NAMIC Wiki - User contributions [en]

2008 Summer Project Week

2008-06-27T13:45:24Z

Grandjoldes: /* 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
** 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]].
** 1:00-4:00pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Stata 32-D451) (Daniel Marcus)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Stata Kiva Conference Room) (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-rigid Registration]] (Stata Kiva Conference Room) (Stephen Aylward)
** 4:00-5:30pm: Project Week 2008 Special topic breakout: CMake/CPack/CTest/CDash, KWWidgets (Stata Kiva Conference Room) (Julien Jomier, Sebastien Barre)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Stata Kiva Conference Room) (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** Misc:
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***[http://grants.nih.gov/grants/guide/pa-files/PAR-08-184.html Collaborator RFA has been renewed]
***[[Events:TutorialContestJan2009]]
***Next Project Week [[AHM_2009| in Utah, January 5-9, 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, Serdar Balci MIT, Sylvain Bouix BWH, 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: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]] (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]] (Vidya Rajagopalan, Chris Wyatt, Kilian Pohl)
#[[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
#[[IGT_Projects_Discussion]]

===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
# Nicu Archip BWH
# Florin Talos BWH
#Stephen Aylward Kitware

==Pictures==
<gallery perrow="3" widths="150px">
Image:NA-MIC-ProjectWeek1.JPG|Lunch
Image:2008MITProjectWeekOpening-353.jpg|Opening Session
Image:NA-MIC-ProjectWeek2.JPG|Day 1
</gallery>
[http://woofton.rivendel.net/gallery2/main.php?g2_itemId=33261 PICTURES!] taken by Jeffrey Hawley

2008 Summer Project Week

2008-06-27T13:30:56Z

Grandjoldes: /* 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
** 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]].
** 1:00-4:00pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Stata 32-D451) (Daniel Marcus)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Stata Kiva Conference Room) (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-rigid Registration]] (Stata Kiva Conference Room) (Stephen Aylward)
** 4:00-5:30pm: Project Week 2008 Special topic breakout: CMake/CPack/CTest/CDash, KWWidgets (Stata Kiva Conference Room) (Julien Jomier, Sebastien Barre)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Stata Kiva Conference Room) (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** Misc:
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***[http://grants.nih.gov/grants/guide/pa-files/PAR-08-184.html Collaborator RFA has been renewed]
***[[Events:TutorialContestJan2009]]
***Next Project Week [[AHM_2009| in Utah, January 5-9, 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, Serdar Balci MIT, Sylvain Bouix BWH, 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: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]] (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]] (Vidya Rajagopalan, Chris Wyatt, Kilian Pohl)
#[[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, Carling Cheung - 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
#[[IGT_Projects_Discussion]]

===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
# Nicu Archip BWH
# Florin Talos BWH
#Stephen Aylward Kitware

==Pictures==
<gallery perrow="3" widths="150px">
Image:NA-MIC-ProjectWeek1.JPG|Lunch
Image:2008MITProjectWeekOpening-353.jpg|Opening Session
Image:NA-MIC-ProjectWeek2.JPG|Day 1
</gallery>
[http://woofton.rivendel.net/gallery2/main.php?g2_itemId=33261 PICTURES!] taken by Jeffrey Hawley

NA-MIC/Projects/Collaboration/UWA-Perth

2008-06-27T12:54:12Z

Grandjoldes: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:TLED-grabJPG.jpg|thumb|520px|Flow chart of the finite element algorithm with Total Lagrange Explicit Dynamics (TLED) for computing soft organ deformation developed at ISML.]]
|[[Image:ISML.gif|thumb|320px]]
|}

__NOTOC__


===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 from UWA, Will, Jim, Steve from NAMIC

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

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

<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%;" align="justify">

<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 procedures (non-linear explicit dynamics with Total Lagrangian formulation) that do not require solving large systems of equations 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;" align="justify">

<h1>Progress</h1>
The algorithms are already implemented in C/C++ using Visual Studio and MFC. Matlab is used for visualizing the results.

<h1>At the Project Week</h1>
*Learned from Jim Miller about possible solutions for linking our Finite Element (FE) solver for computing soft organ deformations with Slicer. No decision regarding selection of such solution has been made.
*Talked with other groups (from the College of William & Mary, Laboratory of Neuro Imaging at UCLA, and the University of Iowa) about applying the FE analysis in computing soft organ deformations for image registration.
*Learned from Vincent Magnotta about the hexahedral mesh generator developed at the University of Iowa.
*Attended the ITK and Non-rigid Registration topic break-outs.

</div>

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

</div>

===References===
*For complete list of our publication visit here [http://www.mech.uwa.edu.au/ISML/publications.htm]
*[1] Miller, K., Joldes, G., Lance, D., Wittek, A. (2007) Total Lagrangian explicit dynamics finite element algorithm for computing soft tissue deformation, Communications in Numerical Methods in Engineering. Vol. 23, pp. 121-134, doi: 10.1002/cnm.887, available on-line [http://www.sciencedirect.com/].
*[2] Wittek, A., Miller, K., Kikinis, R., Warfield, S. K. (2007) Patient-specific model of brain deformation: Application to medical image registration. Journal of Biomechanics. Vol. 40, pp. 919-929, DOI:10.1016/j.jbiomech.2006.02.021, available on-line [http://www.sciencedirect.com/].
*[3] Joldes, G. R., Wittek, A., Miller, K. (2007) Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2007, Brisbane, Australia, ISBN 13: 978 0 643 09517 5, pp. 65-73.
*[4] Hawkins, T., Wittek, A. and Miller, K. (2006) Comparison of constitutive models of brain tissue for non-rigid image registration, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages.
*[5] Horton, A., Wittek, A. and K. Miller (2006) Computer simulation of brain shift using an element free Galerkin method, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 906-911.
*[6] Horton, A., Wittek, A. and K. Miller (2006) Towards meshless methods for surgery simulation. Linear versus non-linear computation of the brain shift, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 32-40, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[7] Joldes, G., Wittek, A. and Miller, K. (2006) Improved linear tetrahedral element for surgery simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 52-63, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[8] Joldes, G., Wittek, A. and Miller, K. (2006) Towards non-linear finite element, computations in real time, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 894-899.
*[9] Miller, K., Joldes, G. and Wittek, A. (2006) New finite element algorithm for surgical simulation, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages
*[10] Miller, K. Hawkins, T. and Wittek, A. (2006) Linear versus non-linear computation of the brain shift, in CD Proceedings of the 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 888-893.
*[11] Miller, K. and Wittek, A. (2006) Neuroimage registration as displacement - zero traction problem of solid mechanics, Lead Lecture in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 1-12, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[12] Wittek, A., Kikinis, K., Warfield, S. K., and Miller, K. (2005) Brain shift computation using a fully nonlinear biomechanical model, in Proceedings of 8th International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2005 in Lecture Notes in Computer Science 3750 2006, pp. 583-590.

