NAMIC Wiki - User contributions [en]

2008 Summer Project Week

2008-06-11T15:10:31Z

Pkazanzides: /* Attendee List */

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

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

== Logistics ==

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

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

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

'''Registration Method''' Please add your name to the attendee list below (create namic wiki account if you don't have one, by clicking on the "login/create account" link on the top right corner of this page), and then mail a check to Donna Kaufman at the address above.

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

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

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

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

==Introduction to NA-MIC Project Week==

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

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

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

== Preparation ==

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

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

== A History in Wiki Links ==

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

== Projects ==

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

===Other Projects===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#Integraton of groupwise b-spline registration into atlas building (Casey Goodlett, Serdar Balci)
# CVS / SVN auto synchronization
# 3D Widgets in Slicer
## Issues with existing widgets
## Design of new widgets
# Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
# Module Chaining (Marco, Jim, Steve, Dan B., Luca)
# Nonlinear transforms (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# Slicer3, XNAT integration, and desigining XCEDE Web Services (Dan M., Steve, Julien, Dan B.)
## Review and enrich use cases
# Python in Slicer (Dan B., Michael Halle, Steve, Luca)
# Performance Tuning of Fiducials using the EventBroker and other tools (Nicole, Alex, Steve, Will)
# GUI Tweaking (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]
# [[2008_Summer_Project_Week:fMRIconnectivity|fMRI connectivity]] (Bryce Kim, MIT)

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#[[NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Lung Atlas]] (Gary Christensen Group)
#Non-rigid image registration (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
#FMA (Protege) links to Slicer (Vish, Mike, Florin, Jim, Steve, Wendy)
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]]
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga)
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)

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

==Attendee List==
# Ron Kikinis, BWH
# Carl-Fredrik Westin, BWH
# Gary Christensen, The University of Iowa
# Jeffrey Hawley, Gary Christensen's student
# Kate Raising, Gary Christensen's student
# Nathan Fritze, Gary Christensen's student
# Paul Song, Gary Christensen's student
# Cheng Zhang, Gary Christensen's student
# Ying Wei, Gary Christensen's student
# Nathan Burnette, The University of Iowa
# Hans Johnson, The University of Iowa
# Vincent Magnotta, The University of Iowa
# Keith Gunderson, The University of Iowa
# Steve Pieper, Isomics, Core 2/6
# Dana C. Peters, BIDMC Harvard Medical
# Jason Taclas, BIDMC Harvard Medical
# Nicole Aucoin, BWH, Core 2
# Will Schroeder, Kitware, Cores 2/4
# Sebastien Barre, Kitware, Core 2
# Julien Jomier, Kitware, Core 2
# Luis Ibanez, Kitware, Core 2
# Curtis Lisle, KnowledgeVis, Core 2
# Katie Hayes, BWH, Core 2
# Randy Gollub, MGH, Core 5
# Clement Vachet, UNC, Core 3
# Zhexing Liu, UNC, Core 1/3
# Casey Goodlett, Utah, Core 1
# Marcel Prastawa, Utah, Core 1
# Jeffrey Grethe, UCSD, Core 2
# Marco Ruiz, UCSD, Core 2
# Zhen Qian, Rutgers University
# Jinghao Zhou, Rutgers University
# Luca Antiga, Mario Negri Institute
# Adam Wittek, The University of Western Australia
# Grand Joldes, The University of Western Australia
# Jamie Berger, The University of Western Australia
# Serdar Balci, MIT, Core 1
# Bryce Kim, MIT, Core1
# Tina Kapur, BWH, Core 6
# Carling Cheung, Robarts Research Institute / The University of Western Ontario
# Danielle Pace, Robarts Research Institute / The University of Western Ontario
# Sean Megason, Dept of Systems Biology, Harvard Medical School
# Alex Gouaillard, Dept of Systems Biology, Harvard Medical School
# Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School
# Arnaud Gelas, Dept of Systems Biology, Harvard Medical School
# Sonia Pujol, Surgical Planning Laboratory, BWH
# Bjoern Menze, (then) Surgical Planning Laboratory, BWH
# Alex Yarmarkovich, Isomics, Core 2
# Sylvain Bouix, BWH, Core 3
# Priya Srinivasan, BWH, Core 3
# Chris Churas, UCSD, Core 2
# John Melonakos, Georgia Tech, Core 1
# Yi Gao, Georgia Tech, Core 1
# Tauseef Rehman, Georgia Tech, Core 1
# Clare Poynton, MIT, Core 1
# H. Jeremy Bockholt, MRN Lupus DBP Core 3
# Mark Scully, MRN Lupus DBP Core 3
# Gabor Fichtinger, Queen's, Core 3
# David Gobbi, Queen's, Core 3
# Purang Abolmaesumi, Queen's, Core 3, June 23-25
# Siddharth Vikal, Queen's, Core 3
# Daniel Blezek, Mayo
# Csaba Csoma, JHU, Core 3
# Ran Tao, University of Utah, Core 1
# Jim Miller, GE Research, Core 2
# Xiaodong Tao, GE Research, Core 2
# Dirk Padfield, GE Research, Core 2
# Viswanath Avasarala, GE Research, NAC
# Dan Marcus, Washington University (Monday - Wednesday)
# Tim Olsen, Washington University (Monday - Wednesday)
# Kevin Archie, Washington University (Monday - Wednesday)
# Misha Milchenko, Washington University (Monday - Wednesday)
# Wendy Plesniak, BWH, Core 2
# Demian Wasserman, INRIA, LMI-collaborator
# Xenophon Papademetris, Yale, Collaborator
# Xenophon P's postdoc, Yale, Collaborator
# Xenophon P's student, Yale, Collaborator
# Vidya Rajagopalan, Virginia Tech, Student of Chris Wyatt, External Collaborator
# Greg Sharp, MGH, External Collaborator
# Marta Peroni, MGH, External Collaborator
# Toru Higaki, Hiroshima Univ., Japan, External collaborator (Hata)
# Jacek Kukluk, BWH,
# Nobuhiko Hata, BWH
# Junichi Tokuda, BWH
# Haying Liu, BWH
# Ragini Verma, UPenn (June 24)
# Luke Bloy, UPenn (Ragini Verma's student) (June 24)
# Yang Li, UPenn (Ragini's postdoc) (June 24)
# Jack Blevins, Acoustic Med, Collaborator
# Nikos Chrisochoides, College of William and Mary, External collaborator (June 23)
# Andriy Fedorov, College of William and Mary, External collaborator
# Carlos Sánchez Mendoza, BWH
# Kilian Pohl, BWH
# Pratik Patel, Brainlab, Collaborator
# Marianna Jakab, BWH
# Nathan Hageman, UCLA
# Douglas Alan, Harvard IIC, External Collaborator
# Tammy Riklin Raviv, MIT
# Peter Kazanzides, JHU, Collaborator (June 24)
# Scott Hoge, BWH, (Wed, Jun 25)
#*WE HAVE REACHED CAPACITY. REGISTRATION IS CLOSED. [[User:Tkapur|Tkapur]] 19:42, 6 June 2008 (UTC)

