NAMIC Wiki - User contributions [en]

NA-MIC/Projects/Collaboration/SBIA UPenn

2008-06-27T01:00:15Z

Ragini: /* Key Investigators */

== '''DTI and HARDI analysis tools''' ==

{|
|[[Image:ProjectWeek-2008.png|thumb|360px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:DTIReg.JPG|thumb|420px|The non-linear DTI registration plugin.]]
|}
{|
|[[Image:Registration_example.png|thumb|420px|Example of non-linear DTI registration: Row 1 is the template and row 2 is the average of 10 brains after deformable registration. ]]
|}
__NOTOC__
===Key Investigators===
*Ragini Verma, SBIA, UPenn <Ragini.Verma@uphs.upenn.edu>
*Christos Davatzikos <Christos.Davatzikos@uphs.upenn.edu>
*Yang Li <Yang.Li@uphs.upenn.edu> (DTI integration)
*Luke Bloy <lbloy@seas.upenn.edu> (HARDI integration)
*Jinzhong Yang
*Dinggang Shen
*Carl-Fredrik Westin, BWH
*Luis Ibanez, Slicer
*Steve Pieper, Slicer

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

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

<h1>Objective</h1>

To incorporate into Slicer, processing and analysis methods for DTI and HARDI being developed at the Section of Biomedical Image Analysis (SBIA), UPenn [http://www.rad.upenn.edu/sbia]. The main components will be plugins for DTI registration and manifold-based statistics followed by methods for HARDI registration and statistics.

</div>

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

<h1>Approach, Plan</h1>
*'''DTI registration''': has been developed in SBIA over a period of 2 years, mainly using in-house code (not in ITK). This will be incorporated as a plugin.
*'''DTI Statistics''': SPM-like package for statistics on the full tensor. The proposed format is again a plugin as it is based on code already existing in SBIA in C, C++.
*'''HARDI registration''': This is being developed in ITK, building on HARDI representation format currently under development
*'''HARDI statistics''': being developed in ITK

</div>

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

<h1>Progress</h1>
*DTI Registration: plugin is ready and was demonstrated
Two step process:

1. Executable will be provided immediately (in discussion with : Steve Pieper)

2. Source code will be checked in after some licensing issues (as it involves some legacy code) are resolved (in discussion with : Luis Ibanez)

* Tensor Demons registration code was found from Slicer 2.6
1. Luis Ibanez will be looking at reviving it in discussion with C-F Westin.

2. We will help from our end if recoding is necessary.

*ODF estimation code is ready and will be checked into Namic Sandbox after preliminary testing. This will hopefully serve as the backend to Demian Wasserman's visulaization.
</div>

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

</div>

===References===
This work was supported in part by NIH grants R01-MH-079938 and R01-MH-070365.

* Link to [http://www.rad.upenn.edu/sbia SBIA web site: ]
* J. Yang, D. Shen, C. Davatzikos and R. Verma, Diffusion Tensor Image Registration Using Tensor Geometry and Orientation Features, in MICCAI 2008, New York.
* J. Yang, D. Shen, C. Davatzikos and R. Verma, Spatial Normalization of Diffusion Tensor Images Based on Anisotropic Segmentation, in SPIE Medical Imaging 2008, San Diego.
* R. Verma, P. Khurd, C. Davatzikos, [https://www.rad.upenn.edu/sbia/papers/181.pdf On Analyzing Diffusion Tensor Images by Identifying Manifold Structure using Isomaps], IEEE Transactions on Medical Imaging, 772-778, Vol. 26, No. 6, 2007
* P. Khurd, R. Verma and C. Davatzikos, [https://www.rad.upenn.edu/sbia/papers/177.pdf Kernel-based Manifold Learning for Statistical Analysis of Diffusion Tensor Images], Information Processing in Medical Imaging (IPMI), 581-593, Vol. 4584, 2007

2008 Summer Project Week

2008-06-24T03:30:25Z

Ragini: /* External Collaborations */

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

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

== Logistics ==
*'''Dates:''' June 23-27, 2008
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. If you are attending for one day only, the registration fee is not required.
*'''Registration Method''' The event is full. [[User:Tkapur|Tkapur]] 18:12, 17 June 2008 (UTC)
*'''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&key=4FD1B Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2008 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2007_Programming/Project_Week_MIT#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]
*Next Project Week in Utah -- January 5-9, 2009