In Press
*[13] Wittek, A., T. Hawkins, and Miller, K. (2008). On the unimportance of constitutive models in computing brain deformation for image-guided surgery (in press). Biomechanics and Modeling in Mechanobiology: 8 pages, doi: 10.1007/s10237-008-0118-1, Springer.
*[14] Grand Joldes, Karol Miller and Adam Wittek (2007) Efficient hourglass control implementation for an uniform strain hexahedra using Total Lagrangian formulation. Communications in Numerical Methods in Engineering (accepted in June 2007), 9 pages, doi: 10.1002/cnm.1034, Wiley.

2008 Summer Project Week

2008-06-27T12:51:59Z

Grandjoldes: /* External Collaborations */

NA-MIC/Projects/Collaboration/UWA-Perth

2008-06-23T18:07:19Z

Grandjoldes: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:TLED-grabJPG.jpg|thumb|520px|Flow chart of the finite element algorithm with Total Lagrange Explicit Dynamics (TLED) for computing soft organ deformation developed at ISML.]]
|[[Image:ISML.gif|thumb|320px]]
|}

__NOTOC__


===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 from UWA, Will, Jim, Steve from NAMIC

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

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

<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%;" align="justify">

<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 procedures (non-linear explicit dynamics with Total Lagrangian formulation) that do not require solving large systems of equations 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;" align="justify">

<h1>Progress</h1>
The algorithms are already implemented in C/C++ using Visual Studio and MFC. Matlab is used for visualizing the results.

</div>

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

</div>

===References===
*For complete list of our publication visit here [http://www.mech.uwa.edu.au/ISML/publications.htm]
*[1] Miller, K., Joldes, G., Lance, D., Wittek, A. (2007) Total Lagrangian explicit dynamics finite element algorithm for computing soft tissue deformation, Communications in Numerical Methods in Engineering. Vol. 23, pp. 121-134, doi: 10.1002/cnm.887, available on-line [http://www.sciencedirect.com/].
*[2] Wittek, A., Miller, K., Kikinis, R., Warfield, S. K. (2007) Patient-specific model of brain deformation: Application to medical image registration. Journal of Biomechanics. Vol. 40, pp. 919-929, DOI:10.1016/j.jbiomech.2006.02.021, available on-line [http://www.sciencedirect.com/].
*[3] Joldes, G. R., Wittek, A., Miller, K. (2007) Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2007, Brisbane, Australia, ISBN 13: 978 0 643 09517 5, pp. 65-73.
*[4] Hawkins, T., Wittek, A. and Miller, K. (2006) Comparison of constitutive models of brain tissue for non-rigid image registration, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages.
*[5] Horton, A., Wittek, A. and K. Miller (2006) Computer simulation of brain shift using an element free Galerkin method, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 906-911.
*[6] Horton, A., Wittek, A. and K. Miller (2006) Towards meshless methods for surgery simulation. Linear versus non-linear computation of the brain shift, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 32-40, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[7] Joldes, G., Wittek, A. and Miller, K. (2006) Improved linear tetrahedral element for surgery simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 52-63, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[8] Joldes, G., Wittek, A. and Miller, K. (2006) Towards non-linear finite element, computations in real time, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 894-899.
*[9] Miller, K., Joldes, G. and Wittek, A. (2006) New finite element algorithm for surgical simulation, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages
*[10] Miller, K. Hawkins, T. and Wittek, A. (2006) Linear versus non-linear computation of the brain shift, in CD Proceedings of the 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 888-893.
*[11] Miller, K. and Wittek, A. (2006) Neuroimage registration as displacement - zero traction problem of solid mechanics, Lead Lecture in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 1-12, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[12] Wittek, A., Kikinis, K., Warfield, S. K., and Miller, K. (2005) Brain shift computation using a fully nonlinear biomechanical model, in Proceedings of 8th International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2005 in Lecture Notes in Computer Science 3750 2006, pp. 583-590.

In Press
*[13] Wittek, A., T. Hawkins, and Miller, K. (2008). On the unimportance of constitutive models in computing brain deformation for image-guided surgery (in press). Biomechanics and Modeling in Mechanobiology: 8 pages, doi: 10.1007/s10237-008-0118-1, Springer.
*[14] Grand Joldes, Karol Miller and Adam Wittek (2007) Efficient hourglass control implementation for an uniform strain hexahedra using Total Lagrangian formulation. Communications in Numerical Methods in Engineering (accepted in June 2007), 9 pages, doi: 10.1002/cnm.1034, Wiley.

NA-MIC/Projects/Collaboration/UWA-Perth

2008-06-23T18:06:18Z

Grandjoldes: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:TLED-grabJPG.jpg|thumb|520px|Flow chart of the finite element algorithm with Total Lagrange Explicit Dynamics (TLED) for computing soft organ deformation developed at ISML.]]
|[[Image:ISML.gif|thumb|320px]]
|}

__NOTOC__


===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, Will, Jim, Steve

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

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

<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%;" align="justify">

<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 procedures (non-linear explicit dynamics with Total Lagrangian formulation) that do not require solving large systems of equations 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;" align="justify">

<h1>Progress</h1>
The algorithms are already implemented in C/C++ using Visual Studio and MFC. Matlab is used for visualizing the results.