==Pictures==

2008 Summer Project Week

2008-06-06T03:02:09Z

Pkazanzides:

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

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

== Logistics ==

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

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

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

'''Registration Method''' Please add your name to the attendee list below (create namic wiki account if you don't have one, by clicking on the "login/create account" link on the top right corner of this page), and then mail a check to Donna Kaufman at the address above.

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

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

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

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

==Introduction to NA-MIC Project Week==

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

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

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

== Preparation ==

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

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

== A History in Wiki Links ==

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

== Projects ==

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

===Other Projects===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#Integraton of groupwise b-spline registration into atlas building (Casey Goodlett, Serdar Balci)
# CVS / SVN auto synchronization
# 3D Widgets in Slicer
## Issues with existing widgets
## Design of new widgets
# Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
# Module Chaining (Marco, Jim, Steve, Dan B., Luca)
# Nonlinear transforms (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# Slicer3, XNAT integration, and desigining XCEDE Web Services (Dan M., Steve, Julien)
## Review and enrich use cases
# Python in Slicer (Dan B., Michael Halle, Steve, Luca)
# Performance Tuning of Fiducials using the EventBroker and other tools (Nicole, Alex, Steve, Will)
# GUI Tweaking (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#NIREP: Non-rigid Image Registration Evaluation (Gary Christensen Group)
#Lung Atlas (Gary Christensen Group)
#Non-rigid image registration (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
#FMA (Protege) links to Slicer (Vish, Mike, Florin, Jim, Steve, Wendy)
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]]
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga)
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)