==Introduction to NA-MIC Project Week==
Please read an introduction about these events [[Project_Events#Introduction|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: [[2008-Project-Week-Welcome|Welcome]] (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process
** 10-10:30am [http://www.slicer.org/slicerWiki/index.php/Announcements:Slicer3.2 Slicer 3.2 Update] (Jim Miller, Steve Pieper)
** 11-12noon [[Project Week 2008 Slicer Tuning| Performance tuning for Slicer 3.2]] (Jackson Room 38-466) (Ron Kikinis)
** noon lunch
** 1pm: [[2008-Project-Week-SVN-Change|Cut over to a new version of the NA-MIC SVN]]. (Grier Room) Zack Galbreath will provide details and can help with configurations.
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Stata 32-D407) (Daniel Marcus)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-rigid Registration]] (Stephen Aylward)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** Noon: Lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##[[2008_Summer_Project_Week:DWIRegistrationOMT|DWI Registration using Optimal Mass Transport]] (Sylvain Bouix BWH, Tauseef Rehman GATech)
##[[2008_Summer_Project_Week:EddyCurrentCorrection|EPI-DWI Eddy Current distortion correction]] (Sylvain Bouix BWH, Ran Tao Utah)
##[[2008_Summer_Project_Week:LobeParcellation| Parcellation of 3T MR data]](Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
##[[2008_Summer_Project_Week:GMLongDistanceTractography|GM Long Distance Tractography]] (John Melonakos GATech, Marek Kubicki BWH)
##[[2008_Summer_Project_Week:PopulationDTIApplication|Group Analysis of DTI]] (Casey Goodlett Utah, Marek Kubicki BWH)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[2008_Summer_Project_Week:RegionalCorticalThicknessTool|Work Flow Tool for regional cortical thickness pipeline]] (Clement Vachet UNC)
##[[2008_Summer_Project_Week:NITRCRegistration|NITRC registration of cortical thickness modules]] (Clement Vachet UNC)
##[[2008_Summer_Project_Week:DWI-DTI_PrepTools|DWI DTI Prep Tools]] (Zhexing Liu UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[DBP2:MIND:RoadmapProject|Lesion Classification Module]] (Mark Scully MIND)
##[[DBP2:MIND:LongitudinalRegistrationProject|Longitudinal Registration and time course analyses in white matter lesions]] (Mark Scully and Jeremy Bockholt, MIND)
##[[DBP2:MIND:BeyondLesionsProject|Enhancements and extension of white matter lesion classification using DTI scalars]] (Jeremy Bockholt, MIND)
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)
##[[2008_Summer_Project_Week:TransRectal_Prostate_Biopsy_Module|Trans-Rectal Prostate Biopsy module]] (David Gobbi, Gabor Fichtinger, Queens/JHU)
##[[2008_Summer_Project_Week:ProstateSegReg|Prostate Segmentation and Registration]] (Yi Gao GATech, Gabor Fichtinger JHU)
##[[2008_Summer_Project_Week:PerkStation|Hardware/software overlay for percutaneous intervention (PERK Station)]] (Siddharth Vikal, Gabor Fichtinger, Queens/JHU)

===Other Projects===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#[[2008_Summer_Project_Week:GroupwiseBSplineForDTI| Integraton of groupwise b-spline registration into atlas building]] (Casey Goodlett, Serdar Balci)
#[[2008_Summer_Project_Week:GroupwisePortingToNamicKit| Porting groupwise registration project into NAMIC-kit]] (Serdar Balci, Brad Davis)
# [[2008_Summer_Project_Week:CVS_SVN_Synchronization|CVS / SVN auto synchronization]] (Sebastien, Steve, Jim, Will, Bill)
# [[2008_Summer_Project_Week:3DWidgetsInSlicer|3D Widgets in Slicer]] (Nicole Aucoin, Will Schroeder)
## Issues with existing widgets
## Design of new widgets
# [[2008_Summer_Project_Week:Batch_Processing|Batch processing in the NAMIC Kit]] (Julien, Marco, Steve, Jim)
#[[2008_Summer_Project_Week:ModuleChaining|Module Chaining]] (Marco, Jim, Steve, Dan B., Luca)
# [[2008_Summer_Project_Week:Nonlinear transforms | Nonlinear transforms]] (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# [[2008_Summer_Project_Week:XNATandXCEDE| Slicer3, XNAT integration and XCEDE Web Services ]] (Dan M., Wendy, Steve, Julien, Dan B.)
## Review and enrich use cases [[Media: XCEDE-Use-Cases-2008-06-25.ppt | (developing use case ppt)]]
# [[2008_Summer_Project_Week:PythonInSlicer| Python in Slicer]] (Dan B., Michael Halle, Steve, Luca)
# [[2008_Summer_Project_Week:PerformanceTuningFiducials|Performance Tuning of Fiducials]] using the EventBroker and other tools (Nicole Aucoin, Alex Yarmarkovich, Steve Pieper, Will Schroeder)
# [[2008_Summer_Project_Week:FocusedGUIRefinement|Focused GUI Refinement and Strategies for Consistency]] (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]
# [[2008_Summer_Project_Week:fMRIconnectivity|fMRI connectivity]] (Bryce Kim, MIT)
# [[2008_Summer_Project_Week:AtlasFreeSegmentation|Atlas free Segmentation]] (Tammy Riklin-Raviv, MIT)
#[[NA-MIC/Projects/Collaboration/EM Bias Field Correction | New Bias Field Correction in EM]] (Carlos Sánchez Mendoza, Kilian Pohl - SPL, Brad Davis - Kitware)
# [[2008_Summer_Project_Week:FluidMechanicsTractographyUCLA|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman, UCLA)