</div>

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

</div>

===References===
*For complete list of our publication visit here [http://www.mech.uwa.edu.au/ISML/publications.htm]
*[1] Miller, K., Joldes, G., Lance, D., Wittek, A. (2007) Total Lagrangian explicit dynamics finite element algorithm for computing soft tissue deformation, Communications in Numerical Methods in Engineering. Vol. 23, pp. 121-134, doi: 10.1002/cnm.887, available on-line [http://www.sciencedirect.com/].
*[2] Wittek, A., Miller, K., Kikinis, R., Warfield, S. K. (2007) Patient-specific model of brain deformation: Application to medical image registration. Journal of Biomechanics. Vol. 40, pp. 919-929, DOI:10.1016/j.jbiomech.2006.02.021, available on-line [http://www.sciencedirect.com/].
*[3] Joldes, G. R., Wittek, A., Miller, K. (2007) Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2007, Brisbane, Australia, ISBN 13: 978 0 643 09517 5, pp. 65-73.
*[4] Hawkins, T., Wittek, A. and Miller, K. (2006) Comparison of constitutive models of brain tissue for non-rigid image registration, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages.
*[5] Horton, A., Wittek, A. and K. Miller (2006) Computer simulation of brain shift using an element free Galerkin method, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 906-911.
*[6] Horton, A., Wittek, A. and K. Miller (2006) Towards meshless methods for surgery simulation. Linear versus non-linear computation of the brain shift, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 32-40, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[7] Joldes, G., Wittek, A. and Miller, K. (2006) Improved linear tetrahedral element for surgery simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 52-63, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[8] Joldes, G., Wittek, A. and Miller, K. (2006) Towards non-linear finite element, computations in real time, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 894-899.
*[9] Miller, K., Joldes, G. and Wittek, A. (2006) New finite element algorithm for surgical simulation, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages
*[10] Miller, K. Hawkins, T. and Wittek, A. (2006) Linear versus non-linear computation of the brain shift, in CD Proceedings of the 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 888-893.
*[11] Miller, K. and Wittek, A. (2006) Neuroimage registration as displacement - zero traction problem of solid mechanics, Lead Lecture in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 1-12, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[12] Wittek, A., Kikinis, K., Warfield, S. K., and Miller, K. (2005) Brain shift computation using a fully nonlinear biomechanical model, in Proceedings of 8th International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2005 in Lecture Notes in Computer Science 3750 2006, pp. 583-590.

In Press
*[13] Wittek, A., T. Hawkins, and Miller, K. (2008). On the unimportance of constitutive models in computing brain deformation for image-guided surgery (in press). Biomechanics and Modeling in Mechanobiology: 8 pages, doi: 10.1007/s10237-008-0118-1, Springer.
*[14] Grand Joldes, Karol Miller and Adam Wittek (2007) Efficient hourglass control implementation for an uniform strain hexahedra using Total Lagrangian formulation. Communications in Numerical Methods in Engineering (accepted in June 2007), 9 pages, doi: 10.1002/cnm.1034, Wiley.

NA-MIC/Projects/Collaboration/UWA-Perth

2008-06-23T16:50:31Z

Grandjoldes: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:TLED-grabJPG.jpg|thumb|520px|Flow chart of the finite element algorithm with Total Lagrange Explicit Dynamics (TLED) for computing soft organ deformation developed at ISML.]]
|[[Image:ISML.gif|thumb|320px]]
|}

__NOTOC__


===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%;" align="justify">

<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%;" align="justify">

<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 procedures (non-linear explicit dynamics with Total Lagrangian formulation) that do not require solving large systems of equations 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;" align="justify">

<h1>Progress</h1>
The algorithms are already implemented in C/C++ using Visual Studio and MFC. Matlab is used for visualizing the results.

</div>

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

</div>

===References===
*For complete list of our publication visit here [http://www.mech.uwa.edu.au/ISML/publications.htm]
*[1] Miller, K., Joldes, G., Lance, D., Wittek, A. (2007) Total Lagrangian explicit dynamics finite element algorithm for computing soft tissue deformation, Communications in Numerical Methods in Engineering. Vol. 23, pp. 121-134, doi: 10.1002/cnm.887, available on-line [http://www.sciencedirect.com/].
*[2] Wittek, A., Miller, K., Kikinis, R., Warfield, S. K. (2007) Patient-specific model of brain deformation: Application to medical image registration. Journal of Biomechanics. Vol. 40, pp. 919-929, DOI:10.1016/j.jbiomech.2006.02.021, available on-line [http://www.sciencedirect.com/].
*[3] Joldes, G. R., Wittek, A., Miller, K. (2007) Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2007, Brisbane, Australia, ISBN 13: 978 0 643 09517 5, pp. 65-73.
*[4] Hawkins, T., Wittek, A. and Miller, K. (2006) Comparison of constitutive models of brain tissue for non-rigid image registration, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages.
*[5] Horton, A., Wittek, A. and K. Miller (2006) Computer simulation of brain shift using an element free Galerkin method, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 906-911.
*[6] Horton, A., Wittek, A. and K. Miller (2006) Towards meshless methods for surgery simulation. Linear versus non-linear computation of the brain shift, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 32-40, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[7] Joldes, G., Wittek, A. and Miller, K. (2006) Improved linear tetrahedral element for surgery simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 52-63, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[8] Joldes, G., Wittek, A. and Miller, K. (2006) Towards non-linear finite element, computations in real time, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 894-899.
*[9] Miller, K., Joldes, G. and Wittek, A. (2006) New finite element algorithm for surgical simulation, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages
*[10] Miller, K. Hawkins, T. and Wittek, A. (2006) Linear versus non-linear computation of the brain shift, in CD Proceedings of the 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 888-893.
*[11] Miller, K. and Wittek, A. (2006) Neuroimage registration as displacement - zero traction problem of solid mechanics, Lead Lecture in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 1-12, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[12] Wittek, A., Kikinis, K., Warfield, S. K., and Miller, K. (2005) Brain shift computation using a fully nonlinear biomechanical model, in Proceedings of 8th International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2005 in Lecture Notes in Computer Science 3750 2006, pp. 583-590.

