NAMIC Wiki - User contributions [en]

Event:2011-Registration-Retreat-Wednesday

2011-02-25T15:40:50Z

Lzollei: wed meeting notes

[[Event:2011_Registration_Retreat| Back to Registration Brainstorming 2011]]

==Some relevant links==
* Survey of the available data from NCI: https://wiki.nci.nih.gov/display/CIP/CIP+Survey+of+Biomedical+Imaging+Archives
* FDA guidance RFC on getting a drug development device through the regulatory approval: http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/UCM230597.pdf

=Wednesday registration topics=

==Multi-modal registration (A. Fedorov)==
The task of multi-parametric MRI prostate registration is an example of a problem where the clinical case numbers are low, subject positioning is highly variable, and image resolution is also quite low. One of the biggest challenges at present is the lack of a validation mechanism. What kind of measures, techniques, ... could we introduce to measure performance in the case of this complex problem?

Diverging from this discussion a bit, what guidelines / principles should standard validation pipelines all follow?

* Could multi-center studies be helpful in non-brain centered image analysis? How could we catalyze their collection?
* Should the final step be to be used in an FDA approved system?
* We should probably separate scenarios where working on thousands of data is feasible and those where solution needs to be offered to unique problems, challenging interventions, where large numbers are not available.
* Should we also work on a "proper experimental design" paper so that data collection and collaboration with the clinical side would smoother.
* http://nipy.sourceforge.net/ (wrapper around tools and to test and compare registration techniques)

==Poly-affine / multi-affine registration (CF Westin)==
Why hasn't the poly-/multi-affine techniques caught up more over the past ~10 years? It seems we mostly focus on the two extremes: rigid/affine and dense / diffeomorphic warps.

* direct displacement averaging
* infinitessimal displacement averaging

==Wrap up discussions==

=== White paper details ===

# Target audience
## NIH
## clinicians, RAs, end users
## tech developers looking for gap in development (PhD candidates, junior scientists, ...)

# Contents
## What works at present
## What should be funded
## What open question are out there

Can we advance new and existing techniques through setting up a framework?
What to do about non-brain areas?
Appropriate inappropriate users

# Paper details and contents
## define "registration" and its scope
## educate clinicians about "it is not magic"
## describe a single or a couple of successful case studies (ADNI, OASIS, MNI pediatric, AFIB, cardiac JHU, ...) so that investigators can plan ahead of time and data become more usable and consistent
## more annotated data sets are needed!
## how quickly could we get new data sets if an announcement went out?
## list / reference of available data sets (indicated above)
## require data sets being accompanied by problem definition and data parameters
## promote the idea of papers being accompanied by data and code; they seem to be more useful and more heavily cited / downloaded currently. We should set an example doing that more, but it difficult to require it from all conf / journal submissions because of IRB issues.
## identify environments in which comparing results and techniques is easier (eg.: NIREP http://www.nirep.org/index.php?id=22)
## promote the aim for graceful failure and detailed feedback to the user about performance

# Misc
## should we include extensive terminology in the paper?
## could more extensive clinical and engineering partnership to move things forward?
## we need to establish "bridges" between the two collaborating sides
## "cost centers" could be an example workable model
## new challenges: new acquisition techniques, longitudinal data sets
## it is important to also describe when and how things fail
## "computational steering": there is a need for interactive rigid and non-rigid registration tools; visualization is very important besides registration technique; can we borrow examples from the gaming industry? (can we validate certain results / outcomes with real-time feedback?)

===What is next? ===
People sign up for working on sections; smaller group will come up with an introduction and conclusion draft

2007 Programming/Project Week MIT

2007-06-18T06:59:59Z

Lzollei: /* Attendee List */

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007]]
== Logistics ==

'''Dates:''' June 25-29, 2007

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

'''Registration Fee:''' $200 (this will cover the cost of breakfast,lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

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

'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

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

===Introduction to NA-MIC Project Week===

This is a week of hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. A full week of hands on activities is held in the summer at MIT (typically the last week of June), and for half a week in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

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

=== Agenda===

* Monday June 25
** noon-1pm lunch
** 1-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
** 4:30-5:30pm [[Special topic breakout: New DBP Introduction to NA-MIC Engineering]]
* Tuesday June 26
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman, special guest speaker [http://www.boost-consulting.com/about/people David Abrahams] of [http://www.boost-consulting.com/ Boost Consulting])
** 10-10:30am Slicer 3.0 Update(Jim Miller, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1-2pm: [[Special topic breakout: KWWidgets]]
** 2-3pm: [[Special topic breakout: Non-Linear Registration]]
** 3-4pm: [[Special topic breakout: Atlases]]
** 4-5pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday June 27
** 8:30am breakfast
** noon lunch
** 1-2pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday June 28
** 8:30am breakfast
** noon lunch
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2008| in Utah the week of Jan 7, 2008]])

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## 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. (Andy)
# By 3pm ET on June 21, 2007: [[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.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# 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...

== Projects ==

=== Template ===

http://www.na-mic.org/Wiki/index.php/NA-MIC/Projects/Theme/Template - Please use this template intead of the 4-block ppts.

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:MIND | Longitudinal Classification of White Matter Lesions in Lupus]] (MIND/UNM)
#[[DBP2:JHU | Segmentation and Registration Tools for Robotic Prostate Interventions]] (JHU/Queen's)
#[[DBP2:UNC |Longitudinal MRI study of early brain development in neuropsychiatric disorder: UNC Autism Study]] (UNC)
#[[DBP2:Harvard|Velocardiofacial Syndrome (VCFS) as a genetic model for schizophrenia]] (Harvard)

===Structural Analysis===
#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)
#[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|vtkITK wrapper for rule based segmentation]] (John Melonakos GATech, Tauseef Rehman GATech, Brad Davis Kitware, Marek Kubicki BWH)

===Diffusion Image Analysis===
# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH)
#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)

===NA-MIC Kit===
#Slicer3
##[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
##[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
## [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
## [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Steve, Nicole, Alex, Curt)
## [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Luca, Steve, Dan)
## [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Bill Hoffman, Katie, Steve)
## [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
## [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Scalars and Tensors]] (Katharina, Sylvain, Steve)
## [[Projects/Slicer3/2007_Project_Week_Support for electron microscopy | Dendritic Spine Morphometrics]] (Bryan Smith)
# Slicer2

===External Collaborations===
# Meshing
## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
# Image-Guided Therapy
## [[Collaboration/BWH/Tracker Integration]] (Noby, Haiying, Katie Hayes BWH)
## [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
## [[Collaboration/JHU/Brachytherapy needle positioning robot integration|Brachytherapy needle positioning robot integration]] (Csaba Csoma, Peter Kazanzides JHU, David Gobbi Queen's, Katie Hayes BWH)
## [[Collaboration/BWH/RadVision and Tracker Integration|RadVision and Tracker Integration]] (Jack Blevins, Noby)
# Registration
## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)
# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)

===Non-Medical Collaborations===
* [[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)

==Attendee List==
#John Melonakos, Georgia Tech, Core 1
#Tauseef Rehman, Georgia Tech, Core 1
#Casey Goodlett, UNC, Core 1,
#Serdar K Balci, MIT, Core 1
#Elliot Uvero, MIT, Core 1
#Ran Tao, Utah, Core 1
#Kevin Teich, MGH, Core 1
#W. Bryan Smith, UCSD/NCMIR, Core 2
#Jeffrey Grethe, UCSD, Core 2
#Marco Ruiz, UCSD, Core 2
#Neil Jones, UCSD, Core 2
#Jim Miller, GE Core 2,
#Dan Blezek, GE Core 2
#Steve Pieper, Isomics, Core 2
#Alex Yarmarkovich, Isomics, Core 2
#Katie Hayes, BWH, Core 2
#Nicole Aucoin, BWH, Core 2
#Will Schroeder, Kitware, Core 2
#Yumin Yuan, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Luis Ibanez, Kitware, Core 2
#Bill Hoffman, Kitware, Core 2 (Mon, Tue)
#Sylvain Bouix, BWH, Core 3
#Marek Kubicki, BWH, Core 3
#Katharina Quintus, BWH, Core 3
#Marc Niethammer, BWH. Core 3
#Clement Vachet, UNC Core 3 (II)
#David Gobbi, Queen's University, Core 3 (II)
#Csaba Csoma, Johns Hopkins University, Core 3 (II)
#H. Jeremy Bockholt, The MIND Institute, Core 3 (II)
#Mark Scully, The MIND Institute, Core 3 (II)
#Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01
#Zack Galbreath, Kitware, Core 4 (Mon, Tue)
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
#Chris Wyatt, Virginia Tech, Collaborator R01
#Vincent Magnotta, University of Iowa, Collaborator R01
#Kiran Shivanna, University of Iowa, Collaborator R01
#Peter Kazanzides, JHU, Collaborator (Wed or Thurs)
#Luca Antiga, Mario Negri Institute, Collaborator
#Stephen Aylward, Kitware, Collaborator
#Douglas Alan, Harvard IIC, Collaborator
#Michael Halle, BWH/IIC, Collaborator
#Wendy Plesniak, BWH, Collaborator
#Kilian Pohl, BWH Collaborator
#Raimundo Sierra, BWH, Collaborator
#Lauren O'Donnell, BWH, Collaborator
#Raul San Jose, BWH, Collaborator
#Clare Tempany, BWH Collaborator (Tuesday, June 26th only)
#Noby Hata, BWH Collaborator (Monday, June 25th only)
#Haiying Liu, BWH Collaborator
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Kai Ding, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Skip Talbot, Northwestern University, Collaborator
#Alex Kogan, Northwestern University, Collaborator
#Vladimir Kleper, Northwestern University, Collaborator
#Pat Mongkolwat, Northwestern University, Collaborator
#Greg Sharp, MGH, Collaborator
#Lilla Zollei, MGH, Collaborator (Monday, Tuesday)
#James Ross, GE, Collaborator
#Alex Gouaillard, CEGS Caltech, Collaborator
#Sean Megason, CEGS caltech, Collaborator
#Clif Burdette, Acousticmed, Collaborator
#Jack Blevins, Acousticmed, Collaborator
No more attendees. We have reached capacity.