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

==Attendee List==
# Ron Kikinis, BWH
# Carl-Fredrik Westin, BWH
# Gary Christensen, The University of Iowa
# Jeffrey Hawley, Gary Christensen's student
# Kate Raising, Gary Christensen's student
# Nathan Fritze, Gary Christensen's student
# Paul Song, Gary Christensen's student
# Cheng Zhang, Gary Christensen's student
# Ying Wei, Gary Christensen's student
# Nathan Burnette, The University of Iowa
# Hans Johnson, The University of Iowa
# Vincent Magnotta, The University of Iowa
# Keith Gunderson, The University of Iowa
# Steve Pieper, Isomics, Core 2/6
# Dana C. Peters, BIDMC Harvard Medical
# Jason Taclas, BIDMC Harvard Medical
# Nicole Aucoin, BWH, Core 2
# Will Schroeder, Kitware, Cores 2/4
# Sebastien Barre, Kitware, Core 2
# Julien Jomier, Kitware, Core 2
# Luis Ibanez, Kitware, Core 2
# Curtis Lisle, KnowledgeVis, Core 2
# Katie Hayes, BWH, Core 2
# Randy Gollub, MGH, Core 5
# Clement Vachet, UNC, Core 3
# Zhexing Liu, UNC, Core 1/3
# Casey Goodlett, Utah, Core 1
# Marcel Prastawa, Utah, Core 1
# Jeffrey Grethe, UCSD, Core 2
# Marco Ruiz, UCSD, Core 2
# Zhen Qian, Rutgers University
# Jinghao Zhou, Rutgers University
# Luca Antiga, Mario Negri Institute
# Adam Wittek, The University of Western Australia
# Grand Joldes, The University of Western Australia
# Jamie Berger, The University of Western Australia
# Serdar Balci, MIT, Core 1
# Bryce Kim, MIT, Core1
# Tina Kapur, BWH, Core 6
# Carling Cheung, Robarts Research Institute / The University of Western Ontario
# Danielle Pace, Robarts Research Institute / The University of Western Ontario
# Sean Megason, Dept of Systems Biology, Harvard Medical School
# Alex Gouaillard, Dept of Systems Biology, Harvard Medical School
# Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School
# Arnaud Gelas, Dept of Systems Biology, Harvard Medical School
# Sonia Pujol, Surgical Planning Laboratory, BWH
# Bjoern Menze, (then) Surgical Planning Laboratory, BWH
# Alex Yarmarkovich, Isomics, Core 2
# Sylvain Bouix, BWH, Core 3
# Priya Srinivasan, BWH, Core 3
# Chris Churas, UCSD, Core 2
# John Melonakos, Georgia Tech, Core 1
# Yi Gao, Georgia Tech, Core 1
# Tauseef Rehman, Georgia Tech, Core 1
# Clare Poynton, MIT, Core 1
# H. Jeremy Bockholt, MRN Lupus DBP Core 3
# Mark Scully, MRN Lupus DBP Core 3
# Gabor Fichtinger, Queen's, Core 2
# David Gobbi, Queen's, Core 2
# Purang Abolmaesumi, Queen's, Core 2
# Siddharth Vikal, Queen's, Core 2
# Daniel Blezek, Mayo
# Csaba Csoma, JHU, Core 2
# Ran Tao, University of Utah, Core 1
# Jim Miller, GE Research, Core 2
# Xiaodong Tao, GE Research, Core 2
# Dirk Padfield, GE Research, Core 2
# Viswanath Avasarala, GE Research, NAC
# Dan Marcus, Washington University
# Tim Olsen, Washington University
# Kevin Archie, Washington University
# Misha Milchenko, Washington University
# Wendy Plesniak, BWH, Core 2
# Demian Wasserman, INRIA, LMI-collaborator
# Xenophon Papademetris, Yale, Collaborator
# Xenophon P's postdoc, Yale, Collaborator
# Xenophon P's student, Yale, Collaborator
# Vidya Rajagopalan, Virginia Tech, Student of Chris Wyatt, External Collaborator
# Greg Sharp, MGH, External Collaborator
# Marta Peroni, MGH, External Collaborator
# Toru Higaki, Hiroshima Univ., Japan, External collaborator (Hata)
# Jacek Kukluk, BWH,
# Nobuhiko Hata, BWH
# Junichi Tokuda, BWH
# Haying Liu, BWH
# Ragini Verma, UPenn (June 24)
# Luke Bloy, UPenn (Ragini Verma's student) (June 24)
# Yang Li, UPenn (Ragini's postdoc) (June 24)
# Jack Blevins, Acoustic Med, Collaborator
# Nikos Chrisochoides, College of William and Mary, External collaborator (June 23)
# Andriy Fedorov, College of William and Mary, External collaborator
# Carlos Sánchez Mendoza, BWH
# Kilian Pohl, BWH
# Pratik Patel, Brainlab, Collaborator
# Marianna Jakab, BWH
# Nathan Hageman, UCLA
# Douglas Alan, Harvard IIC, External Collaborator
# Tammy Riklin Raviv, MIT
# Peter Kazanzides, JHU, Collaborator

==Pictures==

2007 December Slicer IGT Programming

2007-12-13T16:38:16Z

Pkazanzides: /* 1000-10:30am Demonstrations */

__NOTOC__
=Dates.Location.Hotels=
December 12-14, 2007

SPL at 1249 Boylston Street, Boston MA. ([http://www.spl.harvard.edu/Directions#Getting_to_1249_Boylston_Street Directions])

Area hotels: [[Boston_Hotels]]

=Goal=
*Continued [[Leadership:SlicerIGT_2007|'''discussion''']] of Slicer IGT infrastructure, applications, and timelines
*Introduce each team's effort in Slicer in the context of IGT
*active funding&future submissions
*on-going technical development
*find unmet needs
*find how we can share the work
*Learning IGSK-Slicer
*Interface to scanners

=Agenda=
==Wednesday, December 12 ==
'''Theme: Where are we?'''
*12noon: lunch
*12:55pm: Welcome (Ron Kikinis)
*1-2pm:
**Slicer: overview of architecture, current status, and future plans (Pieper, Hata)
***History
***Clinical applications
***transition from 2.6 to 3
***resource
***[[media:Pieper-IGT-retreat-2007-12-12.ppt | Slicer Core]] + [[Slicer3:Loadable_Modules | Loadable Modules]]
**IGSTK
*** [[Media:IGSTK-Architecture-IGT-Meeting-Dec-12-2007.ppt‎|Architecture Overview]] (Ibanez)
*** Current status, and future plans (Cheng) [http://public.kitware.com/IGSTKWIKI/index.php/Design_Discussion Refactoring Design Discussion]
***IGSTK has time stamping for tracker and event.
***Monitors to ensure the minimal latency between display and data acquisition (possible take away from IGSTK to Slicer).
***works on FLTK, Qt

*215-330pm: Setting goals for meeting: Each IGT group present what they want to achieve at this meeting.
**2:30-3:00pm - NCIGT CIGL Stoll and Demo
**3:00-3:15 - NA-MIC Collaborator Georgetown Cleary/Yaniv
**3:15-3:30 - NA-MIC DBP Queens/JHU Gobbi/Csoma/Kazanzides
*3:30pm-3:45pm: Review of today's progress
** Did you find what the others are doing with Slicer?

