2009 Summer Project Week

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Introduction to the FIRST JOINT PROJECT WEEK

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the NA-MIC Kit, algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on Thursday, April 16th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of NA-MIC, NCIGT, NAC, Harvard Catalyst, and CIMIT. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available here.

Agenda

  • Monday
    • noon-1pm lunch
    • 1pm: Welcome (Ron Kikinis)
    • 1:05-3:30pm Introduce Projects using templated wiki pages (all Project Leads) (Wiki Template)
    • 3:30-5:30pm Start project work
  • Tuesday
    • 8:30am breakfast
    • 9:30-10am: NA-MIC Kit Overview (Jim Miller)
    • 10-10:30am Slicer 3.4 Update (Steve Pieper)
    • 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
    • 11am-12:00pm Breakout Session: 2009 Project Week Breakout Session: Slicer-Python (Demian W)
    • noon lunch
    • 2:30pm-4pm: Data Clinic (Ron Kikinis)
    • 4:30pm CIMIT Forum (at BWH Shapiro Center) Open Source Software for Translational IGT Research and Commercial Use, Clif Burdette, Acoustic MedSystems, Inc.

At BWH / Carl J. and Ruth Shapiro Cardiovascular Cente

Projects

  1. Cortical Thickness Pipeline (Clement Vachet UNC)
  2. Lupus Lesion Segmentation (Jeremy Bockholt MRN)
  3. Stochastic Tractography to study VCFS and Schizophrenia (Marek Kubicki BWH)
  4. Prostate Robotics (Junichi Tokuda BWH)
  5. Segmentation of Knee Structures (Harish Doddi Stanford)
  6. Liver Ablation in Slicer (Ziv Yaniv Georgetown)
  7. Measuring Alcohol Stress Interaction (Vidya Rajgopalan Virginia Tech)
  8. White Matter Lesion segmentation (Minjeong Kim UNC)
  9. Skull Stripping (Snehasish Roy JHU)
  10. IAFE Mesh Modules - improvements and testing (Curt Lisle Knowledge Vis)
  11. Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp MGH)
  12. SLicer3, BioImage Suite and Brainlab - Introduction and Demo to UCLA (Haiying Liu BWH)
  13. Segmentation of thalamic nuclei from DTI (Ion-Florin Talos BWH)
  14. Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev BWH)
  15. Fluid mechanics tractography and visualization (Nathan Hageman UCLA)
  16. DWI/DTI QC and Preparation Tool: DTIPrep (Zhexing Liu UNC)
  17. DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman UCLA)
  18. EPI Correction in Slicer3 (Ran Tao Utah)
  19. FastMarching for brain tumor segmentation (Andrey Fedorov BWH)
  20. EM Segment (Sylvain Jaume MIT, Nicolas Rannou BWH)
  21. Meningioma growth simulation (Andrey Fedorov BWH)
  22. Automatic brain MRI processing pipeline (Marcel Prastawa Utah)
  23. HAMMER Registration (Guorong Wu UNC)
  24. Spherical Mesh Diffeomorphic Demons Registration (Luis Ibanez Kitware)
  25. BSpline Registration in Slicer3 (Samuel Gerber Utah)
  26. 4D Imaging (Perfusion, Cardiac, etc.) (Junichi Tokuda BWH)
  27. MRSI Module (Bjoern Menze MIT)
  28. Gated 4D ultrasound reconstruction for Slicer3 (Danielle Pace Robarts Institute)
  29. Integration of stereo video into Slicer3 (Mehdi Esteghamatian Robarts Institute)
  30. multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego Cantor Robarts Institute)
  31. Using ITK in python (Steve Pieper BWH)
  32. Taking advantage of multicore machines & clusters with python (Julien de Siebenthal BWH)
  33. Deferring heavy computational tasks with Slicer python (Julien de Siebenthal BWH)
  34. Accelerating python with cython: application to stochastic tractography (Julien de Siebenthal BWH)
  35. VTK 3d Widgets in Slicer3 (Nicole Aucoin BWH)
  36. Updates to Slicer3 Colors module (Nicole Aucoin BWH)
  37. Plug-in 3D Viewer based on XIP (Lining Yang Siemens Research)
  38. Slicer3 Informatics Workflow Design & XNAT updates for Slicer (Wendy Plesniak BWH)
  39. Registration reproducibility in Slicer3 (Andrey Fedorov BWH)
  40. The Vascular Modeling Toolkit in 3D Slicer (Daniel Haehn BWH)
  41. Extension of the Command Line XML Syntax/Interface (Bennett Landman)
  42. XNAT user interface improvements for NA-MIC (Dan Marcus WUSTL)
  43. XNAT File System with FUSE (Dan Marcus WUSTL)
  44. XNAT integration into Harvard Catalyst i2b2 framework (Yong Harvard)
  45. GWE-XNAT Integration (Marco Ruiz UCSD)
  46. Slicer 3 registration (Andrew Rausch)
  47. Transrectal Prostate Biopsy (Andras Lasso Queen's)
  48. 3D GRASE (Scott Hoge BWH)
  49. Atlas to CT Registration in Trigeminal Neuralgia (Marta Peroni PoliMI, Maria Francesca Spadea UMG, Greg Sharp MGH)
  50. Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients (Doug Terry, Marek Kubicki BWH)
  51. Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer (Jayender Jagadeesan BWH)
  52. Orthogonal Planes in Reformat Widget (Michal Depa MIT)
  53. New Level Framework in ITK (Arnaud Gelas, Harvard Medical School)
  54. Tubular Surface Segmentation in Slicer (Vandana Mohan, Georgia Tech)
  55. Prostate Registration Slicer Module (Yi Gao, Georgia Tech)