2007 Programming/Project Week MIT

2007-06-18T06:59:29Z

Lzollei: /* Attendee List */

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007]]
== Logistics ==

'''Dates:''' June 25-29, 2007

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

'''Registration Fee:''' $200 (this will cover the cost of breakfast,lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

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

'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

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

===Introduction to NA-MIC Project Week===

This is a week of hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. A full week of hands on activities is held in the summer at MIT (typically the last week of June), and for half a week in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

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

=== Agenda===

* Monday June 25
** noon-1pm lunch
** 1-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
** 4:30-5:30pm [[Special topic breakout: New DBP Introduction to NA-MIC Engineering]]
* Tuesday June 26
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman, special guest speaker [http://www.boost-consulting.com/about/people David Abrahams] of [http://www.boost-consulting.com/ Boost Consulting])
** 10-10:30am Slicer 3.0 Update(Jim Miller, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1-2pm: [[Special topic breakout: KWWidgets]]
** 2-3pm: [[Special topic breakout: Non-Linear Registration]]
** 3-4pm: [[Special topic breakout: Atlases]]
** 4-5pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday June 27
** 8:30am breakfast
** noon lunch
** 1-2pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday June 28
** 8:30am breakfast
** noon lunch
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2008| in Utah the week of Jan 7, 2008]])

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## 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. (Andy)
# By 3pm ET on June 21, 2007: [[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.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# 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...

== Projects ==

=== Template ===

http://www.na-mic.org/Wiki/index.php/NA-MIC/Projects/Theme/Template - Please use this template intead of the 4-block ppts.

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:MIND | Longitudinal Classification of White Matter Lesions in Lupus]] (MIND/UNM)
#[[DBP2:JHU | Segmentation and Registration Tools for Robotic Prostate Interventions]] (JHU/Queen's)
#[[DBP2:UNC |Longitudinal MRI study of early brain development in neuropsychiatric disorder: UNC Autism Study]] (UNC)
#[[DBP2:Harvard|Velocardiofacial Syndrome (VCFS) as a genetic model for schizophrenia]] (Harvard)

===Structural Analysis===
#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)
#[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|vtkITK wrapper for rule based segmentation]] (John Melonakos GATech, Tauseef Rehman GATech, Brad Davis Kitware, Marek Kubicki BWH)

===Diffusion Image Analysis===
# [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett UNC, Jim Miller GE, Marek Kubicki BWH)
#[[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos GATech, Marc Niethammer BWH, Marek Kubicki BWH)
# [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich)
# [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich)

===NA-MIC Kit===
#Slicer3
##[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
##[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
## [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
## [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Steve, Nicole, Alex, Curt)
## [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Luca, Steve, Dan)
## [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Bill Hoffman, Katie, Steve)
## [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
## [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Scalars and Tensors]] (Katharina, Sylvain, Steve)
## [[Projects/Slicer3/2007_Project_Week_Support for electron microscopy | Dendritic Spine Morphometrics]] (Bryan Smith)
# Slicer2

===External Collaborations===
# Meshing
## [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
## [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
# [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
# Image-Guided Therapy
## [[Collaboration/BWH/Tracker Integration]] (Noby, Haiying, Katie Hayes BWH)
## [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
## [[Collaboration/JHU/Brachytherapy needle positioning robot integration|Brachytherapy needle positioning robot integration]] (Csaba Csoma, Peter Kazanzides JHU, David Gobbi Queen's, Katie Hayes BWH)
## [[Collaboration/BWH/RadVision and Tracker Integration|RadVision and Tracker Integration]] (Jack Blevins, Noby)
# Registration
## [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
## [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
## [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
# [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek GE)
# [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
# [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)

===Non-Medical Collaborations===
* [[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)

==Attendee List==
#John Melonakos, Georgia Tech, Core 1
#Tauseef Rehman, Georgia Tech, Core 1
#Casey Goodlett, UNC, Core 1,
#Serdar K Balci, MIT, Core 1
#Elliot Uvero, MIT, Core 1
#Ran Tao, Utah, Core 1
#Kevin Teich, MGH, Core 1
#W. Bryan Smith, UCSD/NCMIR, Core 2
#Jeffrey Grethe, UCSD, Core 2
#Marco Ruiz, UCSD, Core 2
#Neil Jones, UCSD, Core 2
#Jim Miller, GE Core 2,
#Dan Blezek, GE Core 2
#Steve Pieper, Isomics, Core 2
#Alex Yarmarkovich, Isomics, Core 2
#Katie Hayes, BWH, Core 2
#Nicole Aucoin, BWH, Core 2
#Will Schroeder, Kitware, Core 2
#Yumin Yuan, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Luis Ibanez, Kitware, Core 2
#Bill Hoffman, Kitware, Core 2 (Mon, Tue)
#Sylvain Bouix, BWH, Core 3
#Marek Kubicki, BWH, Core 3
#Katharina Quintus, BWH, Core 3
#Marc Niethammer, BWH. Core 3
#Clement Vachet, UNC Core 3 (II)
#David Gobbi, Queen's University, Core 3 (II)
#Csaba Csoma, Johns Hopkins University, Core 3 (II)
#H. Jeremy Bockholt, The MIND Institute, Core 3 (II)
#Mark Scully, The MIND Institute, Core 3 (II)
#Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01
#Zack Galbreath, Kitware, Core 4 (Mon, Tue)
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
#Chris Wyatt, Virginia Tech, Collaborator R01
#Vincent Magnotta, University of Iowa, Collaborator R01
#Kiran Shivanna, University of Iowa, Collaborator R01
#Peter Kazanzides, JHU, Collaborator (Wed or Thurs)
#Luca Antiga, Mario Negri Institute, Collaborator
#Stephen Aylward, Kitware, Collaborator
#Douglas Alan, Harvard IIC, Collaborator
#Michael Halle, BWH/IIC, Collaborator
#Wendy Plesniak, BWH, Collaborator
#Kilian Pohl, BWH Collaborator
#Raimundo Sierra, BWH, Collaborator
#Lauren O'Donnell, BWH, Collaborator
#Raul San Jose, BWH, Collaborator
#Clare Tempany, BWH Collaborator (Tuesday, June 26th only)
#Noby Hata, BWH Collaborator (Monday, June 25th only)
#Haiying Liu, BWH Collaborator
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Kai Ding, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Skip Talbot, Northwestern University, Collaborator
#Alex Kogan, Northwestern University, Collaborator
#Vladimir Kleper, Northwestern University, Collaborator
#Pat Mongkolwat, Northwestern University, Collaborator
#Greg Sharp, MGH, Collaborator
#Lilla Zollei, MGH, Collaborator (monday, Tuesday)
#James Ross, GE, Collaborator
#Alex Gouaillard, CEGS Caltech, Collaborator
#Sean Megason, CEGS caltech, Collaborator
#Clif Burdette, Acousticmed, Collaborator
#Jack Blevins, Acousticmed, Collaborator
No more attendees. We have reached capacity.

Publications

2007-06-08T01:41:50Z

Lzollei: /* Peer Reviewed Conference Proceedings */

__NOTOC__
The following publications gratefully acknowledge the support of NA-MIC. Please see [[Publications:NIH_Roadmap_acknowledgement|'''NA-MIC acknowledgement instructions''']] for instructions on how to acknowledge NA-MIC in your publications.

= '''Search Medline'''=

The majority of our papers are listed in Medline. Please click the link below to see them.

[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=EB005149 Search Medline for NAMIC-enabled publications]

= '''Search the Insight Journal'''=

[http://www.insight-journal.org/InsightJournalManager/search.php?texte=namic%20OR%20na-mic%20OR%20EB005149&onlysponsors=1 Search the Insight Journal for NA-MIC enabled publications]

='''Publications not indexed by Medline'''=
'''Note: Many technical journals are not listed in Medline. Medline therefore only holds a subset of NA-MIC related refereed publications. The rest of this page contains publications that do not appear in Medline.'''

== Peer Reviewed Journal Papers ==

# Taylor WD, MacFall JR, Gerig G, Krishnan KR. Structural integrity of the uncinate fasciculus in geriatric depression: Relationship with age of onset. In press, Neuropsychiatric Disease and Treatment.
# Niethammer M, Vela P, Tannenbaum A. On the evolution of closed curves by means of vector distance functions. Int. Journal Computer Vision, 2006. [[Media:Niethammer_etal_VISI849-04I.pdf| PDF]]
# Niethammer M, Tannenbaum A, Angenent S. Dynamic active contours. IEEE Trans. Automatic Control. 2006; 51:562-579. [[Media:Niethammer_paper1.pdf| PDF]]
# Turner JA, Smyth P, Macciardi F, Fallon JH, Kennedy JL, Potkin SG. Imaging phenotypes and genotypes in schizophrenia. Neuroinformatics. 2006;4(1):21-49. [[Media:Media-Turner_paper.pdf| PDF]]
# Corouge I, Fletcher PT, Sarang J, Gouttard S, Gerig G. Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis. Medical Image Analysis), 768-798. [http://www.cs.unc.edu/~gerig/publications/Corouge-DTI-Original-MedIA-2006.pdf| PDF]
# Martin K, Hoffman B. An Open Source Approach to Developing Software in a Small Organization. IEEE Software. January/February 2007 (Vol. 24, No. 1).
# Rathi Y., Vaswani N., Tannenbaum A. Generic Framework for Tracking Using Particle Filter with Dynamic Shape Prior. IEEE Transactions on Image Processing. 2007: 16:1370-1382.
# Szymczak A., Stillman A., Mischaikow K. Tannenbaum A. Coronary Vessel Cores from 3D Imagery: A Topological Approach. Medical Image Analysis. 2006; 10:548-559.
# Angenent S., Pichon E., Tannenbaum A. Mathematical Methods in Medical Imaging. Bull. Amer. Math. Soc. 2006; 43: 365-396.
# Niethammer M, Tannenbaum A, Kalies W, Mischaikow K. Detecting simple points in higher dimensions. IEEE Trans. Image Processing, 2006. 15: 2462- 2469.