Adjourn
*4-6pm (optional) demonstration of Slicer for control and display of MRI scanner (prostate module) @Advanced MRI center, 221 Longwood
**See [[2007_December_Slicer_IGT_Programming_MRI_DEMO| slicer-MRI demo]]

==Thursday, December 13==
===Morning===

Theme: Where are we?'''
*9:00am breakfast, start work

===9-10:00am Demos:===
*Hata (Tracking at BWH)
*Freudling (Pieper) (Volume rendering)

===1000-10:30am Demonstrations===
**[[Media:Neuro-Dec07.pdf‎|Robot-assisted neurosurgery with Slicer ]] (Kazanzides)
**Robot connected to Slicer via Robot control unit (with Real time OS)
**Slicer CT coords != Stealthstation CT coords
**Needs rasToIjk matrix from xml file
**Inter-computer communication

*Slicer 3 IGT update

===10:30am: Identifying the unmet needs===
(At this point, representatives from each site should start thinking which part of the unment needs they can take primary responsibility, and take home as homework.)

#Queens: NA-MIC DBP
#JHU: BRP
#BWH: NCIGT etc.
#Georgetown: Liver RF
#Kitware-BWH

*Identify the unique needs in IGT
*Identify commonality among the projects
*which one is to be covered by actively funded project?

*Identity and prioritize unmet needs
*Find commonality among the needs, consolidate if necessary
*Identify 2x three focus groups for afternoon

====List 1====
** Plug-in mechanism
** Data/communication/event...
*** Data Workflow I/O
*** ticking and latency management
*** Threads to read-in tracker info
*** Special DICOM and PACS
*** Priority control of events? -> Event Manager
*** Realtime needs
*** Inter-communication mechanism to/from Slicer

** GUI
*** GUI-Workflow (see [[Slicer3:IGTdesign| possible topics for discussion ]]) (David)
*** human interface
*** Overlay of tools in 2D view of Slicer

** Testing/Quality assurance, GUI Testing (Slicer), Tracker Testing (Robot)

====List 2====
** Inter-communication mechanism to/from Slicer
** Volume rendering
** Abdominal registration
** (Regulartory approval) (Legal issue/ form / guideline)

===12:00-1pm First round of break out session===
(topics to be decided in the morning session)

Report template

http://wiki.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming:report-template

===1pm: lunch===

===Afternoon===

*1:30-2:30pm Second round of break-out session (topics to be decided in the morning session)
*3-4pm: Coffee break (and NA-MIC TCON)
*3-4pm: session leaders put together reports in wiki

*4:00 review of outcome from break out sessions

*5pm: Review day and plan for Friday (Hata)

*5:30pm: adjourn

==Friday, December 14==
----
*9:00am: breakfast, work
*9:00-10:00am
*Identify the homework for each team (NCIGT, NA-MIC, Georgetown, Queens, JHU)
*Identify the new initiative, i.e. new funding: who will do what
*review this meeting
*discuss how we can continue this effort in what way.
*Plan for Hands on IGT Week

*11:15am-noon: Wrapup/Suggestion to NAC, NCIGT, NAC, and ultimately NIH(Hata)
*noon: adjourn and head out to group lunch

----

==Confirmed Attendees==
#Noby Hata, BWH (NCIGT)
#Steve Pieper, Isomics - (All Days) (NAMIC, NAC)
#Patrick Cheng, Georgetown (NAMIC Collab)
#Ziv Yaniv, Georgetown (NAMIC Collab)
#Kevin Cleary, Georgetown (Wed only) (NAMIC Collab)
#Luis Ibanez, Kitware (NAMIC)
#Sebastien Barre, Kitware (NCIGT)
#Stephen Aylward, Kitware (NCIGT)
#Jeff Stoll (except Thursday), BWH/CIMIT (NCIGT)
#Haiying Liu, BWH (NCIGT)
#Katie Hayes, BWH (NAC)
#Peter Kazanzides (except Friday), JHU (NAMIC Collab)
#Csaba Csoma, JHU (NAMIC/NCIGT Collab)
#David Gobbi, Queens (NAMIC/NCIGT Collab)
#Tina Kapur,BWH (NAMIC/NCIGT)
#Ron Kikinis, BWH (NAMIC/NCIGT)
#Junichi Tokuda, BWH (NCIGT)
#Raul San Jose, BWH (NAC)
#Neculai Archip, BWH (Wed only) (NCIGT)
#Nicholas Ayache (NCIGT) (Wed only)

File:Neuro-Dec07.pdf

2007-12-13T16:37:34Z

Pkazanzides: Presentation about robot-assisted neurosurgery, Dec 13, 2007, Peter Kazanzides.

Presentation about robot-assisted neurosurgery, Dec 13, 2007, Peter Kazanzides.

