than once/sec.
***Still 25% slower, but not 100x slower
**Rendering time has been increased by an order of magnitude
* OK for Kitware to put Slicer3 screenshots on Flickr? (see [http://flickr.com/photos/kitware/ Kitware's Flickr account])
** => I (Seb) did a quick pass at the files uploaded in 2008, and copied them to a [http://flickr.com/photos/kitware/sets/72157604594177467/detail/ Slicer3 photoset].

==2008-04-03==

Jim, Curt, Tina, Nicole, Wendy, Steve, Brad, Xiaodong, Vince, Ron, Nathan

Agenda
* discussion of xcede web services and mBIRN
* [[2008_Engineering_review_at_Utah:FollowUp]]
* New! [[Slicer3:DTMRI |glyphs on slices movie!]]
** made using wink from http://www.debugmode.com/wink/
** add something like the following to your wiki page after uploading the .swf file to the wiki
<pre><flash>file=dti_glyphs.swf|width=800|height=600|quality=best|loop=true|play=true</flash></pre>
* CMake 2.6 release candidates have been cut with .rpm and .deb output targets!
** Will will work with Katie on this
* Jim is going to visit Kitware to talk about BSpline registration

==2008-03-27==
Attendees: Steve, Will, Xiaodong, Nathan, Katie, Wendy, Tina, Nicole, Marco, Sebastien
* Nathan will discuss presentation of fluid mechanics projects.
* Update from Core 1 + Core 2 [[2008_Engineering_review_at_Utah | meetings in Utah]] earlier this week.
* [[Slicer3:Chain_CLMs | Discussion of Module Chaining]] (Marco and All)
** Requested by Core 1 to systematize common use case
** Need several steps in an analysis process to act like a single command
** Would like something akin to the EMSegment workflow wizard, but as command line module rather than built-in module

Highlights:

Nathan's overview: discussing visualization options for his fluid velocity vector fields for tractography algorithm. Steve mentions a few options:
* A LDDMM module in Slicer2 that does animated vector field visualization (work done in collaboration with Johns Hopkins: Anthony Kolasny, Mike Miller, et al.).
* Another option would be to try using ParaView as a way to flesh out specifics, and then build a more custom tool for tractography later. Will will point Nathan to documentation for file formats, data formats, etc. or help with any questions, and Nathan will try this out.

Discussion of these topics at the engineering review in Utah:

* chaining modules together
* grid wizard (Marco) for grid and batch computing
* Bspline registration
* setting up repositories for collecting slicer modules (as technology transition mechanism)
* how this will fit into the slicer build process
* diffusion weighted imaging, shape analysis, and segmentation
* dicom to nrrd converter...

Milestones were set for April-end, Project week, and AHM.

Module chaining discussion (see link above):

* Java version as first goal -- eventually C++ implementation.
* Discussion about module discovery process and how will chained modules be packaged: (c++ stub programs? or
or discovery find chain-descriptor xml files? shell scripts? (cross-platform issues)...)
* Goal: By project week in June we would like to be able to chain modules developed by Core 1.

Sebastien's update on module building: Wiki will be updated today with status. (link)

==2008-03-20==
Attendees: Tina, Jim, Will, Wendy, Xiaodong, Nathan, Martin, Marco
* [[2008_Annual_Scientific_Report|Progress Report]] - read over the assignments. We will look for progress from June 1, 2007 to May 30, 2008.
* June 23-27 is the summer project week. We will make first pass on projects in late April.
* Module discussion: Martin wanted to understand the state of module creation and usage within Slicer. Sebastien is working on modules that are built against an installed module. Terry is working on built-in modules for Slicer. Jim is working on modules using CMake in the NTRIC repository.
* Nathan- write a command line, Slicer module that is a wrapper to a web service. Nathan thinks he can get this done prior to the June AHM. We referred to Jim's presentation at the Utah SLC Core 1/Core 2 meeting.
* We will talk about grid wizard next week at SLC

==2008-03-13==
Attendees: Jim, Nicole, Dan, Xiaodong, Vince, Sebastian, Alex, Curt, Steve, Will, Terry
* Update on [[Slicer3:Loadable_Modules |Loadable Modules]] project (Terry) and [[Slicer3:Build/Modules | CMake updates for module builds]] (Sebastien)
* [[2008_Engineering_review_at_Utah | Engineering trip to Utah]]
* We are starting to use Categories to bin our pages. [[SuggestedCategories]] - suggestions?

==2008-03-06==
Attendees: Steve, Jim, Katie, Nicole, Tina, Xiaodong, Marco, Ron

Highlights:
*Slicer page on wikipedia - http://en.wikipedia.org/wiki/3DSlicer. All engineering core members should visit this page and edit as needed. ASAP.
*dicom to nrrd converter in progress. Xiaodong working on it and expecting to complete in a few weeks.
* [[2008_Engineering_review_at_Utah|March 24-26 Meeting in Utah]]

==2008-02-28==

* Attendees: Jim, Steve, Wendy, Katie, Tina, Jeff, and Marco (Grid Wizard Guy)
* Discussion on time series analysis (viewer, scene markup). Initial viewer will be a general tool for comparing images.
* Avalanche of new features in [http://gridwizard.org/gwe/index.html grid wizard and GSlicer3]
** Proxy around Command Line Modules
** Extends command line with specifications for ranges of values as well as specify remote resources (data) that need to be transferred to/from the grid.
** Uses Velocity for parameter template engine
** Grid selection and authentication still being refined for Slicer
** Could be extended to other grid types (LSF, etc.)
** Lots of information on the website. Instructions for installation. A bit daunting for non-grid people. Some of us will have to work through the instructions step by step to evaluate.

==2008-02-21==

* Attendees: Xiaodong, Jim, Katie, Nicole, Will, Steve, Nathan, Tina, Ron, Padma, Marco

- Nathan brought us up to date on fluid mechanics tractography

- Padma Sundaram: SCIrun environment supports EEG processing

- Marco is releasing Grid Wizard alpha version

- Nathan brought up the helical digital phantom web service. Currently the thinking is that it can be accessed through a web service. We suggested that Nathan write a wrapper, consistent with Slicer's execution module, to invoke the web service. However, since it is not available in source form, NAMIC cannot accept it as part of the NAMIC Kit proper. We can guide Nathan in the execution of this module.

==2008-02-14==
* Attendees: Xiaodong, Katie, Will, Sebastien, Steve, Mike, Wendy, Haiyi, Dan, Curt, Tina

=== Other NA-MIC Projects ===

16 - CPack (Katie): Slicer3 compiles and packs using the new C-tools with some bug fixes. Using CMake to select desired modules, using something similar to cygwin. Official Slicer3 snapshot tagged. Different Tcl/Tk versions are currently used for different platform. This need to be addressed.

17 - Slicer GUI Style Guide and Cookbook {Wendy}: This will be a long term effort. During the programming week, the design and implementation details were discussed. The Cookbook will be launched from Slicer, act like KWWidget tour.

18 - Volume rendering (Steve): UI is fairly stable.

19 - Volume rendering using Cuda (Steve):

20 - 3D W Widgets and Picking (Will): found a list of candidates of widgets for Slicer. A few bug fixes for VTK.

21 - XNAT Integration (Dan): Requirements were gathered for a XNAT application that organizes files and caches files from XNAT repositories. Some XML format issues have been addressed.

22 - KWWidgets Roadmap (Sebastien): Gathered requirements. Been working down the list of the feature requirements.

=== External Collaboration ===

1 - Astronomical coordinate system support [Harvard IIC] (Mike): Astronomical datasets are quite different from medical dataset. Wendy helped with re-centering data. Made progress in converting between coordinate systems (Cartesian to Spherical).

2 - New Meshing Techniques into NA-MIC [Univ. of Iowa]

3 - Meshing Workflow into Slicer [Univ. of Iowa] (Curt): Will be integrated into Slicer soon. Command line program using VTK.

4 - Evaluating NA-MIC Tools for Small Animal Imaging Workflows [NCI] (Curt):

5 - IGSTK-Slicer [Georgetown] (Haiyi): Successful tracking data using IGSTK.

6 - Japanese Intelligent Surgical Instrument Project [AIST]

7 - GoFigure:High-Level Microscopy Image analysis Application and Algorithms [CalTech-Harvard Medical School]

8 - Doing microscopy image analysis with Slicer3 [The Ohio State University]

9 - fMRI Analysis with Slicer 3 [The Ohio State University]

10 - Resampling DTIs with Slicer 3 [BWH]

11 - Analyzing fMRI and concurrent EEG with Slicer and SCIRun [BWH]

12 - Bayesian hierarchical models for fMRI variance components analysis [BWH]

==2008-02-07==
* Attendees: Ron, Will, Steve, Wendy, Nicole, David G, Mark S., Casey, Sebastien, Curt, Luca

* Look at [http://www.vtk.org/Wiki/VTK_Widget_Examples upcoming VTK 3D widgets]
* Review of projects from SLC AHM 2008 http://wiki.na-mic.org/Wiki/index.php/2008_Winter_Project_Week

===DBPs===

1 - Stochastic Tractography in Schizophrenia (need to be invited to follow-up TCon)

2 - Cortical thickness analysis - testing EM segmenter to their data. They estimated parameters and tested during the week. The goal now is to compare ITK-MS and EM segment module to see how these two tools compare for cortical thickness. They are reviewing the tools using the same patient data.

3 - (Mark Scully) Legion segmentation using EM segmenter and other options - worked with Brad using 2 channels of data. Flare as 3rd channel caused problems. Desired to have T1/T2/Flair together as three channel dataset. Marcel is going to deliver his segmentation algorithm software to them to compare results.

4 - Robotic Prostate Interventions - (David Gobbi) Working on transrectal biopsy module for Slicer. They had a previous module for transcranial biopsies. One of the most exciting developments was a new prototol "open IGT-Link" which will replace navitrack inside Slicer. Image transfer is working over this protocol. A simulator is being developed for the robot. A few VTK bugs may have been discovered during this process, but it isn't on the top priority list right now.