In Press
*[13] Wittek, A., T. Hawkins, and Miller, K. (2008). On the unimportance of constitutive models in computing brain deformation for image-guided surgery (in press). Biomechanics and Modeling in Mechanobiology: 8 pages, doi: 10.1007/s10237-008-0118-1, Springer.
*[14] Grand Joldes, Karol Miller and Adam Wittek (2007) Efficient hourglass control implementation for an uniform strain hexahedra using Total Lagrangian formulation. Communications in Numerical Methods in Engineering (accepted in June 2007), 9 pages, doi: 10.1002/cnm.1034, Wiley.

NA-MIC/Projects/Collaboration/UWA-Perth

2008-06-23T16:49:46Z

Grandjoldes: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:TLED-grabJPG.jpg|thumb|520px|Flow chart of the finite element algorithm with Total Lagrange Explicit Dynamics (TLED) for computing soft organ deformation developed at ISML.]]
|[[Image:ISML.gif|thumb|320px]]
|}

__NOTOC__


===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%;" align="justify">

<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%;" align="justify">

<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 procedures (non-linear explicit dynamics with Total Lagrangian formulation) that do not require solving large systems of equations 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;" align="justify">

<h1>Progress</h1>
The algorithms are already implemented in C/C++ using Visual Studio and MFC.

</div>

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

</div>

===References===
*For complete list of our publication visit here [http://www.mech.uwa.edu.au/ISML/publications.htm]
*[1] Miller, K., Joldes, G., Lance, D., Wittek, A. (2007) Total Lagrangian explicit dynamics finite element algorithm for computing soft tissue deformation, Communications in Numerical Methods in Engineering. Vol. 23, pp. 121-134, doi: 10.1002/cnm.887, available on-line [http://www.sciencedirect.com/].
*[2] Wittek, A., Miller, K., Kikinis, R., Warfield, S. K. (2007) Patient-specific model of brain deformation: Application to medical image registration. Journal of Biomechanics. Vol. 40, pp. 919-929, DOI:10.1016/j.jbiomech.2006.02.021, available on-line [http://www.sciencedirect.com/].
*[3] Joldes, G. R., Wittek, A., Miller, K. (2007) Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2007, Brisbane, Australia, ISBN 13: 978 0 643 09517 5, pp. 65-73.
*[4] Hawkins, T., Wittek, A. and Miller, K. (2006) Comparison of constitutive models of brain tissue for non-rigid image registration, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages.
*[5] Horton, A., Wittek, A. and K. Miller (2006) Computer simulation of brain shift using an element free Galerkin method, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 906-911.
*[6] Horton, A., Wittek, A. and K. Miller (2006) Towards meshless methods for surgery simulation. Linear versus non-linear computation of the brain shift, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 32-40, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[7] Joldes, G., Wittek, A. and Miller, K. (2006) Improved linear tetrahedral element for surgery simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 52-63, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[8] Joldes, G., Wittek, A. and Miller, K. (2006) Towards non-linear finite element, computations in real time, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 894-899.
*[9] Miller, K., Joldes, G. and Wittek, A. (2006) New finite element algorithm for surgical simulation, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages
*[10] Miller, K. Hawkins, T. and Wittek, A. (2006) Linear versus non-linear computation of the brain shift, in CD Proceedings of the 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 888-893.
*[11] Miller, K. and Wittek, A. (2006) Neuroimage registration as displacement - zero traction problem of solid mechanics, Lead Lecture in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 1-12, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[12] Wittek, A., Kikinis, K., Warfield, S. K., and Miller, K. (2005) Brain shift computation using a fully nonlinear biomechanical model, in Proceedings of 8th International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2005 in Lecture Notes in Computer Science 3750 2006, pp. 583-590.

In Press
*[13] Wittek, A., T. Hawkins, and Miller, K. (2008). On the unimportance of constitutive models in computing brain deformation for image-guided surgery (in press). Biomechanics and Modeling in Mechanobiology: 8 pages, doi: 10.1007/s10237-008-0118-1, Springer.
*[14] Grand Joldes, Karol Miller and Adam Wittek (2007) Efficient hourglass control implementation for an uniform strain hexahedra using Total Lagrangian formulation. Communications in Numerical Methods in Engineering (accepted in June 2007), 9 pages, doi: 10.1002/cnm.1034, Wiley.

NA-MIC/Projects/Collaboration/UWA-Perth

2008-06-23T16:41:08Z

Grandjoldes: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:TLED-grabJPG.jpg|thumb|520px|Flow chart of the finite element algorithm with Total Lagrange Explicit Dynamics (TLED) for computing soft organ deformation developed at ISML.]]
|[[Image:ISML.gif|thumb|320px]]
|}

__NOTOC__


===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%;" align="justify">

<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%;" align="justify">

<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 procedures (non-linear explicit dynamics with Total Lagrangian formulation) that do not require solving large systems of equations 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;" align="justify">

<h1>Progress</h1>
Some of the algorithms are already implemented in C/C++ using Visual Studio and MFC.