2007 December Slicer IGT Programming

2007-12-07T02:32:33Z

Pkazanzides: /* Thursday, December 13 */

__NOTOC__
==Dates.Location.Hotels==
December 12-14, 2007

SPL at 1249 Boylston Street, Boston MA. ([http://www.spl.harvard.edu/Directions#Getting_to_1249_Boylston_Street Directions])

Area hotels: [[Boston_Hotels]]

==Goal==
*Continued [[Leadership:SlicerIGT_2007|'''discussion''']] of Slicer IGT infrastructure, applications, and timelines
*Introduce each team's effort in Slicer in the context of IGT
*active funding&future submissions
*on-going technical development
*find unmet needs
*find how we can share the work

=Agenda=
==Wednesday, December 12 ==
'''Theme: Where are we?'''
*12noon: lunch
*12:55pm: Welcome (Ferenc Jolesz)
*1-2pm:
**Slicer: overview of architecture, current status, and future plans (Pieper, Hata)
***History
***Clinical applications
***transition from 2.6 to 3
***resource
***Slicer Core + [[Slicer3:Loadable_Modules | Loadable Modules]]
**IGSTK: overview of architecture, current status, and future plans (Ibanez, Cheng)
*2-3pm: Setting goals for meeting: Each IGT group present what they want to achieve at this meeting.
**2-2:15 - NA-MIC DBP Queens/JHU Gobbi/Csoma/Kazanzides
**2:15-2:30 - NA-MIC Collaborator Georgetown Cleary/Yaniv
**2:30-2:45 - NCIGT BWH Hata
**2:45-3:00 - Kitware
**3:00-3:15pm - NCIGT CIGL Stoll and Demo

*3:15-3:30pm: Coffee Break
*3:30pm Adjourn
*4-6pm (optional) demonstration of Slicer for control and display of MRI scanner (prostate module) @Advanced MRI center, 221 Longwood
**See [[2007_December_Slicer_IGT_Programming_MRI_DEMO| slicer-MRI demo]]

==Thursday, December 13==
'''Morning Theme: Where are we?'''
*9:00am breakfast, start work

*9-1030am Discussion over Demos:
**Stoll (laproscopic ultrasound)
**Hata (Tracking at BWH)
**Yaniv (Tracking at Georgetown)
**Freudling (Pieper) (Volume rendering)

*10:30am: coffee break
*11am: continue work
Review of demos
**which function is cool?
**which functionality has to be shared
**what is the common needs?
**who has those missing functions outside of IGT?

*12:30: lunch
*1:30pm: continue work
'''Afternoon Theme: Where are we going?'''
**1:30-1:45: Proposal for robot-assisted neurosurgery (Kazanzides)
**Resource sharing
**priority tasks
**Hypothetical RO1

*3-4pm: Coffee break (and NA-MIC TCON)
*4:00pm: Plan for Hands on IGT Week
*5pm: Review day and plan for Friday (Hata)
*5:30pm: adjourn

==Friday, December 14==
----
*9:00am: breakfast, work
**Focus group discussion ('''What do we do now?''')
**Report to NCIGT
**Action items
*11:15am-noon: Wrapup/Suggestion to NCIGT PIs (Hata)
*noon: adjourn and head out to group lunch

----

==Confirmed Attendees==
#Noby Hata, BWH (NCIGT)
#Steve Pieper, Isomics - (All Days) (NAMIC, NAC)
#Patrick Cheng, Georgetown (NAMIC Collab)
#Ziv Yaniv, Georgetown (NAMIC Collab)
#Kevin Cleary, Georgetown (Wed only) (NAMIC Collab)
#Luis Ibanez, Kitware (NAMIC)
#Sebastien Barre, Kitware (NCIGT)
#Stephen Aylward, Kitware (NCIGT)
#Jeff Stoll (except Thursday), BWH/CIMIT (NCIGT)
#Haiying Liu, BWH (NCIGT)
#Katie Hayes, BWH (NAC)
#Peter Kazanzides (except Friday), JHU (NAMIC Collab)
#Csaba Csoma, JHU (NAMIC/NCIGT Collab)
#David Gobbi, Queens (NAMIC/NCIGT Collab)
#Tina Kapur,BWH (NAMIC/NCIGT)
#Ron Kikinis, BWH (NAMIC/NCIGT)
#Junichi Tokuda, BWH (NCIGT)
#Raul San Jose, BWH (NAC)
#Ferenc Jolesz, BWH (Wed only) (NCIGT/NAC)

2007 December Slicer IGT Programming

2007-11-29T03:39:35Z

Pkazanzides: /* Confirmed Attendees */

==Dates.Location.Hotels==
December 12-14, 2007
(Scheduled based on: http://www.doodle.ch/participation.html?pollId=a6pt4zn4wydey8kv)

SPL at 1249 Boylston Street, Boston MA. ([http://www.spl.harvard.edu/Directions#Getting_to_1249_Boylston_Street Directions])

Area hotels: [[Boston_Hotels]]

==Goal==
Continued [[Leadership:SlicerIGT_2007|'''discussion''']] of Slicer IGT infrastructure, applications, and timelines

==Agenda==
===Wednesday, December 12===
*12noon: lunch
*1-2pm: Setting goals for meeting: Each IGT group present what they want to achieve at this meeting.
**1-1:15 - NA-MIC DBP Queens/JHU Gobbi/Csaba/Kazanzides
**1:15-1:30 - NA-MIC Collaborator Georgetown Cleary/Cheng
**1:30-1:45 - NCIGT BWH Hata
**1:45-2pm - NCIGT CIMIT Stoll
*2-3pm:
**Slicer: overview of architecture, current status, and future plans
**IGSTK: overview of architecture, current status, and future plans
*3-3:15pm: Break
*3:15-4:15pm Demos:
**Jeff Stoll (virtual colonoscopy, ?)
**volume rendering

===Thursday, December 13===
*9-5: work
*12:30: lunch
*4:30pm: Plan for Hands on IGT Week