5 - Prostate Cancer - Wrote new ITK filter that has been submitted to the Sandbox. They are looking at spherical wavelets for shape segmentation. The wiki page will be updated soon.

=== Other NA-MIC Projects ===

1 - Groupwise Registration - (Casey) New Bspline registration method is being developed here. It has been used for another project by Casey (#6). Page needs to be updated.

2 - (Need to be invited to follow-up TCon)

3 - (Need to be invited to follow-up TCon))

4 - (Need to be invited to follow-up TCon). Page needs to be updated

5 - Incorporating DTI tools into NAMIC toolkit - They are gathering a dataset that has both structural and DTI data in agreement. Previous dataset was missing part of cortex. UNCDB2 dataset has full coverage of the brain. Resolution is a bit lower, but full coverage is an advantage. Page is close to up to data. Just submitted a paper to ISBI 2008 and working on MICCAI paper, as well.

* NITRIC is g-forge and would be a good place for automated build process for Slicer modules. This could make it easier to configure Slicer in client labs without need to build from source. This is still being developed by the NA-MIC core team. There is an entry on the collaboration section of the NA-MIC website. Also www.slicer.org/Documentation link.

6 - (Casey) Worked with Serdar using groupwise registration tool. They are currently evaluating results of this study. More images will be added.

7 - (John Melanakos) Spent last week working with collaborators on the MICCAI paper. Project page is well filled.

8 - (Need to be invited to follow-up TCon)

9 - (Need to be invited to follow-up TCon)

10 - MRML scenes for execution model. Some of the issues Brad was having have been resolved. Alex is making adjustments to MRML library as needed for the EM segmentation model.

11 - (Curt) Unstructured Grids in Slicer - Finite Element modeling process was originally in a standalone VTK application. The first Slicer module integration did not use MRML based storage. We are now creating subclasses of Model and Unstructured grid data for storage and display in Slicer. Some minor issues need to be worked out, but the MRML extensions for UnstructuredGrid datatypes are working.

12 - Python (Luca) MatPlotLib plots are close to happening within Slicer. Steve believes it is 80% complete. Python command line modules are working now. Multiple arguments had to be worked by Luca. He has developed Python-based CLI modules. The event broker is discussed here because it affects the interaction with Python, because a Mutex lock has to be placed on the MRML scene. Dan has been helping with metamodules - a single Python module which calls other mothers (hierarchical execution, recipes, etc.).

* Ron asked about using this scripting technique for the ModelMaker. Some of the parameter setting, etc. could be set in the top module. Nicole will look at this. Kilian said that he wanted to call the "modelmaker" from another module.

* A need was identified for new wiki pages: (1) scripted modules, (2) metamodules, (2) python scripted modules

13 - (Luca) Transform hardening - Sometimes images are not XYZ alligned. How will command line modules treat an object if it is the child of a transform. The module needs to be able to apply xforms to data (after hierarchy is flattened) to get xformed data. Jim and Steve talked through this lately becomes of the transforms access two-directions (from parents / to parents, etc.) They are looking at how to change the model.

14 - (Steve) MRML support for out-of-core processing - Steve put a link to a new page. Dan, Jim, Wendy, Steve, etc. working through NAC renewal grant (5 years). Multiresolution and asynchronous data are likely targets for this effort, but it will be a long-term effort.

15 - Event Broker discussion - Steve has made process on this, but this wiki page is older. See the event broker page. (look at link under Objective). New term "observation" : completely introspectable. A full dependency between objects is implemented. When a subject issues a "modified" event, Delete events are maintained. Complete "relationship" management of the interaction between objects. This helps by allowing asynchronous event processing. MRML has been converted to use the event broker with asynchronous events managed by the Slicer GUI (async events invoked after GUI events are done). This hasn't broken anything so far, but should improve scalability. Dot logfile format can be generated for inter-object dependencies. This can be used to help provide "who called who" traces. Some special magic is done in MRML Display nodes. They set "observation nodes"

=== Next Week ===
Continue through project review. Request missing project members to attend. Review wiki pages.

==2008-01-31==
Attendees: Jim, Steve, Stephen, Wendy, Xiaodong, Nicole, Katie, Ron
* Project week follow-up
** Half of tcon on Feb 7
** Half of tcon on Feb 14
* Registration
** Viola-Wells optimizations need to be enabled
** Stephen needs to check-in and publish recent changes
** Stephen needs to update the wiki
** Luis continues to make optimizations (main focus is memory reduction)
* BatchMake
** Grid Wizard - meeting on Monday
** Integration with Slicer delivered via getbuildtest2
* New webpages
** http://slicer.org
** Uses wiki-to-web
** Feel free to edit/improve
* Slicer-specific wiki
** Migrating appropriate info from Na-mic to slicer
** Hold off on adding to Slicer-wiki until notified
*** Continue using Na-mic wiki
* New Nitrc project
** Jim Miller is leading
** "Slicer3 plug-in examples" project
** http://nitrc.org - search for slicer3
*** Includes demo/stub for ITK filtering data, etc.
** Collection associated with an ITK course being taught
** Requires CVS version of ITK
** Works with Slicer build and Slicer install
** Steve P is the liaison with NITRC
* Slicer tutorial at UNC, April 14th
** Working with UNC's BRIC (http://www.bric.unc.edu)
** Sonja, Randy, Martin, Stephen
* User-level Slicer training - Feb 20 at BWH
** 1249 Boyleston
** Release version of Slicer3

==2008-01-24==
Attendees: Jim, Steve, Wendy, Xiaodong, Nicole, Katie, Alex, Luis, Ron, Will
* Project week follow-up (Next week?)
** Will will send email invitations for first half of projects for next week's tcon
* Loadable modules
** Alex and Terry are rearranging Slicer3.cxx to support loadable modules
** Separate branch for built-in module discovery process
** Sebastien is working on build issues for modules whose code is outside Slicer3
* GenerateCLP - Thanks Hans for changes to support building modules
** Hans is running a class this semester where the students will build Slicer CLI modules.
** Jim is working on an ExampleModule for people to use as a template for building modules outside of Slicer3. Perhaps NITRC.
* XML library
** What to do with libaries that are too big to include in the source directory?
* AHM 2009, Jan 5-9, 2009
* Summer Project Week, Jun 23-27, 2008
* New server architecture for wiki, svn, publication database

==2008-01-17==
Attendees: Jim, Katie, Sebastien, Stephen, Luis, Steve, Wendy, Will

* Luis and Bill Hoffman are making progress in making ITK installation relocatable. This is needed to finish the work on building plugins from an installation.
* What's in VTK 5.2?
** Infovis - Tables, Graphs, Views, IO
** Refinements to WWidgets. Client/Server connections within the widgets. Event translation. New widgets (text, caption, affine, checkerboard, rectilinear wipe, annotation, key frame, contour, measurement, point/placer, plot)
** Build now? Or wait until 5.2 released?
** Repository freeze in March
** Release on April 1, 2008
* ITK release
** Patches to ITK 3.4
*** Nine component/six component tensor conversion in IO has been patched to ITK 3.4
** 1/19-2/1 moving contributions on Insight Journal for ITK 3.6
** Move items from Review directory to main tree (QuadMesh, TransformIO) for ITK 3.6
** Freeze repository 2/29 for ITK 3.6
** Slicer3 will need to build against the Review directory.
* CMake release
** Version 2.6 on the horizon - release candidate in 3 weeks.
* Tcl/Tk 8.5
** Sebastien has a Windows build
** Steve will try it out
** Wait to switch to 8.5 until we have a good reason
* Loadable modules
** Sebastien - working on CMake issues on building modules as loadable modules
** Terry - working on loading modules and reworking Slicer3.cxx
* [[Slicer3:EventBroker | Event Broker]]
* DWI DICOM as part of the Load Volume. Xiaodong is working on it.
* ITKFactories directory in build and installs to hold ImageIO plugin libraries. Should increase the speed of executable plugins on the Mac.
* OpenIGTLink
** Protocol on the wiki (message format)
** Put code in Sandbox, SourceForge, NITRC, Google Code???
* Will schedule a time to go over the Project Week results

==2008-01-10==
No tcon due to AHM

==2008-01-03==
* Attendees: Jim, Steve, Will, Brad Davis
* Topics:
** Jim and Will talked about leading the Monday and Friday sessions, and who would do what.
** We are going to send out reminders to the project leads to ensure that their project descriptions are up to date
** We discussed the software process project to make sure that we have a chance to address the Slicer build process, dashboards, etc.
** We decided not to hold the project wrap-up presentation at AHM; we will do that later at subsequent TCons. (We decided that we needed the time to actually work. We are concerned that we are starting to see too many break-outs and not enough time to work.)
** We keenly missed Tina and hope that she and her family are doing well.