</div>

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

</div>

===References===
*For complete list of our publication visit here [http://www.mech.uwa.edu.au/ISML/publications.htm]
*[1] Miller, K., Joldes, G., Lance, D., Wittek, A. (2007) Total Lagrangian explicit dynamics finite element algorithm for computing soft tissue deformation, Communications in Numerical Methods in Engineering. Vol. 23, pp. 121-134, doi: 10.1002/cnm.887, available on-line [http://www.sciencedirect.com/].
*[2] Wittek, A., Miller, K., Kikinis, R., Warfield, S. K. (2007) Patient-specific model of brain deformation: Application to medical image registration. Journal of Biomechanics. Vol. 40, pp. 919-929, DOI:10.1016/j.jbiomech.2006.02.021, available on-line [http://www.sciencedirect.com/].
*[3] Joldes, G. R., Wittek, A., Miller, K. (2007) Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2007, Brisbane, Australia, ISBN 13: 978 0 643 09517 5, pp. 65-73.
*[4] Hawkins, T., Wittek, A. and Miller, K. (2006) Comparison of constitutive models of brain tissue for non-rigid image registration, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages.
*[5] Horton, A., Wittek, A. and K. Miller (2006) Computer simulation of brain shift using an element free Galerkin method, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 906-911.
*[6] Horton, A., Wittek, A. and K. Miller (2006) Towards meshless methods for surgery simulation. Linear versus non-linear computation of the brain shift, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 32-40, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[7] Joldes, G., Wittek, A. and Miller, K. (2006) Improved linear tetrahedral element for surgery simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 52-63, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[8] Joldes, G., Wittek, A. and Miller, K. (2006) Towards non-linear finite element, computations in real time, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 894-899.
*[9] Miller, K., Joldes, G. and Wittek, A. (2006) New finite element algorithm for surgical simulation, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages
*[10] Miller, K. Hawkins, T. and Wittek, A. (2006) Linear versus non-linear computation of the brain shift, in CD Proceedings of the 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 888-893.
*[11] Miller, K. and Wittek, A. (2006) Neuroimage registration as displacement - zero traction problem of solid mechanics, Lead Lecture in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 1-12, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[12] Wittek, A., Kikinis, K., Warfield, S. K., and Miller, K. (2005) Brain shift computation using a fully nonlinear biomechanical model, in Proceedings of 8th International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2005 in Lecture Notes in Computer Science 3750 2006, pp. 583-590.

In Press
*[13] Wittek, A., T. Hawkins, and Miller, K. (2008). On the unimportance of constitutive models in computing brain deformation for image-guided surgery (in press). Biomechanics and Modeling in Mechanobiology: 8 pages, doi: 10.1007/s10237-008-0118-1, Springer.
*[14] Grand Joldes, Karol Miller and Adam Wittek (2007) Efficient hourglass control implementation for an uniform strain hexahedra using Total Lagrangian formulation. Communications in Numerical Methods in Engineering (accepted in June 2007), 9 pages, doi: 10.1002/cnm.1034, Wiley.

NA-MIC/Projects/Collaboration/UWA-Perth

2008-06-23T16:31:20Z

Grandjoldes: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:TLED-grabJPG.jpg|thumb|520px|Flow chart of the finite element algorithm with Total Lagrange Explicit Dynamics (TLED) for computing soft organ deformation developed at ISML.]]
|[[Image:ISML.gif|thumb|320px]]
|}

__NOTOC__


===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 procedures (non-linear explicit dynamics with Total Lagrangian formulation) that do not require solving large systems of equations 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>
Some of the algorithms are already implemented in C/C++ using Visual Studio and MFC.

</div>

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

</div>

===References===
*For complete list of our publication visit here [http://www.mech.uwa.edu.au/ISML/publications.htm]
*[1] Miller, K., Joldes, G., Lance, D., Wittek, A. (2007) Total Lagrangian explicit dynamics finite element algorithm for computing soft tissue deformation, Communications in Numerical Methods in Engineering. Vol. 23, pp. 121-134, doi: 10.1002/cnm.887, available on-line [http://www.sciencedirect.com/].
*[2] Wittek, A., Miller, K., Kikinis, R., Warfield, S. K. (2007) Patient-specific model of brain deformation: Application to medical image registration. Journal of Biomechanics. Vol. 40, pp. 919-929, DOI:10.1016/j.jbiomech.2006.02.021, available on-line [http://www.sciencedirect.com/].
*[3] Joldes, G. R., Wittek, A., Miller, K. (2007) Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2007, Brisbane, Australia, ISBN 13: 978 0 643 09517 5, pp. 65-73.
*[4] Hawkins, T., Wittek, A. and Miller, K. (2006) Comparison of constitutive models of brain tissue for non-rigid image registration, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages.
*[5] Horton, A., Wittek, A. and K. Miller (2006) Computer simulation of brain shift using an element free Galerkin method, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 906-911.
*[6] Horton, A., Wittek, A. and K. Miller (2006) Towards meshless methods for surgery simulation. Linear versus non-linear computation of the brain shift, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 32-40, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[7] Joldes, G., Wittek, A. and Miller, K. (2006) Improved linear tetrahedral element for surgery simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 52-63, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[8] Joldes, G., Wittek, A. and Miller, K. (2006) Towards non-linear finite element, computations in real time, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 894-899.
*[9] Miller, K., Joldes, G. and Wittek, A. (2006) New finite element algorithm for surgical simulation, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages
*[10] Miller, K. Hawkins, T. and Wittek, A. (2006) Linear versus non-linear computation of the brain shift, in CD Proceedings of the 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 888-893.
*[11] Miller, K. and Wittek, A. (2006) Neuroimage registration as displacement - zero traction problem of solid mechanics, Lead Lecture in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 1-12, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[12] Wittek, A., Kikinis, K., Warfield, S. K., and Miller, K. (2005) Brain shift computation using a fully nonlinear biomechanical model, in Proceedings of 8th International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2005 in Lecture Notes in Computer Science 3750 2006, pp. 583-590.

In Press
*[13] Wittek, A., T. Hawkins, and Miller, K. (2008). On the unimportance of constitutive models in computing brain deformation for image-guided surgery (in press). Biomechanics and Modeling in Mechanobiology: 8 pages, doi: 10.1007/s10237-008-0118-1, Springer.
*[14] Grand Joldes, Karol Miller and Adam Wittek (2007) Efficient hourglass control implementation for an uniform strain hexahedra using Total Lagrangian formulation. Communications in Numerical Methods in Engineering (accepted in June 2007), 9 pages, doi: 10.1002/cnm.1034, Wiley.

NA-MIC/Projects/Collaboration/UWA-Perth

2008-06-23T16:25:27Z

Grandjoldes: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:TLED-grabJPG.jpg|thumb|520px|Flow chart of the finite element algorithm with Total Lagrange Explicit Dynamics (TLED) for computing soft organ deformation developed at ISML.]]
|[[Image:ISML.gif|thumb|320px]]
|}

__NOTOC__


===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 solving large systems of equations 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>
Some of the algorithms are already implemented in C/C++ using Visual Studio and MFC.