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Grand Joldes)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#[[NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Lung Atlas]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Non-rigid image registration]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
#[[FMA (Protege) links to Slicer]] (Vish, Mike, Florin, Jim, Steve, Wendy)
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]]
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga, Dan Blezek, Mike Halle, Steve Pieper)
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)
#[[NA-MIC/Projects/Collaboration/Carto_scar_BIDMC]] (Dana Peters Group)
#[[NA-MIC/Projects/Collaboration/3D Ultrasound Module in Slicer3]] (Junichi, Haiying and Noby - SPL, David and Siddharth - Queen's, Danielle - Robarts)
#[[NA-MIC/Projects/Collaboration/MGH RadOnc]] (Greg Sharp, MGH)
#[[NA-MIC/Projects/External Collaboration/W&M CRTC]] Non-rigid registration for neurosurgery (Nikos Chrisochoides, Andriy Fedorov, College of William&Mary)
#[[NA-MIC/Projects/Collaboration/SBIA UPenn]] DTI and HARDI Analysis tools(Ragini Verma, SBIA Upenn)
#[[Projects/Diffusion/2008 Project Week DiffusionMRI QBall]] Diffusion QBall framework integration( Demian Wassermann, Rachid Deriche, Odyssée INRIA, CF Westin, LMI

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

== Preparation ==

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

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

==Attendee List==
# Jack Blevins Acoustic Med
# Pratik Patel Brainlab
# Mark Anderson BWH
# Nicole Aucoin BWH
# Sylvain Bouix BWH
# Michael Halle BWH
# Nobuhiko Hata BWH
# Katie Hayes BWH
# Scott Hoge BWH
# Marianna Jakab BWH
# Tina Kapur BWH
# Ron Kikinis BWH
# Jacek Kukluk BWH
# Haying Liu BWH
# Bjoern Menze BWH
# Wendy Plesniak BWH
# Kilian Pohl BWH
# Sonia Pujol BWH
# Carlos Sánchez Mendoza BWH
# Priya Srinivasan BWH
# Junichi Tokuda BWH
# Demian Wassermann BWH (INRIA)
# C-F Westin BWH
# Xiaodong Tao GE
# Dirk Padfield GE
# Jim Miller GE
# Surprise Guest from EAB
# Viswanath Avasarala GE
# John Melonakos GA Tech
# Yi Gao GA Tech
# Tauseef Rehman GA Tech
# Sean Megason Harvard Med
# Alex Gouaillard Harvard Med
# Kishore Mosaliganti Harvard Med
# Arnaud Gelas Harvard Med
# Dana Peters Harvard Med
# Jason Taclas Harvard Med
# Douglas Alan Harvard
# Toru Higaki Hiroshima U
# Daniel Blezek Isomics
# Curtis Lisle Isomics
# Steve Pieper Isomics
# Alex Yarmarkovich Isomics
# Csaba Csoma JHU
# Peter Kazanzides JHU
# Will Schroeder Kitware
# Sebastien Barre Kitware
# Julien Jomier Kitware
# Bill Hoffman Kitware
# Luis Ibanez Kitware
# Luca Antiga Mario Negri Inst
# Randy Gollub MGH
# Silas Mann MGH
# Greg Sharp MGH
# Marta Peroni MGH
# Serdar Balci MIT
# Bryce Kim MIT
# Clare Poynton MIT
# Tammy Riklin Raviv MIT
# Polina Golland MIT
# Jeremy Bockholt MRN Lupus DBP
# Mark Scully MRN Lupus DBP
# Gabor Fichtinger Queen's
# David Gobbi Queen's
# Purang Abolmaesumi Queen's
# Siddharth Vikal Queen's
# Zhen Qian Rutgers
# Jinghao Zhou Rutgers
# Jeffrey Grethe UCSD
# Marco Ruiz UCSD
# Chris Churas UCSD
# Nathan Hageman UCLA
# Keith Gunderson U Iowa
# Gary Christensen U Iowa
# Jeffrey Hawley U Iowa
# Kate Raising U Iowa
# Nathan Fritze U Iowa
# Paul Song U Iowa
# Cheng Zhang U Iowa
# Ying Wei U Iowa
# Nathan Burnette U Iowa
# Hans Johnson U Iowa
# Vincent Magnotta U Iowa
# Clement Vachet UNC
# Zhexing Liu UNC
# Ragini Verma U Penn
# Luke Bloy U Penn
# Yang Li U Penn
# Ran Tao Utah
# Marcel Prastawa Utah
# Casey Goodlett Utah
# Ross Whitaker Utah
# John Hale U Tulsa
# Cody Pollet U Tulsa
# Nikeisha Schimke U Tulsa
# Adam Wittek Western Australia
# Grand Joldes Western Australia
# Jamie Berger Western Australia
# Carling Cheung Western Ontario
# Danielle Pace Western Ontario
# Vidya Rajagopalan VA Tech
# Nikos Chrisochoides William and Mary
# Andriy Fedorov William and Mary
# Dan Marcus Washington U
# Tim Olsen Washington U
# Kevin Archie Washington U
# Misha Milchenko Washington U
# Xenophon Papademetris Yale U
# John Onofrey Yale U
# Yifeng Jiang Yale U
# Dustin Scheinost Yale U
#* Please note that Registration is closed. Do not add names here. [[User:Tkapur|Tkapur]] 18:19, 19 June 2008 (UTC)