Engineering:TCON 2008

2008-05-29T14:27:12Z

Wyatt:

Back to [[TCON:Main|TCON:Main]]
__NOTOC__
== Slicer 3 Dartboard ==
Link to the Slicer 3 Dartboard [http://www.na-mic.org/Dart/Slicer3/Dashboard/ here]

==2008-06-19==
*Agenda: Project Week Prep Loose Ends

==2008-06-12==
Agenda: Discuss NEW EXTERNAL Collaboration projects for project week
*3:00-3:15pm Rutgers (Jinghao)
*3:15-3:45pm UIowa (Gary Christensen)
*3:45-4:00pm regular NAMIC engr business

==2008-06-05==
Agenda: Discuss FUNDED EXTERNAL Collaboration projects for project week
*3:00-3:15pm Meshing Collaboration (Iowa)
*3:15-3:30pm RF Ablation Liver Collaboration (Georgetown)
*3:30-3:45pm Vervet EM Segmentation (WFU/VT)
*3:45-4:00pm regular NAMIC engr business

==2008-05-29==
Agenda: Discuss ALGORITHM CORE lead projects for project week
*3:00-3:15pm
*3:15-3:30pm
*3:30-3:45pm
*3:45-4:00pm
* Status of Slicer 3.2: Steve Pieper et al.
** Status
** Bug squashing

==2008-05-22==
[[Image:Slicer3Dashboard-5-20.png||thumb|right|Dashboard]]
Agenda:
* <big>'''A round of applause for Sebastian, Steve and all the code freezers'''</big>
*http://www.slicer.org/slicerWiki/index.php/Announcements:Slicer3.2 documentation assignments and schedule for the 3.2 release:
**Outstanding issues in release
***EM Segment Wizard - Button Issues
***EM Segment Command line is in the wrong directory - should be put in bin
***EM Segment Template Builders
****First, second and 3rd steps do not work correctly - pull down list
****Possible issue with MRML manager changes
***Feature Request
****Can not changes the name of the parameters because it references the node ID and not the name
****EM Segment simple - images are specified by XML type file and not image - requires reloading and does not use images loaded within Slicer3
****Loading parameter set - Add a hierarchy of the nodes for better visualization of parameters
**registration,
**loadable modules,
**interactive editor,
**volume rendering
*New Slice Control Widget added by Wendy - last GUI based change
*Issues with Resize of Slicer and 3D Widgets
*Discuss Engineering Core Projects for the Project Week
*Discuss Jeremy's request to add Support Vector Machine library to NA-MIC Kit. http://www.csie.ntu.edu.tw/~cjlin/libsvm/

Highlights:
*Attendees: Will, Sebastien, katie, tina, brad, steve, xiadong, vince, jim, nicole, dan marcus, Ron, Sonia.

==2008-05-15==
Agenda:
*DBP II update and plans for project week. 2 DBPs and engr+algo core liaisons should attend.
**3-3:20 Harvard. Marek, Brad, Polina confirmed.
**3:20-3:40 UNC. Heather confirmed. Jim, Martin, Heather, Clement held offline mtg already.
**3:40-4pm regular NAMIC engr business
***Slicer code freeze and release
***Focus during the upcoming months on "ruggedizing" Slicer

Attendees: Tina, Katie, Nicole, Vince, Will, Marek, Sylvain, Polina, Clement, Brad, Ron, Alex, Sebastien

Highlights:
*Harvard DBP projects for Project Week
*#Probabilistic Tractography - on hold since Tri left
*#Slicer3 - Need bug fix for why Slicer 3 can't load and run UNC data that Martin tried
*#EPI Distortion correction (Sylvain, Tauseef GATech)
*#Eddy CUrrent distortion correction (Sylvain, Ran Tao Utah)
*# Parcellation - need help parametrization (Sylvain, Brad)
*# fmri - apply polina's algorithm to Marek's data (Marek, Bryce Kim)
*# Finsler method (John Melonakos, Eric Melonakos)
*# Group Analysis on DTI (Casey Goodlett, Marek)
*Code Freeze: scheduled for tomorrow
*RSNA Demo
*#editor, lightbox, data fusion
*#Sonia is developing the curriculum for course
*UNC DBP Projects
*#Cortical thickness pipeline
*#workflow module
*#NITRC - need to talk to Steve pieper
*#batchmake pipeline in Slicer
*#use Bspline module in ITK

==2008-05-08==
Agenda:
*DBP II update and plans for project week. 2 DBPs and engr+algo core liaisons should attend.
**3:00-3:20 MIND. Jeremy, Ross, Steve Confirmed.
*** Testing lots of methods. None working well.
*** Bayesian labeling seems to be working the best.
*** Close the look on itkEMS method
**3:20-3:40 JHU. David G, Allen T., Katie H. confirmed.
*** Prostate really difficult task
*** Delphine's work was originally on prostate.
*** Optimal mass transport registration project at project week
**3:40-4pm: regular na-mic engr core business
*** Short update on UNC DBP needs: registration, module chaining
*** Discussion on plans for chaining. Prototype for project week?

==2008-05-01==

Attendees: Steve, Jim, Will, Tina, Xiaodong, Katie, Danielle, Sebastian, Sonia,

* Slicer 3 stable release schedule planning (Slicer 3.2)
** We would like a stable version before the [[Events:June-Germany | Mid-June German training event]] that includes all the latest namic technology (CMake 2.6, ITK 3.6, VTK 5.2, Tcl/Tk 8.5, KWWidgets...). Some problems were fixed this week for ITK3.6 and VTK 5.2; Slicer3 was successfully built using CMake 2.6 against VTK 5.2, ITK 3.6, and Tcl/TK on Linux, Windows, and Mac (by Sebastien). Need more coverage on Slicer. TODOs: Developing tutorial material for the new Slicer release. Testing, automated part plus user interaction part.
** [[2008_Summer_Project_Week | Project Week]] projects can go into the trunk after the release is branched. GUI changes to show "axial", "sagittal", "coronal" slices in the acquisition orientation.
** Proposed schedule:
*** May 16: Feature Freeze of the trunk followed by group debugging/testing
*** May 23: Create Release Branch for Slicer 3.2
*Danielle Pace @ Robarts Inst. joined NCIGT/SNR to develop [[LEGO_IGT_and_Medical_Robotics_Tutorial | Slicer IGT Tutorial]].

==2008-04-24==

Attendees: Steve, Katie, Nicole, Tina, Nathan, Jim, Vince, Brad, Louis, Marco

Agenda
* Slicer3D Wikipedia page discussion. Check it out [http://en.wikipedia.org/wiki/Slicer here].
** Need to tone it down a little so it sounds less like ad copy.
** Needs more pawprints on it from unique editors/authors for Wikipedia to keep it online.

* Nathan
** Helical phantom available to LONI web service.
** Should we make the link available through Slicer or not?

* Project pages need to be updated.
** Deadline: May 15th for NA-MIC, a week earlier is preferred
** [[2008_Annual_Scientific_Report | Progress report link]]
** Project week pages need to be linked off the progress report (indirectly)

* Waiting for CMake and ITK releases to be finalized
** Probably will be cut tomorrow

* Set up special T-con time for Oz

* What's the deal with the CMake Policy Change warnings?
** Copy three lines before CMAKE_MINIMAL_REQUIRED
** Ask the CMake list

==2008-04-17==

Attendees: Jim, Dan Marcus, Xiaodong, Nicole, Tina, Steve, Katie, Jeff, Sebastien, Vince

Topics:

*[[2008_Annual_Scientific_Report]]
*[[2008_Summer_Project_Week]]
*VTK (5.2) and CMake (2.6) release schedules
**VTK Plan on branching next week
**CMake is on RC8, guessing will branch in 1-2 weeks
*VTK (5.2) performance issues when rendering
**In the meshing project we have seen a significant reduction in the rendering of a large number of vtkSphereSource and vtkPointWidgets in 5.2 as compared to 5.0
***100x performance hit in debug mode on Linux
***Jeff added code to make sure the check doesn't happen more than once/sec.
***Still 25% slower, but not 100x slower
**Rendering time has been increased by an order of magnitude
* OK for Kitware to put Slicer3 screenshots on Flickr? (see [http://flickr.com/photos/kitware/ Kitware's Flickr account])
** => I (Seb) did a quick pass at the files uploaded in 2008, and copied them to a [http://flickr.com/photos/kitware/sets/72157604594177467/detail/ Slicer3 photoset].

==2008-04-03==

Jim, Curt, Tina, Nicole, Wendy, Steve, Brad, Xiaodong, Vince, Ron, Nathan

Agenda
* discussion of xcede web services and mBIRN
* [[2008_Engineering_review_at_Utah:FollowUp]]
* New! [[Slicer3:DTMRI |glyphs on slices movie!]]
** made using wink from http://www.debugmode.com/wink/
** add something like the following to your wiki page after uploading the .swf file to the wiki
<pre><flash>file=dti_glyphs.swf|width=800|height=600|quality=best|loop=true|play=true</flash></pre>
* CMake 2.6 release candidates have been cut with .rpm and .deb output targets!
** Will will work with Katie on this
* Jim is going to visit Kitware to talk about BSpline registration

==2008-03-27==
Attendees: Steve, Will, Xiaodong, Nathan, Katie, Wendy, Tina, Nicole, Marco, Sebastien
* Nathan will discuss presentation of fluid mechanics projects.
* Update from Core 1 + Core 2 [[2008_Engineering_review_at_Utah | meetings in Utah]] earlier this week.
* [[Slicer3:Chain_CLMs | Discussion of Module Chaining]] (Marco and All)
** Requested by Core 1 to systematize common use case
** Need several steps in an analysis process to act like a single command
** Would like something akin to the EMSegment workflow wizard, but as command line module rather than built-in module

Highlights:

Nathan's overview: discussing visualization options for his fluid velocity vector fields for tractography algorithm. Steve mentions a few options:
* A LDDMM module in Slicer2 that does animated vector field visualization (work done in collaboration with Johns Hopkins: Anthony Kolasny, Mike Miller, et al.).
* Another option would be to try using ParaView as a way to flesh out specifics, and then build a more custom tool for tractography later. Will will point Nathan to documentation for file formats, data formats, etc. or help with any questions, and Nathan will try this out.

Discussion of these topics at the engineering review in Utah:

* chaining modules together
* grid wizard (Marco) for grid and batch computing
* Bspline registration
* setting up repositories for collecting slicer modules (as technology transition mechanism)
* how this will fit into the slicer build process
* diffusion weighted imaging, shape analysis, and segmentation
* dicom to nrrd converter...

Milestones were set for April-end, Project week, and AHM.

Module chaining discussion (see link above):

* Java version as first goal -- eventually C++ implementation.
* Discussion about module discovery process and how will chained modules be packaged: (c++ stub programs? or
or discovery find chain-descriptor xml files? shell scripts? (cross-platform issues)...)
* Goal: By project week in June we would like to be able to chain modules developed by Core 1.