</div>

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

</div>

===References===
*For complete list of our publication visit here [http://www.mech.uwa.edu.au/ISML/publications.htm]
*[1] Miller, K., Joldes, G., Lance, D., Wittek, A. (2007) Total Lagrangian explicit dynamics finite element algorithm for computing soft tissue deformation, Communications in Numerical Methods in Engineering. Vol. 23, pp. 121-134, doi: 10.1002/cnm.887, available on-line [http://www.sciencedirect.com/].
*[2] Wittek, A., Miller, K., Kikinis, R., Warfield, S. K. (2007) Patient-specific model of brain deformation: Application to medical image registration. Journal of Biomechanics. Vol. 40, pp. 919-929, DOI:10.1016/j.jbiomech.2006.02.021, available on-line [http://www.sciencedirect.com/].
*[3] Joldes, G. R., Wittek, A., Miller, K. (2007) Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2007, Brisbane, Australia, ISBN 13: 978 0 643 09517 5, pp. 65-73.
*[4] Hawkins, T., Wittek, A. and Miller, K. (2006) Comparison of constitutive models of brain tissue for non-rigid image registration, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages.
*[5] Horton, A., Wittek, A. and K. Miller (2006) Computer simulation of brain shift using an element free Galerkin method, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 906-911.
*[6] Horton, A., Wittek, A. and K. Miller (2006) Towards meshless methods for surgery simulation. Linear versus non-linear computation of the brain shift, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 32-40, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[7] Joldes, G., Wittek, A. and Miller, K. (2006) Improved linear tetrahedral element for surgery simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 52-63, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[8] Joldes, G., Wittek, A. and Miller, K. (2006) Towards non-linear finite element, computations in real time, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 894-899.
*[9] Miller, K., Joldes, G. and Wittek, A. (2006) New finite element algorithm for surgical simulation, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages
*[10] Miller, K. Hawkins, T. and Wittek, A. (2006) Linear versus non-linear computation of the brain shift, in CD Proceedings of the 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 888-893.
*[11] Miller, K. and Wittek, A. (2006) Neuroimage registration as displacement - zero traction problem of solid mechanics, Lead Lecture in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 1-12, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[12] Wittek, A., Kikinis, K., Warfield, S. K., and Miller, K. (2005) Brain shift computation using a fully nonlinear biomechanical model, in Proceedings of 8th International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2005 in Lecture Notes in Computer Science 3750 2006, pp. 583-590.

In Press
*[13] Wittek, A., T. Hawkins, and Miller, K. (2008). On the unimportance of constitutive models in computing brain deformation for image-guided surgery (in press). Biomechanics and Modeling in Mechanobiology: 8 pages, doi: 10.1007/s10237-008-0118-1, Springer.
*[14] Grand Joldes, Karol Miller and Adam Wittek (2007) Efficient hourglass control implementation for an uniform strain hexahedra using Total Lagrangian formulation. Communications in Numerical Methods in Engineering (accepted in June 2007), 9 pages, doi: 10.1002/cnm.1034, Wiley.

NA-MIC/Projects/Collaboration/UWA-Perth

2008-06-23T16:06:02Z

Grandjoldes: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:TLED-grabJPG.jpg|thumb|520px|Flow chart of the finite element algorithm with Total Lagrange Explicit Dynamics (TLED) for computing soft organ deformation developed at ISML.]]
|[[Image:ISML.gif|thumb|320px]]
|}

__NOTOC__


===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 solving large systems of equations 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>
Some of the algorithms are already implemented in C/C++ using Visual Studio and MFC.

</div>

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

</div>

===References===
*For complete list of our publication visit here [http://www.mech.uwa.edu.au/ISML/publications.htm]
*[1] Miller, K., Joldes, G., Lance, D., Wittek, A. (2007) Total Lagrangian explicit dynamics finite element algorithm for computing soft tissue deformation, Communications in Numerical Methods in Engineering. Vol. 23, pp. 121-134, doi: 10.1002/cnm.887, available on-line [http://www.sciencedirect.com/].
*[2] Wittek, A., Miller, K., Kikinis, R., Warfield, S. K. (2007) Patient-specific model of brain deformation: Application to medical image registration. Journal of Biomechanics. Vol. 40, pp. 919-929, DOI:10.1016/j.jbiomech.2006.02.021, available on-line [http://www.sciencedirect.com/].
*[3] Joldes, G. R., Wittek, A., Miller, K. (2007) Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2007, Brisbane, Australia, ISBN 13: 978 0 643 09517 5, pp. 65-73.
*[4] Hawkins, T., Wittek, A. and Miller, K. (2006) Comparison of constitutive models of brain tissue for non-rigid image registration, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages.
*[5] Horton, A., Wittek, A. and K. Miller (2006) Computer simulation of brain shift using an element free Galerkin method, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 906-911.
*[6] Horton, A., Wittek, A. and K. Miller (2006) Towards meshless methods for surgery simulation. Linear versus non-linear computation of the brain shift, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 32-40, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[7] Joldes, G., Wittek, A. and Miller, K. (2006) Improved linear tetrahedral element for surgery simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 52-63, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[8] Joldes, G., Wittek, A. and Miller, K. (2006) Towards non-linear finite element, computations in real time, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 894-899.
*[9] Miller, K., Joldes, G. and Wittek, A. (2006) New finite element algorithm for surgical simulation, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages
*[10] Miller, K. Hawkins, T. and Wittek, A. (2006) Linear versus non-linear computation of the brain shift, in CD Proceedings of the 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 888-893.
*[11] Miller, K. and Wittek, A. (2006) Neuroimage registration as displacement - zero traction problem of solid mechanics, Lead Lecture in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 1-12, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[12] Wittek, A., Kikinis, K., Warfield, S. K., and Miller, K. (2005) Brain shift computation using a fully nonlinear biomechanical model, in Proceedings of 8th International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2005 in Lecture Notes in Computer Science 3750 2006, pp. 583-590.