===Friday, December 14===
*9-noon: work, wrapup
*noon: adjourn

==Confirmed Attendees==
#Noby Hata, BWH
#Steve Pieper, Isomics
#Patrick Cheng, Georgetown
#Kevin Cleary, Georgetown
#Kinh Tieu (except Friday), BWH
#Luis Ibanez, Kitware
#Sebastien Barre, Kitware
#Jeff Stoll (except Thursday), BWH/CIMIT
#Haiying Liu, BWH
#Katie Hayes, BWH
#Peter Kazanzides (except Friday), JHU
#Csaba Csoma, JHU
#Stephen Aylward, JHU
#David Gobbi, Queens
#Tina Kapur,BWH
#Ron Kikinis, BWH
#Junichi Tokuda, BWH
#Raul San Jose, BWH
#Katie Mastrogiocomo, BWH

2007 Programming/Project Week MIT

2007-06-25T19:16:14Z

Pkazanzides: /* One Day */

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===

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

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] 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 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
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
** 4:30-5:30pm [[Special topic breakout: New DBP Introduction to NA-MIC Engineering]]
* Tuesday June 26
** 8:30am breakfast
'''** All Registration Fee Checks are due TODAY at the latest'''
** 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 [[Project Week 2007 Slicer 3.0 Update|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
** 9:00-12pm [[Special topic breakout: ITK]] (Luis Ibanez)
** 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 ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##[[Projects/Diffusion/2007_Project_Week_Contrasting_Tractography_Measures|Contrasting Tractography Measures]] (Marek Kubicki, Doug Markant, Doug Terry, Lauren O'Donnell, Katharina Quintus, Jorge Alvarado Harvard)
## [[Projects/Diffusion/2007_Project_Week_EPI Distortion correction using field maps|EPI Distortion correction using field maps]] (Marek Kubicki BWH)
##[[Projects/Structural/2007_Project_Week_vtkITK Wrapper for Rule Based Segmentation|Dorsolateral Prefrontal Cortex Segmentation in VCFS]] (John Melonakos, Tauseef Rehman, Brad Davis, Marek Kubicki).
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[Projects/Structural/2007_Project_Week_Cortical_Thickness_for_Autism|Cortical Thickness Measurement for UNC Autism Study]] (Clement Vachet UNC, Heather Hazlett UNC, Martin Styner UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[Projects/Structural/2007_Project_Week_Lesion_Classification_in_Lupus|Lesion Classification in Lupus]] (Jeremy Bockholt, Mark Scully)
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI):
##[[Collaboration/JHU/Brachytherapy_needle_positioning_robot_integration | Brachytherapy needle positioning robot integration
]] (David Gobbi Queen's U, Csaba Csoma, JHU, Katie Hayes, BWH, Peter Kazanzides JHU)

===Structural Analysis===
#[[Projects/Structural/2007_Project_Week_EMSegmentation_Validation| EMSegmentation Validation]] (Brad Davis Kitware, Sylvain Bouix BWH)
#[[Projects/Structural/2007_Project_Week_Nonrigid_Groupwise_Registration| Non-Rigid Groupwise Registration Tools for ITK]] (Serdar K Balci, Polina Golland)

===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)
# [[Projects/Diffusion/2007_Project_Week_DTI_Registration|Distortion Correction in DWI]] (Ran Tao, Utah)
# [[Projects/Diffusion/2007_Project_Week_Fluid_Mechanics_Based_Tractography|Fluid Mechanics Based Tractography]] (Nathan Hagemen UCLA)

===NA-MIC Kit - Slicer 3===
#[[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, Will)
# [[Projects/Slicer3/2007_Project_Week_Python support in Slicer3|Python Support in Slicer 3]] (Dan, Luca, Steve)
# [[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 Tensors]] (Katharina, Sylvain, Steve)
# [[Projects/Slicer3/2007_Project_Week_Support for electron microscopy | Dendritic Spine Morphometrics]] (Bryan Smith)
# [[Projects/Slicer3/2007_Project_Week_Review of Slicer3 CMake Files | Review of Slicer3 CMake Files]] (Steve, Jim, Luca, Bill)
# [[Projects/Slicer3/2007_Project_Week_ROIs in Slicer3 | ROIs in Slicer3]] (Wendy, Jim, Nicole, Steve, Ron)