Sebastien's update on module building: Wiki will be updated today with status. (link)

==2008-03-20==
Attendees: Tina, Jim, Will, Wendy, Xiaodong, Nathan, Martin, Marco
* [[2008_Annual_Scientific_Report|Progress Report]] - read over the assignments. We will look for progress from June 1, 2007 to May 30, 2008.
* June 23-27 is the summer project week. We will make first pass on projects in late April.
* Module discussion: Martin wanted to understand the state of module creation and usage within Slicer. Sebastien is working on modules that are built against an installed module. Terry is working on built-in modules for Slicer. Jim is working on modules using CMake in the NTRIC repository.
* Nathan- write a command line, Slicer module that is a wrapper to a web service. Nathan thinks he can get this done prior to the June AHM. We referred to Jim's presentation at the Utah SLC Core 1/Core 2 meeting.
* We will talk about grid wizard next week at SLC

==2008-03-13==
Attendees: Jim, Nicole, Dan, Xiaodong, Vince, Sebastian, Alex, Curt, Steve, Will, Terry
* Update on [[Slicer3:Loadable_Modules |Loadable Modules]] project (Terry) and [[Slicer3:Build/Modules | CMake updates for module builds]] (Sebastien)
* [[2008_Engineering_review_at_Utah | Engineering trip to Utah]]
* We are starting to use Categories to bin our pages. [[SuggestedCategories]] - suggestions?

==2008-03-06==
Attendees: Steve, Jim, Katie, Nicole, Tina, Xiaodong, Marco, Ron

Highlights:
*Slicer page on wikipedia - http://en.wikipedia.org/wiki/3DSlicer. All engineering core members should visit this page and edit as needed. ASAP.
*dicom to nrrd converter in progress. Xiaodong working on it and expecting to complete in a few weeks.
* [[2008_Engineering_review_at_Utah|March 24-26 Meeting in Utah]]

==2008-02-28==

* Attendees: Jim, Steve, Wendy, Katie, Tina, Jeff, and Marco (Grid Wizard Guy)
* Discussion on time series analysis (viewer, scene markup). Initial viewer will be a general tool for comparing images.
* Avalanche of new features in [http://gridwizard.org/gwe/index.html grid wizard and GSlicer3]
** Proxy around Command Line Modules
** Extends command line with specifications for ranges of values as well as specify remote resources (data) that need to be transferred to/from the grid.
** Uses Velocity for parameter template engine
** Grid selection and authentication still being refined for Slicer
** Could be extended to other grid types (LSF, etc.)
** Lots of information on the website. Instructions for installation. A bit daunting for non-grid people. Some of us will have to work through the instructions step by step to evaluate.

==2008-02-21==

* Attendees: Xiaodong, Jim, Katie, Nicole, Will, Steve, Nathan, Tina, Ron, Padma, Marco

- Nathan brought us up to date on fluid mechanics tractography

- Padma Sundaram: SCIrun environment supports EEG processing

- Marco is releasing Grid Wizard alpha version

- Nathan brought up the helical digital phantom web service. Currently the thinking is that it can be accessed through a web service. We suggested that Nathan write a wrapper, consistent with Slicer's execution module, to invoke the web service. However, since it is not available in source form, NAMIC cannot accept it as part of the NAMIC Kit proper. We can guide Nathan in the execution of this module.

==2008-02-14==
* Attendees: Xiaodong, Katie, Will, Sebastien, Steve, Mike, Wendy, Haiyi, Dan, Curt, Tina

=== Other NA-MIC Projects ===

16 - CPack (Katie): Slicer3 compiles and packs using the new C-tools with some bug fixes. Using CMake to select desired modules, using something similar to cygwin. Official Slicer3 snapshot tagged. Different Tcl/Tk versions are currently used for different platform. This need to be addressed.

17 - Slicer GUI Style Guide and Cookbook {Wendy}: This will be a long term effort. During the programming week, the design and implementation details were discussed. The Cookbook will be launched from Slicer, act like KWWidget tour.

18 - Volume rendering (Steve): UI is fairly stable.

19 - Volume rendering using Cuda (Steve):

20 - 3D W Widgets and Picking (Will): found a list of candidates of widgets for Slicer. A few bug fixes for VTK.

21 - XNAT Integration (Dan): Requirements were gathered for a XNAT application that organizes files and caches files from XNAT repositories. Some XML format issues have been addressed.

22 - KWWidgets Roadmap (Sebastien): Gathered requirements. Been working down the list of the feature requirements.

=== External Collaboration ===

1 - Astronomical coordinate system support [Harvard IIC] (Mike): Astronomical datasets are quite different from medical dataset. Wendy helped with re-centering data. Made progress in converting between coordinate systems (Cartesian to Spherical).

2 - New Meshing Techniques into NA-MIC [Univ. of Iowa]

3 - Meshing Workflow into Slicer [Univ. of Iowa] (Curt): Will be integrated into Slicer soon. Command line program using VTK.

4 - Evaluating NA-MIC Tools for Small Animal Imaging Workflows [NCI] (Curt):

5 - IGSTK-Slicer [Georgetown] (Haiyi): Successful tracking data using IGSTK.

6 - Japanese Intelligent Surgical Instrument Project [AIST]

7 - GoFigure:High-Level Microscopy Image analysis Application and Algorithms [CalTech-Harvard Medical School]

8 - Doing microscopy image analysis with Slicer3 [The Ohio State University]

9 - fMRI Analysis with Slicer 3 [The Ohio State University]

10 - Resampling DTIs with Slicer 3 [BWH]

11 - Analyzing fMRI and concurrent EEG with Slicer and SCIRun [BWH]

12 - Bayesian hierarchical models for fMRI variance components analysis [BWH]

==2008-02-07==
* Attendees: Ron, Will, Steve, Wendy, Nicole, David G, Mark S., Casey, Sebastien, Curt, Luca

* Look at [http://www.vtk.org/Wiki/VTK_Widget_Examples upcoming VTK 3D widgets]
* Review of projects from SLC AHM 2008 http://wiki.na-mic.org/Wiki/index.php/2008_Winter_Project_Week

===DBPs===

1 - Stochastic Tractography in Schizophrenia (need to be invited to follow-up TCon)

2 - Cortical thickness analysis - testing EM segmenter to their data. They estimated parameters and tested during the week. The goal now is to compare ITK-MS and EM segment module to see how these two tools compare for cortical thickness. They are reviewing the tools using the same patient data.

3 - (Mark Scully) Legion segmentation using EM segmenter and other options - worked with Brad using 2 channels of data. Flare as 3rd channel caused problems. Desired to have T1/T2/Flair together as three channel dataset. Marcel is going to deliver his segmentation algorithm software to them to compare results.

4 - Robotic Prostate Interventions - (David Gobbi) Working on transrectal biopsy module for Slicer. They had a previous module for transcranial biopsies. One of the most exciting developments was a new prototol "open IGT-Link" which will replace navitrack inside Slicer. Image transfer is working over this protocol. A simulator is being developed for the robot. A few VTK bugs may have been discovered during this process, but it isn't on the top priority list right now.

5 - Prostate Cancer - Wrote new ITK filter that has been submitted to the Sandbox. They are looking at spherical wavelets for shape segmentation. The wiki page will be updated soon.

=== Other NA-MIC Projects ===

1 - Groupwise Registration - (Casey) New Bspline registration method is being developed here. It has been used for another project by Casey (#6). Page needs to be updated.

2 - (Need to be invited to follow-up TCon)

3 - (Need to be invited to follow-up TCon))

4 - (Need to be invited to follow-up TCon). Page needs to be updated

5 - Incorporating DTI tools into NAMIC toolkit - They are gathering a dataset that has both structural and DTI data in agreement. Previous dataset was missing part of cortex. UNCDB2 dataset has full coverage of the brain. Resolution is a bit lower, but full coverage is an advantage. Page is close to up to data. Just submitted a paper to ISBI 2008 and working on MICCAI paper, as well.

* NITRIC is g-forge and would be a good place for automated build process for Slicer modules. This could make it easier to configure Slicer in client labs without need to build from source. This is still being developed by the NA-MIC core team. There is an entry on the collaboration section of the NA-MIC website. Also www.slicer.org/Documentation link.

6 - (Casey) Worked with Serdar using groupwise registration tool. They are currently evaluating results of this study. More images will be added.

7 - (John Melanakos) Spent last week working with collaborators on the MICCAI paper. Project page is well filled.

8 - (Need to be invited to follow-up TCon)

9 - (Need to be invited to follow-up TCon)

10 - MRML scenes for execution model. Some of the issues Brad was having have been resolved. Alex is making adjustments to MRML library as needed for the EM segmentation model.

11 - (Curt) Unstructured Grids in Slicer - Finite Element modeling process was originally in a standalone VTK application. The first Slicer module integration did not use MRML based storage. We are now creating subclasses of Model and Unstructured grid data for storage and display in Slicer. Some minor issues need to be worked out, but the MRML extensions for UnstructuredGrid datatypes are working.

12 - Python (Luca) MatPlotLib plots are close to happening within Slicer. Steve believes it is 80% complete. Python command line modules are working now. Multiple arguments had to be worked by Luca. He has developed Python-based CLI modules. The event broker is discussed here because it affects the interaction with Python, because a Mutex lock has to be placed on the MRML scene. Dan has been helping with metamodules - a single Python module which calls other mothers (hierarchical execution, recipes, etc.).

* Ron asked about using this scripting technique for the ModelMaker. Some of the parameter setting, etc. could be set in the top module. Nicole will look at this. Kilian said that he wanted to call the "modelmaker" from another module.

* A need was identified for new wiki pages: (1) scripted modules, (2) metamodules, (2) python scripted modules

13 - (Luca) Transform hardening - Sometimes images are not XYZ alligned. How will command line modules treat an object if it is the child of a transform. The module needs to be able to apply xforms to data (after hierarchy is flattened) to get xformed data. Jim and Steve talked through this lately becomes of the transforms access two-directions (from parents / to parents, etc.) They are looking at how to change the model.