'''''In Press'''''
# Gilmore John H., Lin Weili, Corouge Isabelle, Vetsa Y. Sampath K., Smith J. Keith, Kang Chaeryon, Gu Hongbin, Hamer Robert M., Lieberman Jeffrey A., Gerig Guido, Early Postnatal Development of Corpus Callosum and Corticospinal White Matter Assessed with Quantitative Tractography, accepted AJNR- (American Journal of Neuroradiology), in print
# Liu T, Young G, Huang L, Chen N-K, Wong S. “76-space Analysis of Grey Matter Diffusivity: Methods and Applications,” in press, NeuroImage.
# O’Donnell L, Kubicki M, Shenton ME, Dreusicke MH, Grimson WEL, Westin CF. A method for clustering white matter fiber tracts. AJNR (In Press).
# Koo MS, Levitt JJ, McCarley RW, Seidman LJ, Dickey CC, Niznikiewicz MA, Voglmaier MM, Zamani P, Long KL, Kim SS, Shenton ME. Reduction of caudate volume in neuroleptic-naive female subjects with schizotypal personality disorder. Biol Psychiatry (In Press).
# Kuroki N, Kubicki M, Nestor PG, Salisbury DF, Park HJ, Levitt JJ, Woolston S, Frumin M, Niznikiewicz M, Westin CF, Maier SE, McCarley RW, Shenton ME. Fornix integrity and hippocampal volume in male schizophrenic patients. Biol Psychiatry (In Press).
# Onitsuka T, Niznikiewicz MA, Spencer KM, Frumin M, Kuroki N, Lucia LC, Shenton ME, McCarley RW. Schizophrenia is associated with functional and structural deficits in brain regions subserving face processing. Am J Psychiatry (In Press).
# Rathi Y, Dambreville S, Tannenbaum A. Comparative analysis of kernel methods for statistical shape learning. CVAMIA'06, 2006. (In Press).
# Roth RM, Koven, NS, Randolph JJ, Flashman LA, Pixley HS, Ricketts SM, Wishart HA, Saykin AJ. Event-Related fMRI study of Functional magnetic resonance imaging of executive control in bipolar disorder. NeuroReport, 2006 (In Press).
# Pohl KM, Fisher J, Grimson WEL, Kikinis R, Wells WM. [[Media:Pohl-ni-2006.pdf| A bayesian model for joint segmentation and registration.]] NeuroImage, 2006 (In Press).
# Fletcher PT, Joshi S. Riemannian Geometry for the Statistical Analysis of Diffusion Tensor Data. Signal Processing, 2006. (In Press).
#Keator, D.; Grethe, J.S.; Marcus, D.; Ozyurt, B.; Gadde, S.; Murphy, S.; Pieper, S.; Greve, D.; Notestine, R.; Bockholt, H.J; Papadopoulos, P.; Function BIRN; Morphometry BIRN; BIRNCoordinating Center. A National Human Neuroimaging Collaboratory Enabled By The Biomedical Informatics Research Network (BIRN). IEEE Transactions on Information Technology in Biomedicine Special Bio-Grid edition. 2006 (in press).
# Zhu L., Yang Y., Haker S., Tannenbaum A. An Image Morphing Technique Based on Optimal Mass Preserving Mapping. IEEE Trans. Image Processing. 2007. In Press.
# Melonakos J., Pichon E., Angenent S., Tannenbaum A. Finsler Active Contours. IEEE PAMI. 2007. In Press.
# Georgiou T., Michailovich O., Rathi Y., Tannenbaum A. Distribution Metrics and Image Segmentation. Linear Algebra and Its Applications, 2007. In Press.
# Rathi Y, Vaswani N, Tannenbaum A, Yezzi Y. Tracking Deforming Objects Using Particle Filtering for Geometric Active Contours. IEEE PAMI, 2007. In Press.

== Peer Reviewed Conference Proceedings ==

'''Conferences included here represent the major high quality conferences in medical image analysis (MICCAI, IPMI, MMBIA, ISBI). These conferences only accept submission of full papers and guarantee a peer review process by at least three reviewers and an area chair. Acceptance rates are below 40% for MICCAI, IPMI and MMBIA and around 50% for ISBI.'''