===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)
# [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
# 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==
===Full Week===
#John Melonakos, Georgia Tech, Core 1 (Registration Fee: Received by DK at MIT)
#Tauseef Rehman, Georgia Tech, Core 1 (Registration Fee: Received by DK at MIT)
#Casey Goodlett, UNC, Core 1 (Registration Fee: Received by DK at MIT)
#Serdar K Balci, MIT, Core 1 (Registration Fee: )
#Elliot Uvero, MIT, Core 1 (Registration Fee: )
#Ran Tao, Utah, Core 1 (Registration Fee: )
#Kevin Teich, MGH, Core 1 (Registration Fee: )
#W. Bryan Smith, UCSD/NCMIR, Core 2 (Registration Fee: )
#Jeffrey Grethe, UCSD, Core 2 (Registration Fee: )
#Marco Ruiz, UCSD, Core 2 (Registration Fee: )
#Neil Jones, UCSD, Core 2 (Registration Fee: Received by DK at MIT)
#Jim Miller, GE Core 2 (Registration Fee: )
#Dan Blezek, GE Core 2 (Registration Fee: Received by DK at MIT)
#Steve Pieper, Isomics, Core 2 (Registration Fee: )
#Alex Yarmarkovich, Isomics, Core 2 (Registration Fee: Received by DK at MIT)
#Katie Hayes, BWH, Core 2 (Registration Fee: BWH Check Attendee 1) - confirmed by Ron
#Nicole Aucoin, BWH, Core 2 (Registration Fee: BWH Check Attendee 2) - confirmed by Ron
#Will Schroeder, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 1)
#Yumin Yuan, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 2)
#Brad Davis, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 3)
#Luis Ibanez, Kitware, Core 2 (Registration Fee: Kitware Check Attendee 4)
#Bill Hoffman, Kitware, Core 2 (Mon, Tue) (Registration Fee: Kitware Check Attendee 5)
#Sylvain Bouix, BWH, Core 3 (Registration Fee: ) - to be paid by personal check and reimbursed by MS
#Katharina Quintus, BWH, Core 3 (Registration Fee: )- to be paid by personal check and reimbursed by MS
#Marc Niethammer, BWH. Core 3 (Registration Fee: )- to be paid by personal check and reimbursed by MS
#Clement Vachet, UNC Core 3 (II) (Registration Fee: )
#David Gobbi, Queen's University, Core 3 (II) (Registration Fee: Received by DK at MIT)
#Csaba Csoma, Johns Hopkins University, Core 3 (II) (Registration Fee: Received by DK at MIT)
#H. Jeremy Bockholt, The MIND Institute, Core 3 (II) (Registration Fee: )
#Mark Scully, The MIND Institute, Core 3 (II) (Registration Fee: )
#Sumner Williams, The MIND Institute, Core 3 (II)/Collaborator R01 (Registration Fee: )
#Zack Galbreath, Kitware, Core 4 (Mon, Tue) (Registration Fee: )
#Tina Kapur, BWH, Core 6 (Registration Fee: BWH Check Attendee 3)- confirmed by Ron
#Ron Kikinis, Core 7, PI (Registration Fee: BWH Check Attendee 4)- confirmed by Ron
#Chris Wyatt, Virginia Tech, Collaborator R01 (Registration Fee: Received by DK at MIT)
#Vincent Magnotta, University of Iowa, Collaborator R01 (Registration Fee: )
#Kiran Shivanna, University of Iowa, Collaborator R01 (Registration Fee: )
#Luca Antiga, Mario Negri Institute, Collaborator (Registration Fee: )
#Stephen Aylward, Kitware, Collaborator (Registration Fee: Kitware CHeck Attendee 6)
#Douglas Alan, Harvard IIC, Collaborator (Registration Fee: )
#Michael Halle, BWH/IIC, Collaborator (Registration Fee: )
#Wendy Plesniak, BWH, Collaborator (Registration Fee: BWH Check Attendee 5)- confirmed by Ron
#Kilian Pohl, BWH Collaborator (Registration Fee: BWH Check Attendee 6)- confirmed by Ron
#Raimundo Sierra, BWH, Collaborator (Registration Fee: BWH Check Attendee 7)- confirmed by Ron
#Lauren O'Donnell, BWH, Collaborator (Registration Fee: BWH Check Attendee 8)- confirmed by Ron
#Raul San Jose, BWH, Collaborator (Registration Fee: BWH Check Attendee 9)- confirmed by Ron
#Haiying Liu, BWH Collaborator (Registration Fee: BWH Check Attendee 10)- confirmed by Ron
#Hans Johnson, University of Iowa, Collaborator (Registration Fee: Received by DK at MIT)
#Gary E. Christensen, University of Iowa, Collaborator (Registration Fee: Received by DK at MIT)
#Joo Hyun (Paul) Song, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Xiujuan Geng, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Jake Nickel, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Nick Kiguta, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Kunlin Cao, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#James Harris, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Kai Ding, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Jeff Hawley, University of Iowa, Gary's student (Registration Fee: Received by DK at MIT)
#Skip Talbot, Northwestern University, Collaborator (Registration Fee: )
#Alex Kogan, Northwestern University, Collaborator (Registration Fee: )
#Vladimir Kleper, Northwestern University, Collaborator (Registration Fee: )
#Pat Mongkolwat, Northwestern University, Collaborator (Registration Fee: )
#Greg Sharp, MGH, Collaborator (Registration Fee: )
#James Ross, GE, Collaborator (Registration Fee: )
#Alex Gouaillard, CEGS Caltech, Collaborator (Registration Fee: )
#Sean Megason, CEGS caltech, Collaborator (Registration Fee: )
#Clif Burdette, Acousticmed, Collaborator (Registration Fee: )
#Jack Blevins, Acousticmed, Collaborator (Registration Fee: )
#Curtis Lisle, KnowledgeVis, Collaborator (Registration Fee: )
#C-F Westin, BWH, Collaborator (Registration Fee: BWH Check Attendee 11)- confirmed by Ron
#Demian Wassermann, BWH/INRIA , Collaborator

'''We have reached capacity of this workshop. Any changes made to this list at this point do not translate into space at this meeting. Apologies. If you are interested, check back here for dates of the next NA-MIC event and sign up in advance.'''