14 - (Steve) MRML support for out-of-core processing - Steve put a link to a new page. Dan, Jim, Wendy, Steve, etc. working through NAC renewal grant (5 years). Multiresolution and asynchronous data are likely targets for this effort, but it will be a long-term effort.

15 - Event Broker discussion - Steve has made process on this, but this wiki page is older. See the event broker page. (look at link under Objective). New term "observation" : completely introspectable. A full dependency between objects is implemented. When a subject issues a "modified" event, Delete events are maintained. Complete "relationship" management of the interaction between objects. This helps by allowing asynchronous event processing. MRML has been converted to use the event broker with asynchronous events managed by the Slicer GUI (async events invoked after GUI events are done). This hasn't broken anything so far, but should improve scalability. Dot logfile format can be generated for inter-object dependencies. This can be used to help provide "who called who" traces. Some special magic is done in MRML Display nodes. They set "observation nodes"

=== Next Week ===
Continue through project review. Request missing project members to attend. Review wiki pages.

==2008-01-31==
Attendees: Jim, Steve, Stephen, Wendy, Xiaodong, Nicole, Katie, Ron
* Project week follow-up
** Half of tcon on Feb 7
** Half of tcon on Feb 14
* Registration
** Viola-Wells optimizations need to be enabled
** Stephen needs to check-in and publish recent changes
** Stephen needs to update the wiki
** Luis continues to make optimizations (main focus is memory reduction)
* BatchMake
** Grid Wizard - meeting on Monday
** Integration with Slicer delivered via getbuildtest2
* New webpages
** http://slicer.org
** Uses wiki-to-web
** Feel free to edit/improve
* Slicer-specific wiki
** Migrating appropriate info from Na-mic to slicer
** Hold off on adding to Slicer-wiki until notified
*** Continue using Na-mic wiki
* New Nitrc project
** Jim Miller is leading
** "Slicer3 plug-in examples" project
** http://nitrc.org - search for slicer3
*** Includes demo/stub for ITK filtering data, etc.
** Collection associated with an ITK course being taught
** Requires CVS version of ITK
** Works with Slicer build and Slicer install
** Steve P is the liaison with NITRC
* Slicer tutorial at UNC, April 14th
** Working with UNC's BRIC (http://www.bric.unc.edu)
** Sonja, Randy, Martin, Stephen
* User-level Slicer training - Feb 20 at BWH
** 1249 Boyleston
** Release version of Slicer3

==2008-01-24==
Attendees: Jim, Steve, Wendy, Xiaodong, Nicole, Katie, Alex, Luis, Ron, Will
* Project week follow-up (Next week?)
** Will will send email invitations for first half of projects for next week's tcon
* Loadable modules
** Alex and Terry are rearranging Slicer3.cxx to support loadable modules
** Separate branch for built-in module discovery process
** Sebastien is working on build issues for modules whose code is outside Slicer3
* GenerateCLP - Thanks Hans for changes to support building modules
** Hans is running a class this semester where the students will build Slicer CLI modules.
** Jim is working on an ExampleModule for people to use as a template for building modules outside of Slicer3. Perhaps NITRC.
* XML library
** What to do with libaries that are too big to include in the source directory?
* AHM 2009, Jan 5-9, 2009
* Summer Project Week, Jun 23-27, 2008
* New server architecture for wiki, svn, publication database

==2008-01-17==
Attendees: Jim, Katie, Sebastien, Stephen, Luis, Steve, Wendy, Will

* Luis and Bill Hoffman are making progress in making ITK installation relocatable. This is needed to finish the work on building plugins from an installation.
* What's in VTK 5.2?
** Infovis - Tables, Graphs, Views, IO
** Refinements to WWidgets. Client/Server connections within the widgets. Event translation. New widgets (text, caption, affine, checkerboard, rectilinear wipe, annotation, key frame, contour, measurement, point/placer, plot)
** Build now? Or wait until 5.2 released?
** Repository freeze in March
** Release on April 1, 2008
* ITK release
** Patches to ITK 3.4
*** Nine component/six component tensor conversion in IO has been patched to ITK 3.4
** 1/19-2/1 moving contributions on Insight Journal for ITK 3.6
** Move items from Review directory to main tree (QuadMesh, TransformIO) for ITK 3.6
** Freeze repository 2/29 for ITK 3.6
** Slicer3 will need to build against the Review directory.
* CMake release
** Version 2.6 on the horizon - release candidate in 3 weeks.
* Tcl/Tk 8.5
** Sebastien has a Windows build
** Steve will try it out
** Wait to switch to 8.5 until we have a good reason
* Loadable modules
** Sebastien - working on CMake issues on building modules as loadable modules
** Terry - working on loading modules and reworking Slicer3.cxx
* [[Slicer3:EventBroker | Event Broker]]
* DWI DICOM as part of the Load Volume. Xiaodong is working on it.
* ITKFactories directory in build and installs to hold ImageIO plugin libraries. Should increase the speed of executable plugins on the Mac.
* OpenIGTLink
** Protocol on the wiki (message format)
** Put code in Sandbox, SourceForge, NITRC, Google Code???
* Will schedule a time to go over the Project Week results

==2008-01-10==
No tcon due to AHM

==2008-01-03==
* Attendees: Jim, Steve, Will, Brad Davis
* Topics:
** Jim and Will talked about leading the Monday and Friday sessions, and who would do what.
** We are going to send out reminders to the project leads to ensure that their project descriptions are up to date
** We discussed the software process project to make sure that we have a chance to address the Slicer build process, dashboards, etc.
** We decided not to hold the project wrap-up presentation at AHM; we will do that later at subsequent TCons. (We decided that we needed the time to actually work. We are concerned that we are starting to see too many break-outs and not enough time to work.)
** We keenly missed Tina and hope that she and her family are doing well.

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2008-02-20T14:24:08Z

Wyatt:

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]]

==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

2008-02-07T12:43:12Z

Wyatt: /* Key Personnel */

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, Jenny Long

NAMIC: Kilian Pohl, Sandy Wells

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

==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

2008-02-07T12:41:34Z

Wyatt: /* Resource Links */

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==
Jim Daunais, Chris Wyatt, Bob Kraft, Kilian Pohl, Sandy Wells.

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

==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

2008-02-07T12:38:13Z

Wyatt: /* Projects */

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==
Jim Daunais, Chris Wyatt, Bob Kraft, Kilian Pohl, Sandy Wells.

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

==Resource Links==

* [http://www.slicer.org slicer]

Rhesus EM Segmentation

2008-02-07T12:35:44Z

Wyatt:

'''Objective:'''

* Use the EM segmentation algorithm in slicer to segment Rhesus images.

'''Progress:'''

* [[Collaboration/WFU/NonHuman Primate Neuroimaging| Results from 2007 Project Week]]
* Followingup on a recommendation by Martin Syner, we have extended the algorithm from the project week to use a lobular parcellation map to automate the splitting of regions. We are calling this Lobulated EM Segmentation (LEMS). We are testing this method on a N=7 subject data set currently and a paper is in preparation.

* LEMS was used to segment 7 subjects imaged in alcohol naive and post induction states. No significant changes in the GM-WM volume ratio was obseved.

[[Image:MeanGmWmRatio.jpg|300pix|]]
[[Image:IndGmWmRatio.jpg|300pix|]]

'''Key Investigators:'''

* Virginia Tech: Chris Wyatt
* NAMIC: Kilian Pohl

'''Links:'''
* A tutorial for EMSegment (in Slicer2.X) was developed for non-human primate data. The tutorial and the images are available [http://bsl.ece.vt.edu/download/NHP-EMSTut.zip here]

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2008-02-06T13:17:11Z

Wyatt: /* 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==
Jim Daunais, Chris Wyatt, Bob Kraft, Kilian Pohl, Sandy Wells.

==Projects==
Active projects in this collaboration are:
=== Rhesus Probabalistic Atlas ===
#[[Rhesus_WMGM_Atlas|WM/GM Atlas]]
#[[Rhesus_Subcortical_Atlas|Subcortical 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]]

==Resource Links==

* [http://www.slicer.org slicer]

AHM 2008

2008-01-09T00:19:24Z

Wyatt: /* Agenda */

__NOTOC__
== Introduction ==

{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2"| '''This is the home page for the 2008 NA-MIC all hands meeting (AHM).''' NA-MIC participants meet for a AHM once a year. The purpose of the AHM is to coordinate, discuss plans and report to NIH officers and the external advisory board (EAB). The external advisory board meets with the NA-MIC leadership immediately after the AHM. In parallel, NA-MIC is organizing a project week. These events, with the exception of the EAB meeting, are open to collaborators and potential collaborators.

For more information about the project weeks in general, click [[Engineering:Programming_Events|'''here''']].

For information about the January 2008 project week, see below or click [[2008_Winter_Project_Week|'''here''']].

For information about Utah as a travel destination click [http://www.utah.com '''here'''].
| style="background: #ebeced" colspan="2" align="center"| [[Image:SLC.jpg|center|350px|View of the City]]
|-
| style="background: #ebeced"| <b>SLC</b>
| style="background: #ebeced"|The 2008 AHM, EAB and Project Week will be held in Salt Lake City, UT, January 7-11 2008.
|}
<br />

We have two wireless access points at the AHM. One is named capital-ballroom, the other is named linksys. Both require no password to connect. In general you should connect to whichever access point provides you with a stronger signal. If one access point doesn't let you connect it is probably overloaded. In that case, please try connecting to the other one.