# Goodlett, Casey , Fletcher, P. Thomas , Lin, Weili , and Gerig, Guido, "Quantification of measurement error in DTI: Theoretical predictions and validation", in print MICCAI 2007, to appear Nov. 2007
# M. Maddah, W. M. Wells, S. K. Warfield, C.-F. Westin, and W. E. L. Grimson, Probabilistic Clustering and Quantitative Analysis of White Matter Fiber Tracts, IPMI 2007, Netherlands.
# G. M. Postelnicu, L. Zöllei, R. Desikan and B. Fischl, "Geometry Driven Volumetric Registration", IPMI 2007, Netherlands.
# L. Zöllei, M. Jenkinson, S. Timoner and W. M. Wells:"A marginalized MAP approach and EM optimization for pair-wise registration", IPMI 2007, Netherlands.
# Styner M, Xu SC, El-Sayed M, Gerig G, Correspondence Evaluation in Local Shape Analysis and Structural Subdivision, IEEE Symposium on Biomedical Imaging ISBI 2007, in print
# Zhou C, Park DC, Styner M, Wang YM, ROI Constrained Statistical Surface Morphometry, IEEE Symposium on Biomedical Imaging ISBI 2007, in print
# D. Nain, M. Styner, M. Niethammer, J. J. Levitt, M E Shenton, G Gerig, A. Bobick, A. Tannenbaum. Statistical Shape Analysis of Brain Structures using Spherical Wavelets. Accepted in The Fourth IEEE International Symposium on Biomedical Imaging (ISBI ’07), April 12-15, 2007, Washington DC, USA.
# Kim S, Smyth P. Hierarchical Dirichlet processes with random effects. Advances in Neural Information Processing Systems 19, to appear, 2006. [[Media:Nips_hMDP_RE.pdf| PDF ]]
# Kim S, Smyth P, Stern H. A nonparametric Bayesian approach to detecting spatial activation patterns in fMRI data. To appear in MICCAI, Oct 2-5, 2006.[[Media:InfMM_miccai.pdf| PDF ]]
# Nain D, Haker S, Bobick A, Tannenbaum A. Shape-driven surface segmentation using spherical wavelets. MICCAI, LNCS 4190, Oct 2-5, 2006.
# Goodlett C, Davis B, Jean R, Gilmore J, Gerig G. Improved Correspondence for DTI Population Studies via Unbiased Atlas Building. Proceedings of MICCAI, 2006. [[Media:Goodlett-miccai06.pdf| PDF]]
# Styner M, Jomier M, Gerig G: Closed and Open Source Neuroimage Analysis Tools and Libraries at UNC. IEEE Symposium on Biomedical Imaging ISBI. 2006; 702-705. [[Media:ISBI06_Neurolib.pdf| PDF ]]
# M. Maddah, W. E. L. Grimson, and S. Warfield, Statistical Modeling and EM Clustering of White Matter Fiber Tracts, ISBI 2006: IEEE 2006 International Symposium on Biomedical Imaging, Arlington, VA, April 6-9, 2006
# Gerig G, Joshi S, Fletcher T, Gorczowski K, Xu S, Pizer SM, Styner M. Statistics of populations of images and its embedded objects: Driving applications in neuroimaging. IEEE Symposium on Biomedical Imaging ISBI. 2006; 1120-1123.[[Media:ISBI06-GerigShape.pdf| PDF]]
# Pieper S, Lorensen W, Schroeder W, Kikinis R. [[Media:Pieper-ISBI-2006-revised.pdf| The NA-MIC Kit: ITK, VTK, Pipelines, Grids and 3D Slicer as An Open Platform for the Medical Image Computing Community.]] IEEE Symposium on Biomedical Imaging ISBI. 2006; 698-701.
# Pichon E, Westin CF, and Tannenbaum A. A Hamilton-Jacobi-Bellman approach to high angular diffusion tractography. Proceedings of MICCAI, 2005. [[Media:Pichon-miccai05.pdf| PDF]]
# Yang Y, Zhu L, Haker S, Tannenbaum A. On the harmonic skeleton and vessel data. Proceeedings of MICCAI, 2005. [[Media:YangMICCAI2005.pdf| PDF]]
# Styner M, Gimpel Smith R, Cascio C, Oguz I, Jomier M. Corpus Callosum Subdivision based on a Probabilistic Model of Inter-hemispheric Connectivity. Medical Image Computing and Computer Assisted Interventions MICCAI. 2005 LNCS 3750;765-772. [[Media:MICCAI05CCSubdiv.pdf| PDF]]
# Liu T, Young G, Huang L, Chen N-K, Wong S. “76-space Analysis of Grey Matter Diffusivity: Methods and Applications,” MICCAI 2005.[[Media:MICCAI-2005--461-Liu.pdf| PDF]]
# Pichon E, Tannenbaum A. Curve segmentation using directional information, relation to pattern detection. Proc IEEE International Conference on Image Processing (ICIP), 2005
# Nain D, Haker S, Bobick A, Tannenbaum A. [[Media:Nain.miccai2005.pdf| Multiscale 3D Shape Analysis using Spherical Wavelets]]. Proc MICCAI, LNCS 3750, Oct 26-29 2005; p 459-467.
# Corouge I, Fletcher PT, Joshi S, Gilmore JH, Gerig G. [[Media:Corouge-miccai-2005.pdf| Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis.]] Proc. MICCAI, Oct 26-29 2005; LNCS 3749, pp. 131-139
# Ou W, Golland P. From Spatial Regularization to Anatomical Priors in fMRI Analysis. Proc IPMI, Jul 10-15 2005; LNCS 3565: p 88-100. [[Media:OuGolland_IPMI2005.pdf| PDF]]
# Pohl KM, Fisher J, Levitt JJ, Shenton ME, Kikinis R, Grimson WEL, Wells WM. [[Media:Pohl-miccai-2005.pdf| A Unifying Approach to Registration, Segmentation, and Intensity Correction,]] In Proc. MICCAI 2005: Eigth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, Springer-Verlag, Part I, vol. 3749 of Lecture Notes in Computer Science, pp. 310-318, 2005
# Pohl KM, Bouix S, Shenton ME, Grimson WEL, Kikinis R. [[Media:Pohl-miccai-short-2005.pdf| Automatic Segmentation Using Non-Rigid Registration,]] In short communications of MICCAI 2005: Eighth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, 2005
# Martin-Fernandez M, Bouix S, Ungar L, McCarley RW, Shenton ME. Two Methods for Validating Brain Tissue Classifiers. MICCAI 2005, Palm Springs, CA, USA: Duncan J and Gerig G (Eds.): Lecture Notes in Computer Science, volume 3749, pp 515-522, 2005. Springer-Verlag Berlin Heidelberg, 2005. [[Media:Martin-fernandezMICCAI05.pdf| PDF]]
# Kim S, Smyth P, Stern H, Turner J. Parametric response surface models for analysis of multi-site fMRI data. In Proc. MICCAI 2005: Eighth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, Springer-Verlag, Part I, vol. 3749 of Lecture Notes in Computer Science, pp. 352-359, 2005. [[Media:Seyoung-official.pdf|PDF]]
# O'Donnell L, Westin C-F. White Matter Tract Clustering and Correspondence in Populations. MICCAI 2005, Palm Springs, CA, USA: Duncan J, Gerig G (Eds.): Lecture Notes in Computer Science, volume 3749, pp 140-147, 2005. Springer-Verlag Berlin Heidelberg, 2005. [[Media:OdonnellMICCAI05.pdf| PDF]]
# M. Maddah, A. Mewes, S. Haker, W. E. L. Grimson, and S. Warfield, Automated Atlas-Based Clustering of White Matter Fiber Tracts from DTMRI. MICCAI05, Palm Spring, CA,: Lecture Notes in Computer Science, volume 3749, pp. 188-195, 2005.
# Goodlett C, Fletcher PT, Lin W, and Gerig G. Noise-induced bias in low-direction diffusion tensor MRI: Replication of Monte-Carlo simulation with in-vivo scans. Accepted ISMRM 2007.
# M. Styner, I. Oguz, S. Xu, D. Pantazis, and G. Gerig. Statistical group differences in anatomical shape analysis using hotelling T2 metric. Proc SPIE Medical Imaging Conference, in print, 2007.
# Rathi Y, Olver P, Sapiro G, Tannenbaum A. Affine Invariant Surface Evolutions for 3D Image Segmentation, SPIE 2006
# Rathi Y, Dambreville S, Tannenbaum A. Comparative Analyis of Kernel Methods for Statistical Shape Learning, 2nd Workshop on Computer Vision Approaches to Medical Image Analysis (in conjunction with ECCV) 2006.
# Eric Pichon, Delphine Nain, and Marc Niethammer. [[Media:Pichon-SPIEMI2006-laplace.pdf| A Laplace Equation Approach for Shape Comparison]]. Proc SPIE Medical Imaging, 2006.
# Al-Hakim R, Fallon J, Nain D, Melonakos J, Tannenbaum A. [[Media:Dlpfc-SPIE2006-full.pdf| A Dorsolateral Prefrontal Cortex Semi-Automatic Segmenter]]. Proc SPIE Medical Imaging, 2006.
# Pohl KM, Fisher J, Kikinis R, Grimson WEL, Wells WM. [[Media:Pohl-iccv-ws-2005.pdf| Shape Based Segmentation of Anatomical Structures in Magnetic Resonance Images,]] In Proc. ICCV 2005: Computer Vision for Biomedical Image Applications: Current Techniques and Future Trend, An International Conference on Computer Vision Workshop, Beijing, China, Springer-Verlag, vol. 3765 of Lecture Notes in Computer Science, 2005
# Zöllei L, Learned-Miller E, Grimson WEL, Wells WM III. Efficient Population Registration of 3D Data. Proc ICCV 2005, Computer Vision for Biomedical Image Applications; Beijing, China
# O'Donnell L, Westin C-F. A High-Dimensional Fiber Tract Atlas. accepted to ISMRM 2006.
# Zöllei L, Wells WM III. Multi-modal Image Registration Using Dirichlet-encoded Prior Information. oral presentation at WBIR06
# Fletcher PT, Whitaker RT. Riemannian Metrics on the Space of Solid Shapes. accepted to MICCAI'06 Workshop on Mathematical Foundations of Computational Anatomy (MFCA).
# Cates J, Meyer M, Fletcher PT, Whitaker R. Entropy-Based Particle Systems for Shape Correspondence. accepted to MICCAI'06 Workshop on Mathematical Foundations of Computational Anatomy (MFCA).
# D. Nain, M. Styner, M. Niethammer, J. Levitt, M. Shenton, G. Gerig, A. Tannenbaum. Statistical Shape Analysis of Brain Structures Using Spherical Wavelets. ISBI'07. 2007.
# J. Malcolm , Y. Rathi, A. Tannenbaum, Graph Cut Segmentation with Nonlinear Shape Priors. ICIP`07. In Press.
# O. Michailovich and A. Tannenbaum. Segmentation of Medical Ultrasound Images Using Active Contours. ICIP`07. In Press.
# J. Melonakos, V. Mohan, A. Tannenbaum. Finsler Tractography for White Matter Connectivity Analysis of Cingulum Bundle. MICCAI'07. In Press.
# Y. Rathi, J. Malcolm, A. Tannenbaum. Segmenting Images on the Tensor Manifold. CVPR'07. In Press.

== Book Chapters ==

# Nain D, Tannenbaum A, Unal G, Yezzi A, Zeitouni O. On a stochastic model of geometric snakes. Mathematical Methods in Computer Vision: A Handbook, edited by Faugeras O, Paragios N, Springer-Verlag, 2005.
# Angenent S, Tannenbaum A, Yezzi A, Zeitouni O. Curve shortening and interacting particle systems. Book chapter in a volume edited by Hamid Krim, 2005.
#S. Bouix, K. Siddiqi, A. Tannenbaum, and S. Zucker. Medial axis computation and evolution. Statistics and Analysis of Shape edited by Hamid Krim and A. Yezzi, Birhauser, 2006, pages 1-29.
# S. Dambreville, Y. Rathi, and A. Tannenbaum. A shape-based approach to robust image segmentation. Image Analysis and Recognition, Lecture Notes in Computer Science volume 4141 (2006), pp. 173-183.
# Y. Rathi, S. Dambreville, A. Tannenbaum. Particle filtering with dynamic shape priors. Image Analysis and Recognition, Lecture Notes in Computer Science 4141 (2006), pp. 886-897.

== Submitted and in Preparation ==

# Flashman LA, Roth RM, Pixley HS, Cleavinger HB, Saykin AJ, McAllister TW, Vidaver RM. (submitted). Cavum septum pellucidum in schizophrenia: Clinical and neuropsychological correlates.
# Szymczak A, Tannenbaum A, Stillman A. 3D models of airway trees from CT scans: a point-based approach. submitted to IEEE Trans. Medical Imaging, 2006.
# Michailovich O, Tanenbaum A. Fast approximation of smooth functions from samples of partial derivatives. Submitted for publication to IEEE Signal Processing, 2006.
# Gorczowski K, Gerig G, Fletcher T, Pizer SM, Styner M. Statistics of Pose and Shape in Multi-Object Complexes using Principal Geodesic Analysis. submitted to MICCAI, 2006.
# Gribbin M, Clement M, Muller K, Poe M, Cascio C, Jomier M, Piven J, Gerig G. Statistical analysis of diffusion tensor image data based on first principles, submitted MICCAI'06, March 2006
# Flashman LA, Roth RM, Koven NS, McAllister TW, Vidaver RM, Pendergrass JC. Neural Correlates of Self-Evaluation in Individuals with Schizophrenia. in preparation.
# Basu S, Fletcher PT, Whitaker RT. Rician Noise Removal in Diffusion Tensor MRI, to appear MICCAI'06.
# Han X, Fischl B. Intensity Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms, submitted to IEEE Transactions on Medical Imaging.
# Voineskos AN, Zai G, Bulgin N, Shaikh S, Lang D, Honer WG, Kennedy JL. MAG but not CNP Gene Associated with Total Brain White Matter. In Preparation. Presented in Part at World Congress of Psychiatric Genetics Annual Meeting. October, 2006.
# Michailovich O., Tannenbaum A. Image Segmentation Using Active Contours Driven by Information-Based Criteria. Submitted to IEEE Trans. Image Processing, 2006.
# Michailovich O., Rathi Y., Tannenbaum A. Blind Deconvolution of Medical Ultrasound Images: Parametric Inverse Filtering Approach. Submitted to IEEE Trans. Image Processing, 2007.