In Press
*[13] Wittek, A., T. Hawkins, and Miller, K. (2008). On the unimportance of constitutive models in computing brain deformation for image-guided surgery (in press). Biomechanics and Modeling in Mechanobiology: 8 pages, doi: 10.1007/s10237-008-0118-1, Springer.
*[14] Grand Joldes, Karol Miller and Adam Wittek (2007) Efficient hourglass control implementation for an uniform strain hexahedra using Total Lagrangian formulation. Communications in Numerical Methods in Engineering (accepted in June 2007), 9 pages, doi: 10.1002/cnm.1034, Wiley.

NA-MIC/Projects/Collaboration/UWA-Perth

2008-06-23T16:02:44Z

Grandjoldes: /* References */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:TLED-grabJPG.jpg|thumb|520px|Flow chart of the finite element algorithm with Total Lagrange Explicit Dynamics (TLED) for computing soft organ deformation developed at ISML.]]
|[[Image:ISML.gif|thumb|320px]]
|}

__NOTOC__


===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>
Some of the algorithms are already implemented in C/C++ using Visual Studio and MFC.

</div>

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

</div>

===References===
*For complete list of our publication visit here [http://www.mech.uwa.edu.au/ISML/publications.htm]
*[1] Miller, K., Joldes, G., Lance, D., Wittek, A. (2007) Total Lagrangian explicit dynamics finite element algorithm for computing soft tissue deformation, Communications in Numerical Methods in Engineering. Vol. 23, pp. 121-134, doi: 10.1002/cnm.887, available on-line [http://www.sciencedirect.com/].
*[2] Wittek, A., Miller, K., Kikinis, R., Warfield, S. K. (2007) Patient-specific model of brain deformation: Application to medical image registration. Journal of Biomechanics. Vol. 40, pp. 919-929, DOI:10.1016/j.jbiomech.2006.02.021, available on-line [http://www.sciencedirect.com/].
*[3] Joldes, G. R., Wittek, A., Miller, K. (2007) Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2007, Brisbane, Australia, ISBN 13: 978 0 643 09517 5, pp. 65-73.
*[4] Hawkins, T., Wittek, A. and Miller, K. (2006) Comparison of constitutive models of brain tissue for non-rigid image registration, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages.
*[5] Horton, A., Wittek, A. and K. Miller (2006) Computer simulation of brain shift using an element free Galerkin method, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 906-911.
*[6] Horton, A., Wittek, A. and K. Miller (2006) Towards meshless methods for surgery simulation. Linear versus non-linear computation of the brain shift, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 32-40, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[7] Joldes, G., Wittek, A. and Miller, K. (2006) Improved linear tetrahedral element for surgery simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 52-63, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[8] Joldes, G., Wittek, A. and Miller, K. (2006) Towards non-linear finite element, computations in real time, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 894-899.
*[9] Miller, K., Joldes, G. and Wittek, A. (2006) New finite element algorithm for surgical simulation, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages
*[10] Miller, K. Hawkins, T. and Wittek, A. (2006) Linear versus non-linear computation of the brain shift, in CD Proceedings of the 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 888-893.
*[11] Miller, K. and Wittek, A. (2006) Neuroimage registration as displacement - zero traction problem of solid mechanics, Lead Lecture in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 1-12, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[12] Wittek, A., Kikinis, K., Warfield, S. K., and Miller, K. (2005) Brain shift computation using a fully nonlinear biomechanical model, in Proceedings of 8th International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2005 in Lecture Notes in Computer Science 3750 2006, pp. 583-590.

In Press
*[13] Wittek, A., T. Hawkins, and Miller, K. (2008). On the unimportance of constitutive models in computing brain deformation for image-guided surgery (in press). Biomechanics and Modeling in Mechanobiology: 8 pages, doi: 10.1007/s10237-008-0118-1, Springer.
*[14] Grand Joldes, Karol Miller and Adam Wittek (2007) Efficient hourglass control implementation for an uniform strain hexahedra using Total Lagrangian formulation. Communications in Numerical Methods in Engineering (accepted in June 2007), 9 pages, doi: 10.1002/cnm.1034, Wiley.

NA-MIC/Projects/Collaboration/UWA-Perth

2008-06-23T16:01:50Z

Grandjoldes: /* References */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:TLED-grabJPG.jpg|thumb|520px|Flow chart of the finite element algorithm with Total Lagrange Explicit Dynamics (TLED) for computing soft organ deformation developed at ISML.]]
|[[Image:ISML.gif|thumb|320px]]
|}

__NOTOC__


===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>
Some of the algorithms are already implemented in C/C++ using Visual Studio and MFC.

</div>

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

</div>

===References===
*For complete list of our publication visit here [http://www.mech.uwa.edu.au/ISML/publications.htm]
*[1] Miller, K., Joldes, G., Lance, D., Wittek, A. (2007) Total Lagrangian explicit dynamics finite element algorithm for computing soft tissue deformation, Communications in Numerical Methods in Engineering. Vol. 23, pp. 121-134, doi: 10.1002/cnm.887, available on-line [http://www.sciencedirect.com/].
*[2] Wittek, A., Miller, K., Kikinis, R., Warfield, S. K. (2007) Patient-specific model of brain deformation: Application to medical image registration. Journal of Biomechanics. Vol. 40, pp. 919-929, DOI:10.1016/j.jbiomech.2006.02.021, available on-line [http://www.sciencedirect.com/].
*[3] Joldes, G. R., Wittek, A., Miller, K. (2007) Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2007, Brisbane, Australia, ISBN 13: 978 0 643 09517 5, pp. 65-73.
*[4] Hawkins, T., Wittek, A. and Miller, K. (2006) Comparison of constitutive models of brain tissue for non-rigid image registration, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages.
*[5] Horton, A., Wittek, A. and K. Miller (2006) Computer simulation of brain shift using an element free Galerkin method, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 906-911.
*[6] Horton, A., Wittek, A. and K. Miller (2006) Towards meshless methods for surgery simulation. Linear versus non-linear computation of the brain shift, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 32-40, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[7] Joldes, G., Wittek, A. and Miller, K. (2006) Improved linear tetrahedral element for surgery simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 52-63, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[8] Joldes, G., Wittek, A. and Miller, K. (2006) Towards non-linear finite element, computations in real time, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 894-899.
*[9] Miller, K., Joldes, G. and Wittek, A. (2006) New finite element algorithm for surgical simulation, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages
*[10] Miller, K. Hawkins, T. and Wittek, A. (2006) Linear versus non-linear computation of the brain shift, in CD Proceedings of the 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 888-893.
*[11] Miller, K. and Wittek, A. (2006) Neuroimage registration as displacement - zero traction problem of solid mechanics, Lead Lecture in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 1-12, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[12] Wittek, A., Kikinis, K., Warfield, S. K., and Miller, K. (2005) Brain shift computation using a fully nonlinear biomechanical model, in Proceedings of 8th International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2005 in Lecture Notes in Computer Science 3750 2006, pp. 583-590.