== Agenda ==

{| border="1" cellpadding="5"
|- style="background:#ebeced; color:black" align="left"
| style="width:4%" | '''Time'''
| style="width:12%" | '''Monday, January 7'''
| style="width:12%" | '''Tuesday, January 8'''
| style="width:12%" | '''Wednesday, January 9'''
| style="width:32%" | '''Thursday, January 10 '''
| style="width:12%" | '''Friday, January 11'''
|-
| style="background:#ffffdd; color:black"|
| style="background:#b4d597; color:#522200"| '''[[2008_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#b4d597; color:#522200"| '''[[2008_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#b4d597; color:#522200"| '''[[2008_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#fff6a6; color:#522200"| '''AHM''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol A-B], [[2008_EAB|'''EAB''']] in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus B]
'''[[2008_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus A]
| style="background:#b4d597; color:#522200"|'''[[2008_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
|-
| style="background:#ffffdd; color:black"|'''7:30-'''
| style="background:#ebeced; color:black"|
| style="background:#b4d597; color:black"| Breakfast
| style="background:#b4d597; color:black"| Breakfast
| style="background:#fff6a6; color:black"| Breakfast
| style="background:#b4d597; color:black"| Breakfast
|-
| style="background:#ffffdd; color:black"|'''8:00-10:00'''
| style="background:#ebeced; color:black"|'''9:30''' Core 1 and 2 PI closed session in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol A]
| style="background:#b4d597; color:black"|Project Work <br> [[2008 Winter Project Week Plug-ins for Slicer3|Plug-ins for Slicer3]] in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"|Project Work <br>'''8:00-9:00''' [[2008 Winter Project Week IGT|IGT Breakout Session]] [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
<br>
9am: [[2008 Winter Project Week Tractography|Tractography Breakout Session]] in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 2]
| style="background:#fff6a6; color:black"|<br>
'''8:00''' [[AHM 2008 Introduction|Introduction]], Ron Kikinis <br>

'''Core 1 and 2 Presentations'''<br>
'''8:05''' Utah 1, Ross Whitaker<br>
'''8:20''' Utah 2, Guido Gerig<br>
'''8:30''': MIT, Polina Golland<br>
'''8:45''': Georgia Tech, Allen Tannenbaum<br>
'''9:00''': UNC, Martin Styner<br>
'''9:10''': MGH/WUSTL, Dan Marcus<br>
'''9:25''': Kitware, Will Schroeder<br>
'''9:40''': GE Research, Jim Miller
| style="background:#b4d597; color:black"|Project Work
|-
| style="background:#ffffdd; color:black"|'''10:00-10:30'''
| style="background:#ebeced; color:black"| Core 1 and 2 PI closed session
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#fff6a6; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
|-
| style="background:#ffffdd; color:black"|'''10:30-12:00'''
| style="background:#ebeced; color:black"| Core 1 and 2 PI closed session
| style="background:#b4d597; color:black"|Project Work
| style="background:#b4d597; color:black"|Project Work <br>
[[2008 Winter Project Week Tractography|Tractography Breakout Session contd]]
| style="background:#fff6a6; color:black"|
'''10:30''': Isomics, Steve Pieper<br>
'''10:45''': UCSD, Mark Ellisman<br>
'''11:00''': UCLA, Arthur Toga<br>
'''11:15''': Outreach, Randy Gollub<br>
'''11:25''': Invited speaker: Mike Sherman, Stanford NCBC Simbios, SimTK Architect
| style="background:#b4d597; color:black"|Project Work
|-
| style="background:#ffffdd; color:black"|'''12:00-1:00'''
| style="background:#b4d597; color:black"| Lunch
| style="background:#b4d597; color:black"| Lunch <br> [[DBP Engineering Resource|DPB Engineers Lunch meeting]]
| style="background:#b4d597; color:black"| Lunch<br> [[AHM 2008 fMRI|Birds of a Feather: fMRI]]
| style="background:#fff6a6; color:black"| Lunch
| style="background:#b4d597; color:black"| Adjourn
|-
| style="background:#ffffdd; color:black"|'''1:00-3:00'''
| style="background:#b4d597; color:black"|Introduce Projects and Participants
| style="background:#b4d597; color:black"|Breakout: [[2008 Winter Project Week Geometry and Topology processing of Meshes|Geometry and Topology processing of Meshes]] [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amthyst 1]
| style="background:#b4d597; color:black"|Project Work <br> [[2008 Winter Project Week Tractography|Tractography Breakout Session contd]]
| style="background:#fff6a6; color:black"|
'''DBP results''' <br>
'''1:00''': Queens/JHU, Gabor Fichtinger<br>
'''1:15''':UNC, Heather Cody Hazlett<br>
'''1:30''':Harvard, Marek Kubicki<br>
'''1:45''':MIND/UNM, Jeremy Bockholt<br>

'''NCBC Collaborations'''<br>
'''2:00''': [[Image:NA-MIC_Cleary_RF_Ablation_Georgetown.pdf | Georgetown, Kevin Cleary]]<br>
'''2:15''': [[Media:External-Wyatt-WFUSM.ppt‎|Wake Forest/VT, Chris Wyatt]]<br>
'''2:30''': UIowa, Nicole Grosland,Vincent Magnotta<br>
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''3:30-4:00'''
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#fff6a6; color:black"| Coffee
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''3:00-5:00'''
| style="background:#b4d597; color:black"|'''3:00-4:00''' Slicer Update [[Media:2008 NA-MIC AHM Slicer3.ppt | Slides]]<br>
'''4:00-5:00''' Breakout: [[2008 Winter Project Week EM Segmenter User Group|EM Segmenter User Group]] [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"|Project Work <br>[[2008_Winter_Project_Week_Image_Registration_Update| Registration Breakout]] [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"|Project Work <br>'''3:00-4:00''' [[2008 Winter Project Week Batchmake Update|Batchmake Update]]<br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
[[2008 Winter Project Week Tractography|Tractography Breakout Session contd]] <br>
| style="background:#fff6a6; color:black"|[[2008 EAB|EAB]]<br>[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus B]<br>'''3:00-4:00''' Discussion with NA-MIC Leadership<br> '''4:00-5:00''' Closed Session
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''05:00-07:00'''
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|'''5:00''' Optional: [[2008-SCI-tour|Tour]] of the new SCI building
| style="background:#fff6a6; color:black"|'''6:00''' Optional: [http://www.skisaltlake.com/murphys.htm Beer at Murphy's] (like last year)
| style="background:#ebeced; color:black"|
|}

Please note that there will be a Core 1&2 Site PI Retreat on the morning of Monday, January 7th. This is a closed session for Core 1&2 Site PIs, with no delegates. The topic is the competitive renewal.

== Dates. Venue. Registration ==

'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 10th'''.
* Project Activities will be held rest of the week between '''Monday, January 7th and Friday, January 11th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. To reserve rooms at the meeting rate of $129/night, please either call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting or book online by using the code SCISCIA. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

<big> '''Registration:''' We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click [http://www.sci.utah.edu/namic2008/registration.html '''here'''] for online registration. This registration must be completed by Friday, December 14, 2007. </big>

== Attendees ==

Please note that unlike past events, registration will not be done on the wiki. Instead you need to follow [http://www.sci.utah.edu/namic2008/registration.html this registration link] to complete your online registration. The organizers will periodically publish the list of registered attendees in the space below. Attendees should '''NOT''' add their names in this section.

This is the list of attendees who have registered as of January 5, 2008

===AHM===
# Michael J. Ackerman, Ph.D. National Library of Medicine
# Everette Burdette Acoustic MedSystems, Inc.
# German Cavelier NIHNIMH
# Kevin Cleary Georgetown University collaborator
# Zohara Cohen National Institutes of Health
# Jack Collins SAIC-Frederick, Inc.
# Gabor Fichtinger Queens University
# Chris Johnson External Advisory Board EAB member
# Danial Lashkari MIT MIT
# Mikhail Milchenko Washington University at St Louis 2
# Sandy Napel Stanford EAB member
# Godfrey Pearlson Yale EAB member
# Fred Prior External Advisory Board EAB member
# Mike Sherman Stanford Invited Speaker
# Arthur Toga Laboratory of Neuro Imaging, UCLA
# Chris Wyatt Virginia Tech Collaborator
# Terry S. Yoo National Library of Medicine