==List of publications from other NCBCs:==
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=RR021813 Search Medline for CCB-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=lm008748 Search Medline for I2B2-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=gm072970 Search Medline for SIMBIOS-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=DA021519 Search Medline for NCIBI-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=CA121852 Search Medline for C2B2-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=HG004028 Search Medline for Bioontology-enabled publications]

Publications

2007-06-07T22:37:40Z

Lzollei: /* Peer Reviewed Conference Proceedings */

__NOTOC__
The following publications gratefully acknowledge the support of NA-MIC. Please see [[Publications:NIH_Roadmap_acknowledgement|'''NA-MIC acknowledgement instructions''']] for instructions on how to acknowledge NA-MIC in your publications.

= '''Search Medline'''=

The majority of our papers are listed in Medline. Please click the link below to see them.

[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=EB005149 Search Medline for NAMIC-enabled publications]

= '''Search the Insight Journal'''=

[http://www.insight-journal.org/InsightJournalManager/search.php?texte=namic%20OR%20na-mic%20OR%20EB005149&onlysponsors=1 Search the Insight Journal for NA-MIC enabled publications]

='''Publications not indexed by Medline'''=
'''Note: Many technical journals are not listed in Medline. Medline therefore only holds a subset of NA-MIC related refereed publications. The rest of this page contains publications that do not appear in Medline.'''

== Peer Reviewed Journal Papers ==

# Taylor WD, MacFall JR, Gerig G, Krishnan KR. Structural integrity of the uncinate fasciculus in geriatric depression: Relationship with age of onset. In press, Neuropsychiatric Disease and Treatment.
# Niethammer M, Vela P, Tannenbaum A. On the evolution of closed curves by means of vector distance functions. Int. Journal Computer Vision, 2006. [[Media:Niethammer_etal_VISI849-04I.pdf| PDF]]
# Niethammer M, Tannenbaum A, Angenent S. Dynamic active contours. IEEE Trans. Automatic Control. 2006; 51:562-579. [[Media:Niethammer_paper1.pdf| PDF]]
# Turner JA, Smyth P, Macciardi F, Fallon JH, Kennedy JL, Potkin SG. Imaging phenotypes and genotypes in schizophrenia. Neuroinformatics. 2006;4(1):21-49. [[Media:Media-Turner_paper.pdf| PDF]]
# Corouge I, Fletcher PT, Sarang J, Gouttard S, Gerig G. Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis. Medical Image Analysis), 768-798. [http://www.cs.unc.edu/~gerig/publications/Corouge-DTI-Original-MedIA-2006.pdf| PDF]
# Martin K, Hoffman B. An Open Source Approach to Developing Software in a Small Organization. IEEE Software. January/February 2007 (Vol. 24, No. 1).
# Nain D, Haker S, Bobick A, Tannenbaum A. Multiscale 3D Shape Representation and Segmentation using Spherical Wavelets. IEEE Transactions on Medical Imaging Special issue on Computational Anatomy. 2007; 26:598-618.
# Rathi Y., Vaswani N., Tannenbaum A. Generic Framework for Tracking Using Particle Filter with Dynamic Shape Prior. IEEE Transactions on Image Processing. 2007: 16:1370-1382.
# Szymczak A., Stillman A., Mischaikow K. Tannenbaum A. Coronary Vessel Cores from 3D Imagery: A Topological Approach. Medical Image Analysis. 2006; 10:548-559.
# Angenent S., Pichon E., Tannenbaum A. Mathematical Methods in Medical Imaging. Bull. Amer. Math. Soc. 2006; 43: 365-396.
# Niethammer M, Tannenbaum A, Kalies W, Mischaikow K. Detecting simple points in higher dimensions. IEEE Trans. Image Processing, 2006. 15: 2462- 2469.

'''''In Press'''''
# Gilmore John H., Lin Weili, Corouge Isabelle, Vetsa Y. Sampath K., Smith J. Keith, Kang Chaeryon, Gu Hongbin, Hamer Robert M., Lieberman Jeffrey A., Gerig Guido, Early Postnatal Development of Corpus Callosum and Corticospinal White Matter Assessed with Quantitative Tractography, accepted AJNR- (American Journal of Neuroradiology), in print
# Liu T, Young G, Huang L, Chen N-K, Wong S. “76-space Analysis of Grey Matter Diffusivity: Methods and Applications,” in press, NeuroImage.
# O’Donnell L, Kubicki M, Shenton ME, Dreusicke MH, Grimson WEL, Westin CF. A method for clustering white matter fiber tracts. AJNR (In Press).
# Koo MS, Levitt JJ, McCarley RW, Seidman LJ, Dickey CC, Niznikiewicz MA, Voglmaier MM, Zamani P, Long KL, Kim SS, Shenton ME. Reduction of caudate volume in neuroleptic-naive female subjects with schizotypal personality disorder. Biol Psychiatry (In Press).
# Kuroki N, Kubicki M, Nestor PG, Salisbury DF, Park HJ, Levitt JJ, Woolston S, Frumin M, Niznikiewicz M, Westin CF, Maier SE, McCarley RW, Shenton ME. Fornix integrity and hippocampal volume in male schizophrenic patients. Biol Psychiatry (In Press).
# Onitsuka T, Niznikiewicz MA, Spencer KM, Frumin M, Kuroki N, Lucia LC, Shenton ME, McCarley RW. Schizophrenia is associated with functional and structural deficits in brain regions subserving face processing. Am J Psychiatry (In Press).
# Rathi Y, Dambreville S, Tannenbaum A. Comparative analysis of kernel methods for statistical shape learning. CVAMIA'06, 2006. (In Press).
# Roth RM, Koven, NS, Randolph JJ, Flashman LA, Pixley HS, Ricketts SM, Wishart HA, Saykin AJ. Event-Related fMRI study of Functional magnetic resonance imaging of executive control in bipolar disorder. NeuroReport, 2006 (In Press).
# Pohl KM, Fisher J, Grimson WEL, Kikinis R, Wells WM. [[Media:Pohl-ni-2006.pdf| A bayesian model for joint segmentation and registration.]] NeuroImage, 2006 (In Press).
# Fletcher PT, Joshi S. Riemannian Geometry for the Statistical Analysis of Diffusion Tensor Data. Signal Processing, 2006. (In Press).
#Keator, D.; Grethe, J.S.; Marcus, D.; Ozyurt, B.; Gadde, S.; Murphy, S.; Pieper, S.; Greve, D.; Notestine, R.; Bockholt, H.J; Papadopoulos, P.; Function BIRN; Morphometry BIRN; BIRNCoordinating Center. A National Human Neuroimaging Collaboratory Enabled By The Biomedical Informatics Research Network (BIRN). IEEE Transactions on Information Technology in Biomedicine Special Bio-Grid edition. 2006 (in press).
# Zhu L., Yang Y., Haker S., Tannenbaum A. An Image Morphing Technique Based on Optimal Mass Preserving Mapping. IEEE Trans. Image Processing. 2007. In Press.
# Melonakos J., Pichon E., Angenent S., Tannenbaum A. Finsler Active Contours. IEEE PAMI. 2007. In Press.
# Georgiou T., Michailovich O., Rathi Y., Tannenbaum A. Distribution Metrics and Image Segmentation. Linear Algebra and Its Applications, 2007. In Press.
# Rathi Y, Vaswani N, Tannenbaum A, Yezzi Y. Tracking Deforming Objects Using Particle Filtering for Geometric Active Contours. IEEE PAMI, 2007. In Press.

== Peer Reviewed Conference Proceedings ==

'''Conferences included here represent the major high quality conferences in medical image analysis (MICCAI, IPMI, MMBIA, ISBI). These conferences only accept submission of full papers and guarantee a peer review process by at least three reviewers and an area chair. Acceptance rates are below 40% for MICCAI, IPMI and MMBIA and around 50% for ISBI.'''