==Pictures==
<gallery perrow="3" widths="150px">
Image:NA-MIC-ProjectWeek1.JPG|Lunch
Image:NA-MIC-ProjectWeek2.JPG|Day 1
</gallery>

NA-MIC/Projects/Collaboration/SBIA UPenn

2008-06-24T03:29:39Z

Ragini: /* Non-rigid DTI Registration */

== '''DTI and HARDI analysis tools''' ==

{|
|[[Image:ProjectWeek-2008.png|thumb|360px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:DTIReg.JPG|thumb|420px|The non-linear DTI registration plugin.]]
|}
{|
|[[Image:Registration_example.png|thumb|420px|Example of non-linear DTI registration: Row 1 is the template and row 2 is the average of 10 brains after deformable registration. ]]
|}
__NOTOC__
===Key Investigators===
*Ragini Verma, SBIA, UPenn <Ragini.Verma@uphs.upenn.edu>
*Christos Davatzikos <Christos.Davatzikos@uphs.upenn.edu>
*Yang Li <Yang.Li@uphs.upenn.edu> (DTI integration)
*Luke Bloy <lbloy@seas.upenn.edu> (HARDI integration)
*Jinzhong Yang
*Dinggang Shen
*Carl-Fredrik Westin, BWH
*Luis Ibanez, Slicer
*Steve Pieper, Slicer

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

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

<h1>Objective</h1>

To incorporate into Slicer, processing and analysis methods for DTI and HARDI being developed at the Section of Biomedical Image Analysis (SBIA), UPenn [http://www.rad.upenn.edu/sbia]. The main components will be plugins for DTI registration and manifold-based statistics followed by methods for HARDI registration and statistics.

</div>

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

<h1>Approach, Plan</h1>
*'''DTI registration''': has been developed in SBIA over a period of 2 years, mainly using in-house code (not in ITK). This will be incorporated as a plugin.
*'''DTI Statistics''': SPM-like package for statistics on the full tensor. The proposed format is again a plugin as it is based on code already existing in SBIA in C, C++.
*'''HARDI registration''': This is being developed in ITK, building on HARDI representation format currently under development
*'''HARDI statistics''': being developed in ITK

</div>

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

<h1>Progress</h1>
*DTI Registration: plugin is ready and will be demonstrated
To do: Replace the affine registration component, help file, speed, version control
*Need help with:
1. General representation for registration in ITK

2. Code for Demons DTI registration for comparison

3. Visualization: tensor glyphs and ODFs

</div>

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

</div>

===References===
This work was supported in part by NIH grants R01-MH-079938 and R01-MH-070365.

* Link to [http://www.rad.upenn.edu/sbia SBIA web site: ]
* J. Yang, D. Shen, C. Davatzikos and R. Verma, Diffusion Tensor Image Registration Using Tensor Geometry and Orientation Features, in MICCAI 2008, New York.
* J. Yang, D. Shen, C. Davatzikos and R. Verma, Spatial Normalization of Diffusion Tensor Images Based on Anisotropic Segmentation, in SPIE Medical Imaging 2008, San Diego.
* R. Verma, P. Khurd, C. Davatzikos, [https://www.rad.upenn.edu/sbia/papers/181.pdf On Analyzing Diffusion Tensor Images by Identifying Manifold Structure using Isomaps], IEEE Transactions on Medical Imaging, 772-778, Vol. 26, No. 6, 2007
* P. Khurd, R. Verma and C. Davatzikos, [https://www.rad.upenn.edu/sbia/papers/177.pdf Kernel-based Manifold Learning for Statistical Analysis of Diffusion Tensor Images], Information Processing in Medical Imaging (IPMI), 581-593, Vol. 4584, 2007