===One Day===
#Marek Kubicki, BWH, Core 3 (Monday) (Registration Fee: 0)
#Clare Tempany, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Noby Hata, BWH Collaborator (Monday) (Registration Fee: 0)
#Peter Kazanzides, JHU, Collaborator (Wednesday) (Registration Fee: 0)
#Lilla Zollei, MGH, Collaborator (Tuesday) (Registration Fee: 0)
#Hong Xiang, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Kim Lawson, BWH Collaborator (Tuesday) (Registration Fee: 0)
#Sandy Wells, BWH, Collaborator (Tuesday) (Registration Fee: 0)

2007 Programming/Project Week MIT

2007-06-14T19:03:54Z

Pkazanzides: /* 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
** 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, David Abrahams)
** 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. (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==
#Kilian Pohl, BWH, Core 1
#John Melonakos, Georgia Tech, Core 1
#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 (Wed or Thurs)
#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
#Zack Galbreath, Kitware, Core 4
#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
#Clement Vachet, UNC Core 3 (CS programmer) - 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)
#Serdar K Balci (MIT)
#Jeffrey Grethe, UCSD, Core 2
#Marco Ruiz, UCSD, Core 2
#Neil Jones, UCSD, Core 2
No more attendees. 70 is the last one we can accommodate.

2007 Programming/Project Week MIT

2007-05-18T15:19:16Z

Pkazanzides: /* External Collaborations */

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

== 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 and lunch 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:''' 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]]. 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 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, and those who can help make it happen.
* This is not an introduction to the components of the 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 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 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.

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

* Monday
** noon-1pm lunch
** 1-3:30pm Introduce Projects using 4-block slides (all Project Leads)
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9-10am: NA-MIC Software Process (Bill Hoffman - TBC)
** 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: Non-Linear Registration]]
** 2-3pm: [[Special topic breakout: DWI/DTI]]
** 3-4pm: [[Special topic breakout: KWWidgets]]
** 4-5pm: [[Special topic breakout: Atlases]]
** 5:30pm adjourn for day
* Wednesday
** 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
** 8:30am breakfast
** noon lunch
** 3:30-5pm Special topic breakout: TBD
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using 4-block slides
** 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: Complete the top half of [[media:NA-MIC_Latest_4-Block_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# [[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 ==

===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===
*EMSegmentation Validation (Brad Davis, Sylvain Bouix)
*vtkITK wrapper for rule based segmentation (John Melonakos, Brad Davis, Marek Kubicki)
** Application of the Slicer2 module on DBP data
** Conversion to Slicer3

===Diffusion Image Analysis===
* [[Algorithm:UNC:DTI#Population_Analysis | DTI population analysis]] (Casey Goodlett)
* Slicer3 Whole brain Seeding platform: data representation and pipeline execution (Raul San Jose, Lauren O'Donnell)
* Slicer3 Tractography editor (Lauren O'Donnell, Raul San Jose)

===NA-MIC Kit===
* Slicer3
** [[2007_Project_Week_MIT_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)
** Display Optimization (Raimundo Sierra, David Gobbi, Steve Pieper)
** [[2007_Project_Week_MIT_MRML_Scenes_for_the_Execution_Model]], including transforms (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
** Support for Unstructured Grids (Steve, Nicole, Alex, Curt)
** Python support in Slicer3 (Luca, Steve, depends on Dan's availability)
** CPack, Ctest infrastructure improvements (Andy, Katie, Steve)
** Drafting Human Interface and Slicer Style Guidelines (Wendy)
** Slicer Matlab Pipeline for scalars and tensors (Katharina, Sylvain, Steve)
* Slicer2

===External Collaborations===
* Meshing
** Adding VTK interactive wwidgets to Slicer3 (Will, Vince, Kiran, Curt)
** Migrate Iowa Neural Net code to pure ITK (Vince, Stephen)
*IGT
** [[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)
** [[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===
* 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 (Tentative)
#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
#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
#Rhiannon Carlson, 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
#Csaba Csoma, Johns Hopkins University, Collaborator
#David Gobbi, Queen's University, Collaborator (Hotel at MIT request)
#Kai Ding, University of Iowa, Gary's student
#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

2007 Programming/Project Week MIT

2007-01-21T03:31:23Z

Pkazanzides: /* Attendee List */

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

June 25-29, 2007, MIT

==Please Note==

Programming/Project week is one of the major events in the NA-MIC calendar. This will be our third annual Summer Programmming/Project Week.

* Core 1 - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* Core 2 - bring your code for infrastructure and applications to extend the NA-MIC Kit capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* Core 3 - bring your data to work on with the NA-MIC Kit and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* 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.

== Results ==
Results of this event will be summarized here after it is completed.

== Projects ==

Projects will be added here...

===Structural Analysis===

===Diffusion Image Analysis===

===NA-MIC Kit===
===External Collaborations===
== Logistics ==

'''Dates:''' June 25-29, 2007
'''Registration Fee:''' Registration fee is TBD. It will be payable by check onsite.

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* 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, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# 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#|TBD: Kickoff TCON]]
# TBD: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_2007#|TBD: TCON#2 to discuss projects and verify teams]]
# TBD: 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)
# [[Engineering:TCON_2007#|TBD: TCON#3 last preparation tcon]]
# By June 24, 2007: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

==Attendee List==

#Jim Miller, GE Core 2
#Steve Pieper, Isomics, Core 2,6
#Tina Kapur, BWH, Core 6
#Luis Ibanez, Kitware, Core 2
#Peter Kazanzides, JHU, NA-MIC collaborator