# Goodlett, Casey , Fletcher, P. Thomas , Lin, Weili , and Gerig, Guido, "Quantification of measurement error in DTI: Theoretical predictions and validation", in print MICCAI 2007, to appear Nov. 2007
# M. Maddah, W. M. Wells, S. K. Warfield, C.-F. Westin, and W. E. L. Grimson, Probabilistic Clustering and Quantitative Analysis of White Matter Fiber Tracts, IPMI 2007, Netherlands.
# G. M. Postelnicu, L. Zöllei and B. Fischl, "Geometry Driven Volumetric Registration", IPMI 2007, Netherlands.
# L. Zöllei, M. Jenkinson, S. Timoner and W. M. Wells:"A marginalized MAP approach and EM optimization for pair-wise registration", IPMI 2007, Netherlands.
# Styner M, Xu SC, El-Sayed M, Gerig G, Correspondence Evaluation in Local Shape Analysis and Structural Subdivision, IEEE Symposium on Biomedical Imaging ISBI 2007, in print
# Zhou C, Park DC, Styner M, Wang YM, ROI Constrained Statistical Surface Morphometry, IEEE Symposium on Biomedical Imaging ISBI 2007, in print
# D. Nain, M. Styner, M. Niethammer, J. J. Levitt, M E Shenton, G Gerig, A. Bobick, A. Tannenbaum. Statistical Shape Analysis of Brain Structures using Spherical Wavelets. Accepted in The Fourth IEEE International Symposium on Biomedical Imaging (ISBI ’07), April 12-15, 2007, Washington DC, USA.
# Kim S, Smyth P. Hierarchical Dirichlet processes with random effects. Advances in Neural Information Processing Systems 19, to appear, 2006. [[Media:Nips_hMDP_RE.pdf| PDF ]]
# Kim S, Smyth P, Stern H. A nonparametric Bayesian approach to detecting spatial activation patterns in fMRI data. To appear in MICCAI, Oct 2-5, 2006.[[Media:InfMM_miccai.pdf| PDF ]]
# Nain D, Haker S, Bobick A, Tannenbaum A. Shape-driven surface segmentation using spherical wavelets. MICCAI, LNCS 4190, Oct 2-5, 2006.
# Goodlett C, Davis B, Jean R, Gilmore J, Gerig G. Improved Correspondence for DTI Population Studies via Unbiased Atlas Building. Proceedings of MICCAI, 2006. [[Media:Goodlett-miccai06.pdf| PDF]]
# Styner M, Jomier M, Gerig G: Closed and Open Source Neuroimage Analysis Tools and Libraries at UNC. IEEE Symposium on Biomedical Imaging ISBI. 2006; 702-705. [[Media:ISBI06_Neurolib.pdf| PDF ]]
# M. Maddah, W. E. L. Grimson, and S. Warfield, Statistical Modeling and EM Clustering of White Matter Fiber Tracts, ISBI 2006: IEEE 2006 International Symposium on Biomedical Imaging, Arlington, VA, April 6-9, 2006
# Gerig G, Joshi S, Fletcher T, Gorczowski K, Xu S, Pizer SM, Styner M. Statistics of populations of images and its embedded objects: Driving applications in neuroimaging. IEEE Symposium on Biomedical Imaging ISBI. 2006; 1120-1123.[[Media:ISBI06-GerigShape.pdf| PDF]]
# Pieper S, Lorensen W, Schroeder W, Kikinis R. [[Media:Pieper-ISBI-2006-revised.pdf| The NA-MIC Kit: ITK, VTK, Pipelines, Grids and 3D Slicer as An Open Platform for the Medical Image Computing Community.]] IEEE Symposium on Biomedical Imaging ISBI. 2006; 698-701.
# Pichon E, Westin CF, and Tannenbaum A. A Hamilton-Jacobi-Bellman approach to high angular diffusion tractography. Proceedings of MICCAI, 2005. [[Media:Pichon-miccai05.pdf| PDF]]
# Yang Y, Zhu L, Haker S, Tannenbaum A. On the harmonic skeleton and vessel data. Proceeedings of MICCAI, 2005. [[Media:YangMICCAI2005.pdf| PDF]]
# Styner M, Gimpel Smith R, Cascio C, Oguz I, Jomier M. Corpus Callosum Subdivision based on a Probabilistic Model of Inter-hemispheric Connectivity. Medical Image Computing and Computer Assisted Interventions MICCAI. 2005 LNCS 3750;765-772. [[Media:MICCAI05CCSubdiv.pdf| PDF]]
# Liu T, Young G, Huang L, Chen N-K, Wong S. “76-space Analysis of Grey Matter Diffusivity: Methods and Applications,” MICCAI 2005.[[Media:MICCAI-2005--461-Liu.pdf| PDF]]
# Pichon E, Tannenbaum A. Curve segmentation using directional information, relation to pattern detection. Proc IEEE International Conference on Image Processing (ICIP), 2005
# Nain D, Haker S, Bobick A, Tannenbaum A. [[Media:Nain.miccai2005.pdf| Multiscale 3D Shape Analysis using Spherical Wavelets]]. Proc MICCAI, LNCS 3750, Oct 26-29 2005; p 459-467.
# Corouge I, Fletcher PT, Joshi S, Gilmore JH, Gerig G. [[Media:Corouge-miccai-2005.pdf| Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis.]] Proc. MICCAI, Oct 26-29 2005; LNCS 3749, pp. 131-139
# Ou W, Golland P. From Spatial Regularization to Anatomical Priors in fMRI Analysis. Proc IPMI, Jul 10-15 2005; LNCS 3565: p 88-100. [[Media:OuGolland_IPMI2005.pdf| PDF]]
# Pohl KM, Fisher J, Levitt JJ, Shenton ME, Kikinis R, Grimson WEL, Wells WM. [[Media:Pohl-miccai-2005.pdf| A Unifying Approach to Registration, Segmentation, and Intensity Correction,]] In Proc. MICCAI 2005: Eigth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, Springer-Verlag, Part I, vol. 3749 of Lecture Notes in Computer Science, pp. 310-318, 2005
# Pohl KM, Bouix S, Shenton ME, Grimson WEL, Kikinis R. [[Media:Pohl-miccai-short-2005.pdf| Automatic Segmentation Using Non-Rigid Registration,]] In short communications of MICCAI 2005: Eighth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, 2005
# Martin-Fernandez M, Bouix S, Ungar L, McCarley RW, Shenton ME. Two Methods for Validating Brain Tissue Classifiers. MICCAI 2005, Palm Springs, CA, USA: Duncan J and Gerig G (Eds.): Lecture Notes in Computer Science, volume 3749, pp 515-522, 2005. Springer-Verlag Berlin Heidelberg, 2005. [[Media:Martin-fernandezMICCAI05.pdf| PDF]]
# Kim S, Smyth P, Stern H, Turner J. Parametric response surface models for analysis of multi-site fMRI data. In Proc. MICCAI 2005: Eighth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, Springer-Verlag, Part I, vol. 3749 of Lecture Notes in Computer Science, pp. 352-359, 2005. [[Media:Seyoung-official.pdf|PDF]]
# O'Donnell L, Westin C-F. White Matter Tract Clustering and Correspondence in Populations. MICCAI 2005, Palm Springs, CA, USA: Duncan J, Gerig G (Eds.): Lecture Notes in Computer Science, volume 3749, pp 140-147, 2005. Springer-Verlag Berlin Heidelberg, 2005. [[Media:OdonnellMICCAI05.pdf| PDF]]
# M. Maddah, A. Mewes, S. Haker, W. E. L. Grimson, and S. Warfield, Automated Atlas-Based Clustering of White Matter Fiber Tracts from DTMRI. MICCAI05, Palm Spring, CA,: Lecture Notes in Computer Science, volume 3749, pp. 188-195, 2005.
# Goodlett C, Fletcher PT, Lin W, and Gerig G. Noise-induced bias in low-direction diffusion tensor MRI: Replication of Monte-Carlo simulation with in-vivo scans. Accepted ISMRM 2007.
# M. Styner, I. Oguz, S. Xu, D. Pantazis, and G. Gerig. Statistical group differences in anatomical shape analysis using hotelling T2 metric. Proc SPIE Medical Imaging Conference, in print, 2007.
# Rathi Y, Olver P, Sapiro G, Tannenbaum A. Affine Invariant Surface Evolutions for 3D Image Segmentation, SPIE 2006
# Rathi Y, Dambreville S, Tannenbaum A. Comparative Analyis of Kernel Methods for Statistical Shape Learning, 2nd Workshop on Computer Vision Approaches to Medical Image Analysis (in conjunction with ECCV) 2006.
# Eric Pichon, Delphine Nain, and Marc Niethammer. [[Media:Pichon-SPIEMI2006-laplace.pdf| A Laplace Equation Approach for Shape Comparison]]. Proc SPIE Medical Imaging, 2006.
# Al-Hakim R, Fallon J, Nain D, Melonakos J, Tannenbaum A. [[Media:Dlpfc-SPIE2006-full.pdf| A Dorsolateral Prefrontal Cortex Semi-Automatic Segmenter]]. Proc SPIE Medical Imaging, 2006.
# Pohl KM, Fisher J, Kikinis R, Grimson WEL, Wells WM. [[Media:Pohl-iccv-ws-2005.pdf| Shape Based Segmentation of Anatomical Structures in Magnetic Resonance Images,]] In Proc. ICCV 2005: Computer Vision for Biomedical Image Applications: Current Techniques and Future Trend, An International Conference on Computer Vision Workshop, Beijing, China, Springer-Verlag, vol. 3765 of Lecture Notes in Computer Science, 2005
# Zöllei L, Learned-Miller E, Grimson WEL, Wells WM III. Efficient Population Registration of 3D Data. Proc ICCV 2005, Computer Vision for Biomedical Image Applications; Beijing, China
# O'Donnell L, Westin C-F. A High-Dimensional Fiber Tract Atlas. accepted to ISMRM 2006.
# Zöllei L, Wells WM III. Multi-modal Image Registration Using Dirichlet-encoded Prior Information. oral presentation at WBIR06
# Fletcher PT, Whitaker RT. Riemannian Metrics on the Space of Solid Shapes. accepted to MICCAI'06 Workshop on Mathematical Foundations of Computational Anatomy (MFCA).
# Cates J, Meyer M, Fletcher PT, Whitaker R. Entropy-Based Particle Systems for Shape Correspondence. accepted to MICCAI'06 Workshop on Mathematical Foundations of Computational Anatomy (MFCA).
# D. Nain, M. Styner, M. Niethammer, J. Levitt, M. Shenton, G. Gerig, A. Tannenbaum. Statistical Shape Analysis of Brain Structures Using Spherical Wavelets. ISBI'07. 2007.
# J. Malcolm , Y. Rathi, A. Tannenbaum, Graph Cut Segmentation with Nonlinear Shape Priors. ICIP`07. In Press.
# O. Michailovich and A. Tannenbaum. Segmentation of Medical Ultrasound Images Using Active Contours. ICIP`07. In Press.
# J. Melonakos, V. Mohan, A. Tannenbaum. Finsler Tractography for White Matter Connectivity Analysis of Cingulum Bundle. MICCAI'07. In Press.
# Y. Rathi, J. Malcolm, A. Tannenbaum. Segmenting Images on the Tensor Manifold. CVPR'07. In Press.