In Press
*[13] AWittek, A., T. Hawkins, and Miller, K. (2008). On the unimportance of constitutive models in computing brain deformation for image-guided surgery (in press). Biomechanics and Modeling in Mechanobiology: 8 pages, doi: 10.1007/s10237-008-0118-1, Springer.
*[14] Grand Joldes, Karol Miller and Adam Wittek (2007) Efficient hourglass control implementation for an uniform strain hexahedra using Total Lagrangian formulation. Communications in Numerical Methods in Engineering (accepted in June 2007), 9 pages, doi: 10.1002/cnm.1034, Wiley.

NA-MIC/Projects/Collaboration/UWA-Perth

2008-06-23T15:55:03Z

Grandjoldes:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:TLED-grabJPG.jpg|thumb|520px|Flow chart of the finite element algorithm with Total Lagrange Explicit Dynamics (TLED) for computing soft organ deformation developed at ISML.]]
|[[Image:ISML.gif|thumb|320px]]
|}

__NOTOC__


===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>
Some of the algorithms are already implemented in C/C++ using Visual Studio and MFC.

</div>

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

</div>

===References===
*For complete list of our publication visit here [http://www.mech.uwa.edu.au/ISML/publications.htm]
*[1] Miller, K., Joldes, G., Lance, D., Wittek, A. (2007) Total Lagrangian explicit dynamics finite element algorithm for computing soft tissue deformation, Communications in Numerical Methods in Engineering. Vol. 23, pp. 121-134, doi: 10.1002/cnm.887, available on-line [http://www.sciencedirect.com/].
*[2] Wittek, A., Miller, K., Kikinis, R., Warfield, S. K. (2007) Patient-specific model of brain deformation: Application to medical image registration. Journal of Biomechanics. Vol. 40, pp. 919-929, DOI:10.1016/j.jbiomech.2006.02.021, available on-line [http://www.sciencedirect.com/].
*[3] Joldes, G. R., Wittek, A., Miller, K. (2007) Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2007, Brisbane, Australia, ISBN 13: 978 0 643 09517 5, pp. 65-73.
*[4] Hawkins, T., Wittek, A. and Miller, K. (2006) Comparison of constitutive models of brain tissue for non-rigid image registration, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages.
*[5] Horton, A., Wittek, A. and K. Miller (2006) Computer simulation of brain shift using an element free Galerkin method, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 906-911.
*[6] Horton, A., Wittek, A. and K. Miller (2006) Towards meshless methods for surgery simulation. Linear versus non-linear computation of the brain shift, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 32-40, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[7] Joldes, G., Wittek, A. and Miller, K. (2006) Improved linear tetrahedral element for surgery simulation, in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 52-63, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[8] Joldes, G., Wittek, A. and Miller, K. (2006) Towards non-linear finite element, computations in real time, in CD Proceedings of 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 894-899.
*[9] Miller, K., Joldes, G. and Wittek, A. (2006) New finite element algorithm for surgical simulation, in CD Proceedings of 2nd Workshop on Computer Assisted Diagnosis and Surgery, Santiago, Chile, 4 pages
*[10] Miller, K. Hawkins, T. and Wittek, A. (2006) Linear versus non-linear computation of the brain shift, in CD Proceedings of the 7th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering CMBBE 2006, Antibes, France, ISBN: 0-9549670-2-X, pp. 888-893.
*[11] Miller, K. and Wittek, A. (2006) Neuroimage registration as displacement - zero traction problem of solid mechanics, Lead Lecture in Proceedings of Computational Biomechanics for Medicine Workshop, International Conference on Medical Image Computing and Computer-Assisted Intervention MICCAI 2006, Copenhagen, Denmark, ISBN 10: 87-7611-149-0, pp. 1-12, available on-line [http://www.mech.uwa.edu.au/ISML/publications.htm].
*[12] Wittek, A., Kikinis, K., Warfield, S. K., and Miller, K. (2005) Brain shift computation using a fully nonlinear biomechanical model, in Proceedings of 8th International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI 2005 in Lecture Notes in Computer Science 3750 2006, pp. 583-590.

In Press
*[13] AWittek, A., T. Hawkins, and Miller, K. (2008). On the unimportance of constitutive models in computing brain deformation for image-guided surgery (in press). Biomechanics and Modeling in Mechanobiology: 8 pages, doi: 10.1007/s10237-008-0118-1, Springer.
*[14] Grand Joldes, Karol Miller and Adam Wittek (2007) Efficient hourglass control implementation for an uniform strain hexahedra using Total Lagrangian formulation. Communications in Numerical Methods in Engineering (accepted in June 2007), 9 pages, doi: 10.1002/cnm.1034, Wiley.

2008 Summer Project Week

2008-06-23T15:53:05Z

Grandjoldes:

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 - 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]] Non-rigid DTI Registration(Ragini Verma, SBIA Upenn)

===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 Wasserman 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==
To be added.