NA-MIC/Projects/Collaboration/SBIA UPenn

2008-06-24T02:59:47Z

Ragini: /* Key Investigators */

== '''Non-rigid DTI Registration''' ==

{|
|[[Image:ProjectWeek-2008.png|thumb|360px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:DTIReg.JPG|thumb|420px|The non-linear DTI registration plugin.]]
|}
{|
|[[Image:Registration_example.png|thumb|420px|Example of non-linear DTI registration: Row 1 is the template and row 2 is the average of 10 brains after deformable registration. ]]
|}
__NOTOC__
===Key Investigators===
*Ragini Verma, SBIA, UPenn <Ragini.Verma@uphs.upenn.edu>
*Christos Davatzikos <Christos.Davatzikos@uphs.upenn.edu>
*Yang Li <Yang.Li@uphs.upenn.edu> (DTI integration)
*Luke Bloy <lbloy@seas.upenn.edu> (HARDI integration)
*Jinzhong Yang
*Dinggang Shen
*Carl-Fredrik Westin, BWH
*Luis Ibanez, Slicer
*Steve Pieper, Slicer

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

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

<h1>Objective</h1>

To incorporate into Slicer, processing and analysis methods for DTI and HARDI being developed at the Section of Biomedical Image Analysis (SBIA), UPenn [http://www.rad.upenn.edu/sbia]. The main components will be plugins for DTI registration and manifold-based statistics followed by methods for HARDI registration and statistics.

</div>

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

<h1>Approach, Plan</h1>
*'''DTI registration''': has been developed in SBIA over a period of 2 years, mainly using in-house code (not in ITK). This will be incorporated as a plugin.
*'''DTI Statistics''': SPM-like package for statistics on the full tensor. The proposed format is again a plugin as it is based on code already existing in SBIA in C, C++.
*'''HARDI registration''': This is being developed in ITK, building on HARDI representation format currently under development
*'''HARDI statistics''': being developed in ITK

</div>

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

<h1>Progress</h1>
*DTI Registration: plugin is ready and will be demonstrated
To do: Replace the affine registration component, help file, speed, version control
*Need help with:
1. General representation for registration in ITK

2. Code for Demons DTI registration for comparison

3. Visualization: tensor glyphs and ODFs

</div>

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

</div>

===References===
This work was supported in part by NIH grants R01-MH-079938 and R01-MH-070365.

* Link to [http://www.rad.upenn.edu/sbia SBIA web site: ]
* J. Yang, D. Shen, C. Davatzikos and R. Verma, Diffusion Tensor Image Registration Using Tensor Geometry and Orientation Features, in MICCAI 2008, New York.
* J. Yang, D. Shen, C. Davatzikos and R. Verma, Spatial Normalization of Diffusion Tensor Images Based on Anisotropic Segmentation, in SPIE Medical Imaging 2008, San Diego.
* R. Verma, P. Khurd, C. Davatzikos, [https://www.rad.upenn.edu/sbia/papers/181.pdf On Analyzing Diffusion Tensor Images by Identifying Manifold Structure using Isomaps], IEEE Transactions on Medical Imaging, 772-778, Vol. 26, No. 6, 2007
* P. Khurd, R. Verma and C. Davatzikos, [https://www.rad.upenn.edu/sbia/papers/177.pdf Kernel-based Manifold Learning for Statistical Analysis of Diffusion Tensor Images], Information Processing in Medical Imaging (IPMI), 581-593, Vol. 4584, 2007

NA-MIC/Projects/Collaboration/SBIA UPenn

2008-06-24T02:58:48Z

Ragini: /* Non-rigid DTI Registration */

== '''Non-rigid DTI Registration''' ==

{|
|[[Image:ProjectWeek-2008.png|thumb|360px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:DTIReg.JPG|thumb|420px|The non-linear DTI registration plugin.]]
|}
{|
|[[Image:Registration_example.png|thumb|420px|Example of non-linear DTI registration: Row 1 is the template and row 2 is the average of 10 brains after deformable registration. ]]
|}
__NOTOC__
===Key Investigators===
*Ragini Verma, SBIA, UPenn <Ragini.Verma@uphs.upenn.edu>
*Christos Davatzikos <Christos.Davatzikos@uphs.upenn.edu>
*Yang Li <Yang.Li@uphs.upenn.edu> (DTI integration)
*Luke Bloy <lbloy@seas.upenn.edu> (HARDI integration)
*Jinzhong Yang
*Dinggang Shen
*Carl-Fredrik Westin, LMI & BWH
*Luis Ibanez, Slicer

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

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

<h1>Objective</h1>

To incorporate into Slicer, processing and analysis methods for DTI and HARDI being developed at the Section of Biomedical Image Analysis (SBIA), UPenn [http://www.rad.upenn.edu/sbia]. The main components will be plugins for DTI registration and manifold-based statistics followed by methods for HARDI registration and statistics.