== Book Chapters ==

# Nain D, Tannenbaum A, Unal G, Yezzi A, Zeitouni O. On a stochastic model of geometric snakes. Mathematical Methods in Computer Vision: A Handbook, edited by Faugeras O, Paragios N, Springer-Verlag, 2005.
# Angenent S, Tannenbaum A, Yezzi A, Zeitouni O. Curve shortening and interacting particle systems. Book chapter in a volume edited by Hamid Krim, 2005.
#S. Bouix, K. Siddiqi, A. Tannenbaum, and S. Zucker. Medial axis computation and evolution. Statistics and Analysis of Shape edited by Hamid Krim and A. Yezzi, Birhauser, 2006, pages 1-29.
# S. Dambreville, Y. Rathi, and A. Tannenbaum. A shape-based approach to robust image segmentation. Image Analysis and Recognition, Lecture Notes in Computer Science volume 4141 (2006), pp. 173-183.
# Y. Rathi, S. Dambreville, A. Tannenbaum. Particle filtering with dynamic shape priors. Image Analysis and Recognition, Lecture Notes in Computer Science 4141 (2006), pp. 886-897.

== Submitted and in Preparation ==

# Flashman LA, Roth RM, Pixley HS, Cleavinger HB, Saykin AJ, McAllister TW, Vidaver RM. (submitted). Cavum septum pellucidum in schizophrenia: Clinical and neuropsychological correlates.
# Szymczak A, Tannenbaum A, Stillman A. 3D models of airway trees from CT scans: a point-based approach. submitted to IEEE Trans. Medical Imaging, 2006.
# Michailovich O, Tanenbaum A. Fast approximation of smooth functions from samples of partial derivatives. Submitted for publication to IEEE Signal Processing, 2006.
# Gorczowski K, Gerig G, Fletcher T, Pizer SM, Styner M. Statistics of Pose and Shape in Multi-Object Complexes using Principal Geodesic Analysis. submitted to MICCAI, 2006.
# Gribbin M, Clement M, Muller K, Poe M, Cascio C, Jomier M, Piven J, Gerig G. Statistical analysis of diffusion tensor image data based on first principles, submitted MICCAI'06, March 2006
# Flashman LA, Roth RM, Koven NS, McAllister TW, Vidaver RM, Pendergrass JC. Neural Correlates of Self-Evaluation in Individuals with Schizophrenia. in preparation.
# Basu S, Fletcher PT, Whitaker RT. Rician Noise Removal in Diffusion Tensor MRI, to appear MICCAI'06.
# Han X, Fischl B. Intensity Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms, submitted to IEEE Transactions on Medical Imaging.
# Yu P, Grant P, Qi Y, Han X, Ségonne F, Pienaar R, Busa E, Pacheco J, Makris N, Buckner R, Golland P, Fischl B. Cortical Surface Shape Analysis Based on Spherical Wavelets, submitted to IEEE Transactions on Medical Imaging
# Ségonne F, Pacheco J, Fischl B. Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops, submitted to IEEE Transactions on Medical Imaging
# Voineskos AN, Zai G, Bulgin N, Shaikh S, Lang D, Honer WG, Kennedy JL. MAG but not CNP Gene Associated with Total Brain White Matter. In Preparation. Presented in Part at World Congress of Psychiatric Genetics Annual Meeting. October, 2006.
# Michailovich O., Tannenbaum A. Image Segmentation Using Active Contours Driven by Information-Based Criteria. Submitted to IEEE Trans. Image Processing, 2006.
# Michailovich O., Rathi Y., Tannenbaum A. Blind Deconvolution of Medical Ultrasound Images: Parametric Inverse Filtering Approach. Submitted to IEEE Trans. Image Processing, 2007.

==List of publications from other NCBCs:==
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=RR021813 Search Medline for CCB-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=lm008748 Search Medline for I2B2-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=gm072970 Search Medline for SIMBIOS-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=DA021519 Search Medline for NCIBI-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=CA121852 Search Medline for C2B2-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=HG004028 Search Medline for Bioontology-enabled publications]

2007 Core 1 Meeting

2007-05-29T19:51:11Z

Lzollei: /* Attendees */

== Agenda ==

*May 30 -
** 8:30am Remarks (Whitaker)
*** Introductions
*** Discuss goals and agenda
** 9:00am Driving Biological problems '''[[2007_Core_1_Meeting_DBP_Guidlines|(Guidelines for talks)]]'''
*** Marek Kubicki - Harvard/B&W
*** Gabor Fichtinger - Johns Hopkins
*** (break)
*** H. Jeremy Bockholt - Mind Institute
*** Heather Cody Hazlett - UNC
**11:30pm Core 1 Coordinate Discussion
*** A preliminary discussion in preparation for agenda items on Thurs afternoon. For example --- software dissemination.
**12:00pm Lunch
** 1:00pm Invited Talk: Daniel Rueckert. "Quantification of brain development during early childhood using non-rigid registration". ([http://www.csail.mit.edu/events/eventcalendar/calendar.php?show=event&id=1484 talk announcement])
** 2:00pm Break out sessions with DPBs
** 3:30pm Break
** 3:45-6:00pm Core 1 presentations
*** John Melonakos (Georgia Tech) - TBD
*** Bruce Fischl (MGH) "Predicting architectonic boundaries from folding patterns"
*** MIT Serdar Balci TBA
*** UNC Guido Gerig TBA
*** Tom Fletcher (Utah), "Volumetric Connectivity for analysis of DTI"
*May 31
** 8:30am Core 1 presentations
*** Utah "Nonparametric Shape Modeling of Object Complexes" (Speaker TBD)
*** UNC Guido Gerig TBD
*** (break)
*** Mert Sabuncu (MIT), "Population Analysis of Anatomical Variability"
*** Gheorghe Postelnicu (MGH), "5D warping: integrating volume and surface information"
*** John Melonakos (Georgia Tech) - TBD
** 12:30pm Lunch
** 1pm Strategic planning, software
*** Progress/interactions with DBPs
*** Software contributions and Core 2 interactions
*** Performance assessment and renewal
** 5pm Finish

== Logistics ==

'''Dates:''' May 30-31, 2007.

Please plan to travel on May 29, so that we can start in the morning of May 30.
The meeting will be two full days; please plan to stay until 5pm on May31.

'''Location:''' MIT.

The meeting will take place in the Kiva conference room, on the 4th floor of Stata Center. We will post signs in the building, directing you to the conference room.

'''Food:''' Breakfast and lunch will be provided on May 30-31. We will also organize people into groups to go out for dinner on May 30. There are plenty of restaurants around Central Square and MIT.

'''Hotel:''' There is no official hotel for the meeting. Here is some information about Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Please book your rooms early.

== Attendees ==

#Ross Whitaker (Utah)
#Polina Golland (MIT)
#Ron Kikinis (BWH)
#Guido Gerig(UNC)
#Heather Cody Hazlett (UNC Autism DBP)
#Allen Tannenbaum (Georgia Tech)
#John Melonakos (Georgia Tech)
#H. Jeremy Bockholt (MIND/UNM)
#Harvard Core 3: Marek Kubicki
#Mert R Sabuncu (MIT CSAIL)
#Lilla Zollei (NMR, MGH)
#Serdar K Balci (MIT CSAIL)
#Ulas Ziyan (MIT)
#Tom Fletcher (Utah)
#Josh Cates (Utah - tentative)
#Gabor Fichtinger (JHU)
#Jim Miller (GE Research)
#Dennis Jen (MGH)
#Sandy Wells (BWH, MIT)
#Marc Niethammer (BWH, Core 3)
#Wanmei Ou (MIT)
# Purang Abolmaesumi (Queen's)
# Steve Pieper (Isomics, Core 2)
# Peng Yu (HST/MIT)
# Gheorghe Postelnicu (MGH)

2007 Core 1 Meeting

2007-05-29T19:50:56Z

Lzollei: /* Attendees */

2007 Programming/Project Week MIT

2007-05-28T14:26:32Z

Lzollei: /* Attendee List */

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007]]
== Logistics ==

'''Dates:''' June 25-29, 2007

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

'''Registration Fee:''' $200 (this will cover the cost of breakfast,lunch, and coffee breaks for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

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

'''Hotel:''' We have a group rate of $209/night at the [http://www.hotelatmit.com Hotel at MIT]. (Use group code NAM.) Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.

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

===Introduction to NA-MIC Project Week===

This is a week of hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. A full week of hands on activities is held in the summer at MIT (typically the last week of June), and for half a week in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

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

=== Agenda===
Please note that this agenda is a draft and will be finalized by June 15th.

* Monday June 25
** noon-1pm lunch
** 1-3:30pm 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 June 26
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process (Bill Hoffman)
** 10-10:30am Slicer 3.0 Update(Jim Miller, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1-2pm: [[Special topic breakout: KWWidgets]]
** 2-3pm: [[Special topic breakout: Non-Linear Registration]]
** 3-4pm: [[Special topic breakout: Atlases]]
** 4-5pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday June 27
** 8:30am breakfast
** noon lunch
** 1-2pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday June 28
** 8:30am breakfast
** noon lunch
** 3:30-5pm Special topic breakout: TBD
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## 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. (Andy)
# By 3pm ET on June 21, 2007: [[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.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# 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...

== Projects ==

=== Template ===

http://www.na-mic.org/Wiki/index.php/NA-MIC/Projects/Theme/Template - Please use this template intead of the 4-block ppts.