===AHM and Project Event===
# Douglas Alan Harvard University IIC Collaborator
# Luca Antiga Mario Negri Institute
# Kevin Archie Washington University School of Medicine
# Nicole Aucoin Brigham and Women's Hospital 2
# Stephen Aylward Kitware, Inc.
# Serdar Balci MIT
# Sebastien Barre Kitware, Inc.
# Jack Blevins Acoustic MedSystems, Inc.
# Daniel Blezek Mayo Clinic External
# H Jeremy Bockholt The MIND Research Network MIND DBP2
# Sylvain Bouix Brigham and Womens Hospital Psychiatry Neuroimaging Lab Core 3
# Francois Budin Brigham and Womens Hospital
# Patrick Cheng Georgetown University collaborator
# Kiyoyuki Chinzei AIST, Japan
# Nikos Chrisochoides College of William and Mary
# Csaba Csoma Johns Hopkins University
# Brad Davis Kitware, Inc.
# Preston Tom Fletcher SCI Institute
# Andreas Freudling Brigham and Women's Hospital Leadership Core
# Yi Gao Georgia Tech
# Guido Gerig SCI Institute
# David Gobbi Queens University DBP2
# Polina Golland MIT Core 1
# Randy Gollub MGH Department of Psychiatry Core 5
# Casey Goodlett SCI Institute
# Alexandre Gouaillard Caltech
# Sylvain Gouttard SCI Institute
# Benjamin Grauer Brigham and Women's Hospital Leadership Core
# Jeffrey Grethe UCSD 2
# Nicole Grosland The University of Iowa, CCAD
# Nathan Hageman UCLA
# Michael Halle Brigham and Women's Hospital Leadership Core
# Nobuhiko Hata Brigham and Women's Hospital Leadership Core
# Nobuhiko Hata Brigham and Women's Hospital
# Kathryn Hayes Brigham and Womens Hospital 2 - Engineering
# Heather Cody Hazlett University of North Carolina DBP Core2
# Bill Hoffman Kitware, Inc.
# Jaesung Hong Kyushu University
# Luis Ibanez Kitware, Inc.
# Mustafa Okan Irfanoglu OSU
# Firdaus Janoos ohio-state univ
# Julien Jomier Kitware, Inc.
# Usman Khan Brigham and Womens Hospital
# Ron Kikinis Brigham and Womens Hospital Leadership Core
# Marek Kubicki Brigham and Womens Hospital
# Curtis Lisle KnowledgeVis, LLC 2
# Haiying Liu Brigham and Womens Hospital
# William Lorensen External Advisory Board EAB
# Raghu Machiraju The Ohio State University
# Vincent Magnotta The University of Iowa, CCAD
# Daniel Marcus Washington University Core 2
# Doug Markant Brigham and Women's Hospital Leadership Core
# Katie Mastrogiacomo SPL, Brigham and Women's Hospital Leadership Core
# Sean Megason Caltech
# John Melonakos Georgia Tech
# James V Miller GE Global Research
# Vandana Mohan Georgia Inst of Technology 1
# Kishore Mosaliganti The Ohio State University
# Tri Ngo MIT
# Ipek Oguz UNC 2
# Steve Pieper Isomics, Inc. 2, 6
# Carlo Pierpaoli NIH
# Wendy Plesniak Brigham and Women's Hospital Leadership Core
# Kilian Pohl Brigham and Women's Hospital 1
# Marcel Prastawa SCI Institute
# Sonia Pujol Brigham and Women's Hospital Leadership Core
# Katharina Quintus Brigham and Women's Hospital Leadership Core
# Yogesh Rathi Brigham and Womens Hospital
# Mert Sabuncu MIT
# Will Schroeder Kitware, Inc.
# Mark Scully The MIND Research Network
# Li Shen Indiana University
# Kiran Shivanna The University of Iowa, CCAD
# Martin Styner UNC Chapel Hill 1
# Padma Sundaram Brigham and Womens Hospital Brigham and Womens
# Xiaodong Tao GE
# Kinh Tieu Brigham and Women's Hospital
# Junichi Tokuda Brigham and Women's Hospital Leadership Core
# Clement Vachet UNC Chapel Hill 3
# Koen Van Leemput MIT
# Sandy Wells Brigham and Womens Hospital
# Carl-Fredrik Westin Brigham and Womens Hospital NAC
# Nathan Wilson Cardiovascular Simulation, Inc.
# Alexander Yarmarkovich Isomics, Inc. Engineering Core 2
# Anastasia Yendiki MGH
# Boon Thye Yeo MIT
# Tim Yin Stony Brook University

This is the list of attendees who have registered as of January 5, 2008. Please note that unlike past events, registration will not be done on the wiki. Instead you need to follow [http://www.sci.utah.edu/namic2008/registration.html this registration link] to complete your online registration. The organizers will periodically publish the list of registered attendees in the space above. Attendees should '''NOT''' add their names in this section.

File:External-Wyatt-WFUSM.ppt

2008-01-09T00:16:16Z

Wyatt:

Rhesus Subcortical Atlas

2007-10-16T13:59:57Z

Wyatt:

'''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.

'''Key Investigators:'''

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

'''Links:'''

Rhesus WMGM Atlas

2007-10-16T13:55:00Z

Wyatt:

'''Objective:'''

* Develop an adult WM/GM/CSF atlas from normal subject images.

'''Progress:'''

* N=8 T1,T2,PD subject images acquired
* Using a rhesus tissue atlas provided by the UNC Neuro Image Analysis Laboratory and the UWisc Harlow Primate Laboratory we have segmented the data into WM/GM, and CSF capartments using the Lobulated EM Segmentation method. These segmentations have been averaged to create a study-specific tissue atlas.

'''Key Investigators:'''

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

'''Links:'''

Rhesus EM Segmentation

2007-10-16T13:51:25Z

Wyatt:

Rhesus ICV Extraction

2007-10-16T13:45:37Z

Wyatt:

'''Objective:'''

* Develop an ICV extraction program for Rhesus neuroanatomy.

'''Progress:'''

* Initial algorithm uses segmentation by registration: A manually segmented ICV region from a reference image is mapped onto the subject brain using affine registration. The current algorithm uses the FSL tool flirt todo the registration.

'''Key Investigators:'''

* Virginia Tech: Chris Wyatt
* NAMIC: Kilian Pohl

'''Links:'''

NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction

2007-10-16T13:34:50Z

Wyatt:

'''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 #'''<nowiki>: 1R01AA016748-01 </nowiki>

'''Key Personnel'''<nowiki>: Jim Daunais, Chris Wyatt, Bob Kraft, Kilian Pohl, Sandy Wells. </nowiki>

'''Projects'''<nowiki>: Active projects in this collaboration are listed here: </nowiki>[[NA-MIC_Collaborations#PAR-05-063_Measuring_Alcohol_and_Stress_Interaction_with_Structural_and_Perfusion_MRI]]

'''Publications'''<nowiki>: </nowiki>

'''Meetings and Events Specific to this Collaboration'''<nowiki>: </nowiki>
*[[2007_Programming/Project_Week_MIT|2007 Summer Programming/Project Week at MIT]]

'''Resource Links'''

* [http://www.slicer.org slicer]

Collaboration/WFU/NonHuman Primate Neuroimaging

2007-06-28T16:08:53Z

Wyatt:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|}
Before: [[Image:Nhpbrainexample.png|400px]]

After: [[Image:ProgWeek07NHPResult1.png|400px]]

__NOTOC__
This project is part of an NIH-NIAAA funded "Collaborations with National Centers for Biomedical Computing" grant,
R01-AA016748-01 "Measuring Alcohol and Stress Interactions with Structural and Perfusion MRI" (Jim Daunais PI).

===Key Investigators===
* VT/WFU: Chris Wyatt
* BWH: Kilian Pohl

<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 rhesus macaques
# Develop a custom GM/WM/CSF atlas, bootstrapping from one provided by Martin Styner
# Integrate a sub-cortical atlas
# Segment data from N subjects in the alcohol naive and post-induction state.
# Compare GM/WM volume and ratios between the two states
# Compare hippocampus, putamen, and caudate volumes between states

</div>

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

<h1>Approach, Plan</h1>
We will use the current implementation of the EM Brain classifier 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. The study will be run via VPN on a Sungrid at VT.

</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
* Study data has been skull stripped, ECC masks created, and GM/WM/CSF priors registered to each subject. The ECC masks may need some hand editing and, as a result, the atlas-priors to subject registration is poor in several subjects.

During the project week:
* Nonlinear registration of atlas priors completed using Slicer
* Full EM segmentation model accommodating severe coil inhomogeneity completed
* ITK-based utility to spatially blend prior maps written
* EMSegmenter parameters partially optimized for a single subject
* Scripts prepared to run the full study
</div>

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

</div>

===References===
* K. M. Pohl, J. Fisher, W.E.L. Grimson, R. Kikinis, and W.M. Wells. A Bayesian Model for Joint Segmentation and Registration. NeuroImage, 31(1), pp. 228-239, 2006.
* E. V. Sullivan, H. J. Sable, W. N Strother, D. P. Friedman, A. Davenport, H. Tillman-Smith, R. A. Kraft, C. L. Wyatt, K. T. Szeliga, N. C. Buchheimer, J. B. Daunais, E. Adalsteinsson, A. Pfefferbaum, K. A Grant, Neuroimaging of Rodent and Primate Models of Alcoholism: Initial Reports from the Integrative Neuroscience Initiative on Alcoholism, Alcoholism: Clinical and Experimental Research Vol. 29 No. 2 pgs 287-294 Feb 2005.

File:ProgWeek07NHPResult1.png

2007-06-28T15:49:28Z

Wyatt:

Collaboration/WFU/NonHuman Primate Neuroimaging

2007-06-28T15:42:09Z

Wyatt:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
[[Image:Nhpbrainexample.png|400px]][[Image:Macaque.png]]
|}

__NOTOC__
This project is part of an NIH-NIAAA funded "Collaborations with National Centers for Biomedical Computing" grant,
R01-AA016748-01 "Measuring Alcohol and Stress Interactions with Structural and Perfusion MRI" (Jim Daunais PI).

===Key Investigators===
* VT/WFU: Chris Wyatt
* BWH: Kilian Pohl

<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 rhesus macaques
# Develop a custom GM/WM/CSF atlas, bootstrapping from one provided by Martin Styner
# Integrate a sub-cortical atlas
# Segment data from N subjects in the alcohol naive and post-induction state.
# Compare GM/WM volume and ratios between the two states
# Compare hippocampus, putamen, and caudate volumes between states

</div>

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

<h1>Approach, Plan</h1>
We will use the current implementation of the EM Brain classifier 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. The study will be run via VPN on a Sungrid at VT.

</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
* Study data has been skull stripped, ECC masks created, and GM/WM/CSF priors registered to each subject. The ECC masks may need some hand editing and, as a result, the atlas-priors to subject registration is poor in several subjects.

During the project week:
* Nonlinear registration of atlas priors completed
* Full segmentation model accommodating severe coil inhomogeneity completed
* Paramters optimized for a single subject
* Scripts prepared to run the full study
</div>

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

</div>

===Results===

===References===
* K. M. Pohl, J. Fisher, W.E.L. Grimson, R. Kikinis, and W.M. Wells. A Bayesian Model for Joint Segmentation and Registration. NeuroImage, 31(1), pp. 228-239, 2006.
* E. V. Sullivan, H. J. Sable, W. N Strother, D. P. Friedman, A. Davenport, H. Tillman-Smith, R. A. Kraft, C. L. Wyatt, K. T. Szeliga, N. C. Buchheimer, J. B. Daunais, E. Adalsteinsson, A. Pfefferbaum, K. A Grant, Neuroimaging of Rodent and Primate Models of Alcoholism: Initial Reports from the Integrative Neuroscience Initiative on Alcoholism, Alcoholism: Clinical and Experimental Research Vol. 29 No. 2 pgs 287-294 Feb 2005.