</div>

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

<h1>Approach, Plan</h1>
*'''DTI registration''': has been developed in SBIA over a period of 2 years, mainly using in-house code (not in ITK). This will be incorporated as a plugin.
*'''DTI Statistics''': SPM-like package for statistics on the full tensor. The proposed format is again a plugin as it is based on code already existing in SBIA in C, C++.
*'''HARDI registration''': This is being developed in ITK, building on HARDI representation format currently under development
*'''HARDI statistics''': being developed in ITK

</div>

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

<h1>Progress</h1>
*DTI Registration: plugin is ready and will be demonstrated
To do: Replace the affine registration component, help file, speed, version control
*Need help with:
1. General representation for registration in ITK

2. Code for Demons DTI registration for comparison

3. Visualization: tensor glyphs and ODFs

</div>

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

</div>

===References===
This work was supported in part by NIH grants R01-MH-079938 and R01-MH-070365.

* Link to [http://www.rad.upenn.edu/sbia SBIA web site: ]
* J. Yang, D. Shen, C. Davatzikos and R. Verma, Diffusion Tensor Image Registration Using Tensor Geometry and Orientation Features, in MICCAI 2008, New York.
* J. Yang, D. Shen, C. Davatzikos and R. Verma, Spatial Normalization of Diffusion Tensor Images Based on Anisotropic Segmentation, in SPIE Medical Imaging 2008, San Diego.
* R. Verma, P. Khurd, C. Davatzikos, [https://www.rad.upenn.edu/sbia/papers/181.pdf On Analyzing Diffusion Tensor Images by Identifying Manifold Structure using Isomaps], IEEE Transactions on Medical Imaging, 772-778, Vol. 26, No. 6, 2007
* P. Khurd, R. Verma and C. Davatzikos, [https://www.rad.upenn.edu/sbia/papers/177.pdf Kernel-based Manifold Learning for Statistical Analysis of Diffusion Tensor Images], Information Processing in Medical Imaging (IPMI), 581-593, Vol. 4584, 2007

2008-06-18T03:31:31Z

Ragini: /* Key Investigators */

NA-MIC/Projects/Collaboration/SBIA UPenn

2008-06-18T03:30:44Z

Ragini: /* Key Investigators */

NA-MIC/Projects/Collaboration/SBIA UPenn

2008-06-18T03:30:03Z

Ragini: /* Key Investigators */

NA-MIC/Projects/Collaboration/SBIA UPenn

2008-06-17T19:25:49Z

Ragini: /* Key Investigators */

===Key Investigators===
*Ragini Verma, PhD (ragini.verma at rad.upenn.edu) [http://www.rad.upenn.edu/sbia], Christos Davatzikos, Yang Li, Luke Bloy

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

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

<h1>Objective</h1>

Detailed information about SBIA can be found here [http://www.rad.upenn.edu/sbia]

</div>

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

<h1>Approach, Plan</h1>

</div>

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

<h1>Progress</h1>

</div>

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

</div>

NA-MIC/Projects/Collaboration/SBIA UPenn

2008-06-17T19:21:35Z

Ragini: New page: ===Key Investigators=== *Prof. Karol Miller (kmiller at mech.uwa.edu.au) [http://www.mech.uwa.edu.au/ISML/ Lab Webpages], Dr Adam Wittek, Grand Joldes <div style="margin: 20px;"> <div ...

===Key Investigators===
*Prof. Karol Miller (kmiller at mech.uwa.edu.au) [http://www.mech.uwa.edu.au/ISML/ Lab Webpages], Dr Adam Wittek, Grand Joldes

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

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

<h1>Objective</h1>
The Intelligent Systems of Medicine Laboratory (ISML) mission is to work towards improving clinical outcomes through appropriate use of technology. We are interested in biomechanics (both engineering biomechanics and sport biomechanics), biomedical engineering, computer integrated surgery, medical robotics and related fields. We run exciting research projects in these areas, generously funded by The Australian Research Council and other agencies (including NIH).

Detailed information about the ISML can be found here [http://www.mech.uwa.edu.au/ISML/]

</div>

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

<h1>Approach, Plan</h1>

We intend to contribute to Na-MIC by providing '''algorithms for computing the intra-operative brain deformations''' for image-guided neurosurgery. We treat the brain shift as a continuum mechanics problem involving finite deformations and solve it using non-linear finite element procedures. We use the procedures (non-linear explicit dynamics with Total Lagrangian formulation) that do not require iterations even when applied to non-linear problems and are, therefore, amenable to computing the intra-operative brain deformations in real time (under 150 s) on a standard PC. See also [http://www.mech.uwa.edu.au/ISML/research.htm]
</div>

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

<h1>Progress</h1>

</div>

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

</div>

2008 Summer Project Week

2008-06-17T19:20:13Z

Ragini: /* External Collaborations */

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

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

== Logistics ==

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

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

'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. If you are attending for one day only, the registration fee is not required.