===DBP II===
These are projects by the new set of DBPS:
*[[DBP2:MIND | Longitudinal Classification of White Matter Lesions in Lupus]] (MIND/UNM)
*[[DBP2:JHU | Segmentation and Registration Tools for Robotic Prostate Interventions]] (JHU/Queen's)
*[[DBP2:UNC |Longitudinal MRI study of early brain development in neuropsychiatric disorder: UNC Autism Study]] (UNC)
*[[DBP2:Harvard|Velocardiofacial Syndrome (VCFS) as a genetic model for schizophrenia]] (Harvard)

===Structural Analysis===
*[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis, Sylvain Bouix)
*[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|vtkITK wrapper for rule based segmentation]] (John Melonakos, Brad Davis, Marek Kubicki)

===Diffusion Image Analysis===
* [[Projects/Diffusion/2007_Project_Week_DTI_Population_Analysis| DTI population analysis]] (Casey Goodlett, Jim Miller)
* [[Projects/Diffusion/2007_Project_Week_Geodesic_Tractography| Geodesic Tractography]] (John Melonakos, Marc Niethammer, Marek Kubicki)
* [[Projects/Diffusion/2007_Project_Week_Slicer 3 Whole Brain Seeding|Slicer3 Whole brain Seeding platform: data representation and pipeline execution]] (Raul San Jose, Lauren O'Donnell, Alex Y.)
* [[Projects/Diffusion/2007_Project_Week_Slicer3 Tractography Editor|Slicer 3 Tractography Editor]] (Lauren O'Donnell, Raul San Jose, Alex Y.)

===NA-MIC Kit===
* Slicer3
**[[Projects/Slicer3/2007_Project_Week_QDEC_Slicer3_Integration|QDEC Integration into Slicer3]](Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
**[[Projects/Slicer3/2007_Project_Week_Display_Optimization| Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
** [[Projects/Slicer3/2007_Project_Week_MRML_Scenes_for_the_Execution_Model_including Transforms|MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
** [[Projects/Slicer3/2007_Project_Week_Support for Unstructured Grids|Support for Unstructured Grids]] (Steve, Nicole, Alex, Curt)
** [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Luca, Steve, Dan)
** [[Projects/Slicer3/2007_Project_Week_CPack, Ctest infrastructure improvements|CPack, CTest infrastructure Improvements]] (Bill Hoffman, Katie, Steve)
** [[Projects/Slicer3/2007_Project_Week_Drafting Human Interface and Slicer Style|Drafting Human Interface and Slicer Style]] Guidelines (Wendy,Yumin)
** [[Projects/Slicer3/2007_Project_Week_Slicer Matlab Pipeline for scalars and tensors|Slicer Matlab Pipeline for Scalars and Tensors]] (Katharina, Sylvain, Steve)
* Slicer2

===External Collaborations===
* Meshing
** [[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]] (Will, Vince, Kiran, Curt)
** [[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]] (Vince, Stephen)
*IGT
** [[Collaboration/BWH/Tracker Integration]] (Noby, Haiying, Katie Hayes BWH)
** [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
** [[Collaboration/JHU/Brachytherapy needle positioning robot integration|Brachytherapy needle positioning robot integration]] (Csaba Csoma, Peter Kazanzides JHU, David Gobbi Queen's, Katie Hayes BWH)
** [[Collaboration/BWH/RadVision and Tracker Integration|RadVision and Tracker Integration]] (Jack Blevins, Noby)
* Registration
** [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
** [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe, Wendy)
** [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
* [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek(GE))
* [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
* [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
* [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)

===Non-Medical Collaborations===
* [[Collaboration/Harvard IIC/AstroMed]] (Michael Halle, Douglas Alan)

==Attendee List==
#Kilian Pohl, BWH, Core 1
#John Melonakos, Georgia Tech, Core 1, (Hotel at MIT request)
#Tauseef Rehman, Georgia Tech, Core 1
#Casey Goodlett, UNC, Core 1, (Hotel at MIT request)
#W. Bryan Smith, UCSD/NCMIR, Core 2
#Jim Miller, GE Core 2, Booked at the Hotel At MIT
#Steve Pieper, Isomics, Core 2
#Katie Hayes, BWH, Core 2
#Dan Blezek, GE Core 2, Booked at the Hotel At MIT
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
#Peter Kazanzides, JHU, Collaborator
#Wendy Plesniak, BWH, Collaborator
#Luca Antiga, Mario Negri Institute, Collaborator
#Sylvain Bouix, BWH, Core 3
#Marek Kubicki, BWH, Core 3
#Chris Wyatt, Virginia Tech, Collaborator
#Nicole Aucoin, BWH, Core 2
#Will Schroeder, Kitware, Core 2
#Yumin Yuan, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Stephen Aylward, Kitware, Collaborator
#Luis Ibanez, Kitware, Core 2
#Bill Hoffman, Kitware, Core 2
#Raimundo Sierra, BWH, Core 2
#Clare Tempany, BWH Collaborator (Tuesday, June 26th only)
#Noby Hata, BWH Collaborator (Monday, June 25th only)
#Haiying Liu, BWH Collaborator
#Alex Yarmarkovich, Isomics, Core 2
#Vincent Magnotta, University of Iowa, Collaborator (Hotel at MIT request)
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Kai Ding, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Skip Talbot, Northwestern University, Collaborator (Hotel at MIT request)
#Alex Kogan, Northwestern University, Collaborator (Hotel at MIT request)
#Vladimir Kleper, Northwestern University, Collaborator (Hotel at MIT request)
#Pat Mongkolwat, Northwestern University, Collaborator (Hotel at MIT request)
#Csaba Csoma, Johns Hopkins University, Collaborator (Hotel at MIT request)
#David Gobbi, Queen's University, Collaborator (Hotel at MIT request)
#H. Jeremy Bockholt, The MIND Institute, DBP2:MIND PI
#Mark Scully, The MIND Institute, DBP2:MIND software engineer
#Sumner Williams, The MIND Institute, Magnotta/Johnson/Bockholt BRAINS grant software engineer
#Greg Sharp, MGH, Collaborator
#Lauren O'Donnell, BWH
#Raul San Jose, BWH
#Katharina Quintus, BWH, Core 3
#Marc Niethammer, BWH. Core 3
#Kevin Teich, MGH
#Michael Halle, BWH/IIC
#James Ross, GE
#Kiran Shivanna, University of Iowa, Collaborator (Hotel at MIT request)
#Douglas Alan, Harvard IIC
#Heather Cody Hazlett, UNC Core 3 (only part of week) (Hotel @ MIT request)
#Clement Vachet, UNC Core 3 (CS programmer) - full week (Hotel @ MIT request)
#Rachel G. Smith, UNC Core 3 (image lab manager) - tentative (may not be full week) (Hotel @ MIT request)
#Ran Tao, Utah, Core 1
#Alex. Gouaillard, CEGS caltech Software Engineer, QuadEdgeMesh project Lead (ITK)
#Sean Megason, CEGS caltech PI, (not full week)
#Clif Burdette (Acousticmed, Collaborator)
#Jack Blevins (Acousticmed, Collaborator)
#Lilla Zollei (MGH)

2007 Core 1 Meeting

2007-05-01T19:53:15Z

Lzollei: /* Attendees */

== Agenda ==

*May 30 -
** 8:30am Driving Biological problems
*** Talks '''[[2007_Core_1_Meeting_DBP_Guidlines|(Guidelines)]]'''
*** 15-20 min each with time for questions/discussion
**12:00pm Lunch
** 1:00pm Invited Talk: Daniel Rueckert
** 1:45pm Break out sessions with DPBs
** 4:00pm Core 1 presentations
** 6:00 pm finish
*May 31
** 8:30am Core 1 presentations
** 12pm Lunch
** 1pm Strategic planning, software
*** Progress/interactions with DBPs
*** Software contributions and Core 2 interactions
*** Performance assessment and renewal
** 5pm Finish

== Logistics ==

'''Dates:''' May 30-31, 2007.

Please plan to travel on May 29, so that we can start in the morning of May 30.
The meeting will be two full days; please plan to stay until 5pm on May31.

'''Location:''' MIT.

The meeting will take place in the Kiva conference room, on the 4th floor of Stata Center. We will post signs in the building, directing you to the conference room.

'''Food:''' Breakfast and lunch will be provided on May 30-31. We will also organize people into groups to go out for dinner on May 30. There are plenty of restaurants around Central Square and MIT.

'''Hotel:''' There is no official hotel for the meeting. Here is some information about Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Please book your rooms early.

== Attendees ==

* Ross Whitaker
* Polina Golland
* Ron Kikinis
* UNC Core 1: Martin Styner (tentatively), Guido Gerig
* UNC Core 3: Heather Cody
* Allen Tannenbaum
* John Melonakos
* H. Jeremy Bockholt (MIND/UNM)
* Harvard Core 3: Marek Kubicki
* Mert R Sabuncu (MIT CSAIL)
* Lilla Zollei (NMR, MGH)

P41-2007-Joint-Retreat

2007-01-24T19:43:29Z

Lzollei: /* 11.00-12.30 MGH */

=Joint Retreat =
* What is the objective
**To familiarize the others with the ongoing activties in the respective cores
**To identify opportunities for leverage and augmentation
* Who:
**The MGH Center for Functional Imaging Technologies
**The BWH Neuroimage Analysis Center
**Core PI's for the two centers plus not more than 2 people per core
* Where:
**MIT Stata CEnter, Seminar Room G449 (Patil Conference Room / Kiva)
* When:
**Monday, Jan. 29, 11am-5pm

=Agenda=
==11.00-12.30 MGH==
**Bruce Rosen
**Bruce Fischl
**David Boas
**Larry Wald
**Matti Hamalainen
**Lilla Zollei
*12.30-01.00 pm Break

==01.10-02.30 BWH==
**Ron Kikinis
**Sandy Wells
**CF Westin
**Andrea Mewes
**Mike Halle
**Domink Meier
**Steve Pieper
**Florin Talos

==02.30-03.00 Break==
*03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)
*04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)

=Participants=
#Ron Kikinis, PI, NAC
#Steve Pieper
#Bruce Fischl
#David Boas
#Larry Wald
#Matti Hamalainen
#Bruce Rosen