Collaboration/WFU/NonHuman Primate Neuroimaging

2007-06-25T16:42:45Z

Wyatt:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
[[Image:Nhpbrainexample.png|400px]][[Image:Macaque.png]]
|}

__NOTOC__
This project is part of an NIH-NIAAA funded "Collaborations with National Centers for Biomedical Computing" grant,
R01-AA016748-01 "Measuring Alcohol and Stress Interactions with Structural and Perfusion MRI" (Jim Daunais PI).

===Key Investigators===
* VT/WFU: Chris Wyatt
* BWH: Kilian Pohl

<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 rhesus macaques
# Develop a custom GM/WM/CSF atlas, bootstrapping from one provided by Martin Styner
# Integrate a sub-cortical atlas
# Segment data from N subjects in the alcohol naive and post-induction state.
# Compare GM/WM volume and ratios between the two states
# Compare hippocampus, putamen, and caudate volumes between states

</div>

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

<h1>Approach, Plan</h1>
We will use the current implementation of the EM Brain classifier 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. The study will be run via VPN on a Sungrid at VT.

</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
* Study data has been skull stripped, ECC masks created, and GM/WM/CSF priors registered to each subject. The ECC masks may need some hand editing and, as a result, the atlas-priors to subject registration is poor in several subjects.
Monday:
Tuesday:
Wednesday:
Thursday:
Friday:
</div>

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

</div>

===References===
* K. M. Pohl, J. Fisher, W.E.L. Grimson, R. Kikinis, and W.M. Wells. A Bayesian Model for Joint Segmentation and Registration. NeuroImage, 31(1), pp. 228-239, 2006.
* E. V. Sullivan, H. J. Sable, W. N Strother, D. P. Friedman, A. Davenport, H. Tillman-Smith, R. A. Kraft, C. L. Wyatt, K. T. Szeliga, N. C. Buchheimer, J. B. Daunais, E. Adalsteinsson, A. Pfefferbaum, K. A Grant, Neuroimaging of Rodent and Primate Models of Alcoholism: Initial Reports from the Integrative Neuroscience Initiative on Alcoholism, Alcoholism: Clinical and Experimental Research Vol. 29 No. 2 pgs 287-294 Feb 2005.

Collaboration/WFU/NonHuman Primate Neuroimaging

2007-06-25T16:30:13Z

Wyatt:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|}
[[Image:Nhpbrainexample.png]][[Image:Macaque.png]]

__NOTOC__
This project is part of an NIH-NIAAA funded "Collaborations with National Centers for Biomedical Computing" grant,
R01-AA016748-01 (Jim Daunais PI).

===Key Investigators===
* VT/WFU: Chris Wyatt
* BWH: Kilian Pohl

<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 rhesus macaques
# Develop a custom GM/WM/CSF atlas, bootstrapping from one provided by Martin Styner
# Integrate a sub-cortical atlas
# Segment data from N subjects in the alcohol naive and post-induction state.
# Compare GM/WM volume and ratios between the two states
# Compare hippocampus, putamen, and caudate volumes between states

</div>

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

<h1>Approach, Plan</h1>
We will use the current implementation of the EM Brain classifier 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. The study will be run via VPN on a Sungrid at VT.

</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
* Study data has been skull stripped, ECC masks created, and GM/WM/CSF priors registered to each subject. The ECC masks may need some hand editing and, as a result, the atlas-priors to subject registration is poor in several subjects.
Monday:
Tuesday:
Wednesday:
Thursday:
Friday:
</div>

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

</div>

===References===
* K. M. Pohl, J. Fisher, W.E.L. Grimson, R. Kikinis, and W.M. Wells. A Bayesian Model for Joint Segmentation and Registration. NeuroImage, 31(1), pp. 228-239, 2006.
* E. V. Sullivan, H. J. Sable, W. N Strother, D. P. Friedman, A. Davenport, H. Tillman-Smith, R. A. Kraft, C. L. Wyatt, K. T. Szeliga, N. C. Buchheimer, J. B. Daunais, E. Adalsteinsson, A. Pfefferbaum, K. A Grant, Neuroimaging of Rodent and Primate Models of Alcoholism: Initial Reports from the Integrative Neuroscience Initiative on Alcoholism, Alcoholism: Clinical and Experimental Research Vol. 29 No. 2 pgs 287-294 Feb 2005.

File:Macaque.png

2007-06-25T16:29:19Z

Wyatt:

File:Nhpbrainexample.png

2007-06-25T16:27:31Z

Wyatt:

Collaboration/WFU/NonHuman Primate Neuroimaging

2007-06-25T14:04:48Z

Wyatt:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|}

__NOTOC__
This project is part of an NIH-NIAAA funded "Collaborations with National Centers for Biomedical Computing" grant,
R01-AA016748-01 (Jim Daunais PI).

===Key Investigators===
* VT/WFU: Chris Wyatt
* BWH: Kilian Pohl

<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 rhesus macaques
# Develop a custom GM/WM/CSF atlas, bootstrapping from one provided by Martin Styner
# Integrate a sub-cortical atlas
# Segment data from N subjects in the alcohol naive and post-induction state.
# Compare GM/WM volume and ratios between the two states
# Compare hippocampus, putamen, and caudate volumes between states

</div>

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

<h1>Approach, Plan</h1>
We will use the current implementation of the EM Brain classifier 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. The study will be run via VPN on a Sungrid at VT.

</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
* Study data has been skull stripped, ECC masks created, and GM/WM/CSF priors registered to each subject. The ECC masks may need some hand editing and, as a result, the atlas-priors to subject registration is poor in several subjects.
Monday:
Tuesday:
Wednesday:
Thursday:
Friday:
</div>

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

</div>

===References===
* K. M. Pohl, J. Fisher, W.E.L. Grimson, R. Kikinis, and W.M. Wells. A Bayesian Model for Joint Segmentation and Registration. NeuroImage, 31(1), pp. 228-239, 2006.
* E. V. Sullivan, H. J. Sable, W. N Strother, D. P. Friedman, A. Davenport, H. Tillman-Smith, R. A. Kraft, C. L. Wyatt, K. T. Szeliga, N. C. Buchheimer, J. B. Daunais, E. Adalsteinsson, A. Pfefferbaum, K. A Grant, Neuroimaging of Rodent and Primate Models of Alcoholism: Initial Reports from the Integrative Neuroscience Initiative on Alcoholism, Alcoholism: Clinical and Experimental Research Vol. 29 No. 2 pgs 287-294 Feb 2005.

Collaboration/WFU/NonHuman Primate Neuroimaging

2007-06-25T12:56:36Z

Wyatt: /* References */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|}

__NOTOC__
===Key Investigators===
* VT: Chris Wyatt
* BWH: Kilian Pohl

<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 rhesus macaques
# Develop a custom GM/WM/CSF atlas, bootstrapping from one provided by Martin Styner
# Integrate a sub-cortical atlas
# Segment data from N subjects in the alcohol naive and post-induction state.
# Compare GM/WM volume and ratios between the two states
# Compare hippocampus, putamen, and caudate volumes between states

</div>

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

<h1>Approach, Plan</h1>
We will use the current implementation of the EM Brain classifier 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. The study will be run via VPN on a Sungrid at VT.

</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
* Study data has been skull stripped, ECC masks created, and GM/WM/CSF priors registered to each subject. The ECC masks may need some hand editing and, as a result, the atlas-priors to subject registration is poor in several subjects.
Monday:
Tuesday:
Wednesday:
Thursday:
Friday:
</div>

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

</div>

===References===
* K. M. Pohl, J. Fisher, W.E.L. Grimson, R. Kikinis, and W.M. Wells. A Bayesian Model for Joint Segmentation and Registration. NeuroImage, 31(1), pp. 228-239, 2006.
* E. V. Sullivan, H. J. Sable, W. N Strother, D. P. Friedman, A. Davenport, H. Tillman-Smith, R. A. Kraft, C. L. Wyatt, K. T. Szeliga, N. C. Buchheimer, J. B. Daunais, E. Adalsteinsson, A. Pfefferbaum, K. A Grant, Neuroimaging of Rodent and Primate Models of Alcoholism: Initial Reports from the Integrative Neuroscience Initiative on Alcoholism, Alcoholism: Clinical and Experimental Research Vol. 29 No. 2 pgs 287-294 Feb 2005.

Collaboration/WFU/NonHuman Primate Neuroimaging

2007-06-25T12:48:06Z

Wyatt: /* References */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|}

__NOTOC__
===Key Investigators===
* VT: Chris Wyatt
* BWH: Kilian Pohl

<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 rhesus macaques
# Develop a custom GM/WM/CSF atlas, bootstrapping from one provided by Martin Styner
# Integrate a sub-cortical atlas
# Segment data from N subjects in the alcohol naive and post-induction state.
# Compare GM/WM volume and ratios between the two states
# Compare hippocampus, putamen, and caudate volumes between states

</div>

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

<h1>Approach, Plan</h1>
We will use the current implementation of the EM Brain classifier 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. The study will be run via VPN on a Sungrid at VT.

</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
* Study data has been skull stripped, ECC masks created, and GM/WM/CSF priors registered to each subject. The ECC masks may need some hand editing and the atlas-priors to subject registration is poor in several subjects.
Monday:
Tuesday:
Wednesday:
Thursday:
Friday:
</div>

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

</div>

===References===
* K. M. Pohl, J. Fisher, W.E.L. Grimson, R. Kikinis, and W.M. Wells. A Bayesian Model for Joint Segmentation and Registration. NeuroImage, 31(1), pp. 228-239, 2006.
* E. V. Sullivan, H. J. Sable, W. N Strother, D. P. Friedman, A. Davenport, H. Tillman-Smith, R. A. Kraft, C. L. Wyatt, K. T. Szeliga, N. C. Buchheimer, J. B. Daunais, E. Adalsteinsson, A. Pfefferbaum, K. A Grant, Neuroimaging of Rodent and Primate Models of Alcoholism: Initial Reports from the Integrative Neuroscience Initiative on Alcoholism, Alcoholism: Clinical and Experimental Research Vol. 29 No. 2 pgs 287-294 Feb 2005.