'''Registration Method''' The event and is full. [[User:Tkapur|Tkapur]] 18:12, 17 June 2008 (UTC)

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

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

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

==Introduction to NA-MIC Project Week==

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

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

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process
** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** 11-12noon [[Project Week 2008 Slicer Tuning| Performance tuning for Slicer 3.2]] (Ron Kikinis)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-rigid Registration]] (Stephen Aylward)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])

== Preparation ==

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

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

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

== Projects ==

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

===Other Projects===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#[[2008_Summer_Project_Week:GroupwiseBSplineForDTI| Integraton of groupwise b-spline registration into atlas building]] (Casey Goodlett, Serdar Balci)
# CVS / SVN auto synchronization
# [[2008_Summer_Project_Week:3DWidgetsInSlicer|3D Widgets in Slicer]] (Nicole Aucoin, Will Schroeder)
## Issues with existing widgets
## Design of new widgets
# Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
# Module Chaining (Marco, Jim, Steve, Dan B., Luca)
# Nonlinear transforms (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# Slicer3, XNAT integration, and desigining XCEDE Web Services (Dan M., Steve, Julien, Dan B.)
## Review and enrich use cases
# Python in Slicer (Dan B., Michael Halle, Steve, Luca)
# [[2008_Summer_Project_Week:PerformanceTuningFiducials|Performance Tuning of Fiducials]] using the EventBroker and other tools (Nicole Aucoin, Alex Yarmarkovich, Steve Pieper, Will Schroeder)
# GUI Tweaking (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]
# [[2008_Summer_Project_Week:fMRIconnectivity|fMRI connectivity]] (Bryce Kim, MIT)
# [[2008_Summer_Project_Week:AtlasFreeSegmentation|Atlas free Segmentation]] (Tammy Riklin-Raviv, MIT)
#[[NA-MIC/Projects/Collaboration/EM Bias Field Correction | New Bias Field Correction in EM]] (Carlos Sánchez Mendoza, Kilian Pohl - SPL, Brad Davis - Kitware)
# [[2008_Summer_Project_Week:FluidMechanicsTractographyUCLA|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman, UCLA)

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#[[NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Lung Atlas]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Non-rigid image registration]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
#[[FMA (Protege) links to Slicer]] (Vish, Mike, Florin, Jim, Steve, Wendy)
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]]
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga, Dan Blezek, Mike Halle, Steve Piper)
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)
#[[NA-MIC/Projects/Collaboration/Carto_scar_BIDMC]] (Dana Peters Group)
#[[NA-MIC/Projects/Collaboration/3D Ultrasound Module in Slicer3]] (Junichi, Haiying and Noby - SPL, David - Queen's), Danielle - Robarts) )
#[[NA-MIC/Projects/Collaboration/MGH RadOnc]] (Greg Sharp, MGH)
#[[NA-MIC/Projects/External Collaboration/W&M CRTC]] Non-rigid registration for neurosurgery (Nikos Chrisochoides, Andriy Fedorov, College of William&Mary)
#[[NA-MIC/Projects/Collaboration/SBIA UPenn]] (Ragini Verma, Upenn)

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

==Attendee List==

WE HAVE REACHED CAPACITY. REGISTRATION IS CLOSED. [[User:Tkapur|Tkapur]] 19:42, 6 June 2008 (UTC)

==Pictures==

2008 Summer Project Week

2008-06-02T22:13:04Z

Ragini: /* Attendee List */

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

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

== Logistics ==

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

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

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

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

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

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

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

==Introduction to NA-MIC Project Week==

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

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

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

== Preparation ==

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

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

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

== Projects ==

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

===Structural Analysis===

===Diffusion Image Analysis===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#Integraton of groupwise b-spline registration into atlas building (Casey Goodlett, Serdar Balci)

===Calibration/Validation===

===NA-MIC Kit - Slicer 3===
# CVS / SVN auto synchronization
# 3D Widgets in Slicer
## Issues with existing widgets
## Design of new widgets
# Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
# Module Chaining (Marco, Jim, Steve, Dan B., Luca)
# Nonlinear transforms (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# Slicer3, XNAT integration, and desigining XCEDE Web Services (Dan M., Steve, Julien)
## Review and enrich use cases

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

===Non-Medical Collaborations===

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

==Pictures==

2008 Summer Project Week

2008-06-02T22:08:21Z

Ragini: /* Attendee List */

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

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

== Logistics ==

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

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

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

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

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

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

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

==Introduction to NA-MIC Project Week==

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

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

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

== Preparation ==

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

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

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

== Projects ==

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

===Structural Analysis===

===Diffusion Image Analysis===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#Integraton of groupwise b-spline registration into atlas building (Casey Goodlett, Serdar Balci)

===Calibration/Validation===

===NA-MIC Kit - Slicer 3===
# CVS / SVN auto synchronization
# 3D Widgets in Slicer
## Issues with existing widgets
## Design of new widgets
# Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
# Module Chaining (Marco, Jim, Steve, Dan B., Luca)
# Nonlinear transforms (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# Slicer3, XNAT integration, and desigining XCEDE Web Services (Dan M., Steve, Julien)
## Review and enrich use cases

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

===Non-Medical Collaborations===

==Attendee List==
# Ron Kikinis, BWH
# Carl-Fredrik Westin, BWH
# Gary Christensen, The University of Iowa
# Jeffrey Hawley, Gary Christensen's student
# Kate Raising, Gary Christensen's student
# Nathan Fritze, Gary Christensen's student
# Paul Song, Gary Christensen's student
# Cheng Zhang, Gary Christensen's student
# Ying Wei, Gary Christensen's student
# Nathan Burnette, The University of Iowa
# Hans Johnson, The University of Iowa
# Vincent Magnotta, The University of Iowa
# Keith Gunderson, The University of Iowa
# Steve Pieper, Isomics, Core 2/6
# Dana C. Peters, BIDMC Harvard Medical
# Jason Taclas, BIDMC Harvard Medical
# Nicole Aucoin, BWH, Core 2
# Will Schroeder, Kitware, Cores 2/4
# Sebastien Barre, Kitware, Core 2
# Julien Jomier, Kitware, Core 2
# Luis Ibanez, Kitware, Core 2
# Curtis Lisle, KnowledgeVis, Core 2
# Katie Hayes, BWH, Core 2
# Randy Gollub, MGH, Core 5
# Clement Vachet, UNC, Core 3
# Zhexing Liu, UNC, Core 1/3
# Casey Goodlett, Utah, Core 1
# Marcel Prastawa, Utah, Core 1
# Jeffrey Grethe, UCSD, Core 2
# Marco Ruiz, UCSD, Core 2
# Zhen Qian, Rutgers University
# Jinghao Zhou, Rutgers University
# Luca Antiga, Mario Negri Institute
# Adam Wittek, The University of Western Australia
# Grand Joldes, The University of Western Australia
# Jamie Berger, The University of Western Australia
# Serdar Balci, MIT, Core 1
# Bryce Kim, MIT, Core1
# Tina Kapur, BWH, Core 6
# Carling Cheung, Robarts Research Institute / The University of Western Ontario
# Danielle Pace, Robarts Research Institute / The University of Western Ontario
# Sean Megason, Dept of Systems Biology, Harvard Medical School
# Alex Gouaillard, Dept of Systems Biology, Harvard Medical School
# Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School
# Arnaud Gelas, Dept of Systems Biology, Harvard Medical School
# Sonia Pujol, Surgical Planning Laboratory, BWH
# Bjoern Menze, (then) Surgical Planning Laboratory, BWH
# Alex Yarmarkovich, Isomics, Core 2
# Sylvain Bouix, BWH, Core 3
# Priya Srinivasan, BWH, Core 3
# Chris Churas, UCSD, Core 2
# John Melonakos, Georgia Tech, Core 1
# Yi Gao, Georgia Tech, Core 1
# Tauseef Rehman, Georgia Tech, Core 1
# Clare Poynton, MIT, Core 1
# H. Jeremy Bockholt, MRN Lupus DBP Core 3
# Mark Scully, MRN Lupus DBP Core 3
# Gabor Fichtinger, Queen's, Core 2
# David Gobbi, Queen's, Core 2
# Purang Abolmaesumi, Queen's, Core 2
# Siddharth Vikal, Queen's, Core 2
# Daniel Blezek, Mayo
# Csaba Csoma, JHU, Core 2
# Ran Tao, University of Utah, Core 1
# Jim Miller, GE Research, Core 2
# Xiaodong Tao, GE Research, Core 2
# Dirk Padfield, GE Research, Core 2
# Viswanath Avasarala, GE Research, NAC
# Dan Marcus, Washington University
# Tim Olsen, Washington University
# Kevin Archie, Washington University
# Misha Milchenko, Washington University
# Wendy Plesniak, BWH, Core 2
# Demian Wasserman, INRIA, LMI-collaborator
#Xenophon Papademetris, Yale, Collaborator
#Xenophon P's postdoc, Yale, Collaborator
#Xenophon P's student, Yale, Collaborator
#Vidya Rajagopalan, Virginia Tech, Student of Chris Wyatt, External Collaborator
# Greg Sharp, MGH, External Collaborator
# Marta Peroni, MGH, External Collaborator
#Toru Higaki, Hiroshima Univ., Japan, External collaborator (Hata)
#Jacek Kukluk, BWH,
#Nobuhiko Hata, BWH
#Junichi Tokuda, BWH
#Haying Liu, BWH
#Ragini Verma, UPenn (June 26)
#Luke Bloy, UPenn (Ragini Verma's student) (June 26)
#Yang Li, UPenn (Ragini's postdoc) (June 26)

==Pictures==