CUDA Projects

This is a list of candidate cuda projects that will be discussed with Joe Stam shortly:

  1. 2d/3d Registration (and GPGPU acceleration) for Radiation Therapy (Tina Kapur BWH)
  2. multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego Cantor Robarts Institute)
  3. accelerate calculation for LDR seeds (Jack Blevins Acousticmed)
  4. 2009_Summer_Project_Week_Cone_Beam_backprojection(Zhou Shen U Michigan)
  5. 2009_Summer_project_week_3d_Deformable_alignment(Dan McShan U Michigan)
  6. Developing interactive stochastic tractography using CUDA (Julien de Siebenthal BWH)
  7. acceleration of parallel real time processing of strain and elasticity images for monitoring of ablative therapy (Clif Burdette Acousticmed)

Preparation

  1. Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
  2. Join the kickoff TCON on April 16, 3pm ET.
  3. June 18 TCON at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
  4. By 3pm ET on June 11, 2009: 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.
  5. By 3pm on June 18, 2009: Create a directory for each project on the NAMIC Sandbox (Zack)
    1. 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)
    2. 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.)
    3. 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)
  6. 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...
  7. People doing Slicer related projects should come to project week with slicer built on your laptop.
    1. Projects to develop extension modules should work with the Slicer-3-4 branch (new code should not be checked into the branch).
    2. Projects to modify core behavior of slicer should be done on the trunk.


Logistics

  • Dates: June 22-26, 2009
  • Location: MIT. Grier Rooms A & B: 34-401A & 34-401B.
  • Registration Fee: $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. If this is your first event and you are attending for only one day, the registration fee is waived. Please let us know, so that we can cover the costs with one of our grants.
  • Registration Method Add your name to the Attendee List section of this page
  • Hotel: We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). 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. Summer is tourist season in Boston, so please book your rooms early.
  • 2009 Summer Project Week Template
  • Last Year's Projects as a reference
  • For hosting projects, we are planning to make use of the NITRC resources. See Information about NITRC Collaboration

Attendee List

Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.

John Melonakos AccelerEyes (Wed & Thu morning)
Jack Blevins Acoustic Med
Clif Burdette Acoustic Med (Mon-Wed)
Dana Peters Beth Israel Deaconess
Nicole Aucoin BWH (NAMIC)
Giovanna Danagoulian BWH (NCIGT Collaborator)
Haytham Elhawary BWH (NCIGT Collaborator)
Andriy Fedorov BWH (NAMIC Collaborator)
Daniel Haehn BWH (NAC)
Michael Halle BWH (NAC)
Nobuhiko Hata BWH (NCIGT)
Katie Hayes BWH (NAMIC)
Scott Hoge BWH (NCIGT)
Tina Kapur BWH (NCIGT, NAMIC)
Ron Kikinis BWH (NAMIC, NAC, NCIGT)
Jayender Jagadeesan BWH (NCIGT Collaborator)
Haying Liu BWH (NCIGT)
Lauren O'Donnell BWH (NCIGT)
Wendy Plesniak BWH (NAC)
Megumi Nakao BWH (NAIST)
Sonia Pujol BWH (NAMIC)
Lei Qin BWH (NCIGT Collaborator)
Nicolas Rannou BWH (NAC)
Petter Risholm BWH (NCIGT)
Florin Talos BWH (NAC)
Clare Tempany BWH (NCIGT)
Junichi Tokuda BWH (NCIGT)
Demian Wasserman BWH (INRIA)
Carl-Fredrik Westin BWH (NAC)
Sandy Wells BWH (NAC, NCIGT)
Lilla Zollei MGH (NAC)
Padma Akella BWH (NCIGT)
Sylvain Bouix BWH (PNL)
Julien de Siebenthal BWH (PNL)
Marek Kubicki BWH (NAMIC DBP PNL)
Juhana Frosen BWH Tues only
Sun Woo Lee BWH (PNL)
Jimi Malcolm BWH (PNL)
Eric Melonakos BWH (PNL)
Yogesh Rathi BWH (PNL)
Peter Savadjiev BWH (PNL)
Doug Terry BWH (PNL)
Andrew Rausch BWH (Mon only)
Cal Hisley Des Moines Unive
Jim Miller GE
Xiaodong Tao GE
Vandana Mohan GA Tech
Yi Gao GA Tech
Ivan Kolosev GA Tech
Behnood Gholami GA Tech
Ziv Yaniv Georgetown
Alex Gouaillard Harvard Systems Biology
Arnaud Gelas Harvard Systems Biology
Kishore Mosanliganti Harvard Systems Biology
Lydie Souhait Harvard Systems Biology
Moti Freiman Hebrew University of Jerusalem
Amanda Peters Harvard SEAS
Maria Francesca Spadea Italy
Curtis Lisle KnowledgeVis
Steve Pieper Isomics
Alex Yarmarkovich Isomics
Nathan Cho JHU
Bennett Landman JHU
Snehashis Roy JHU
Sam Song JHU
Sebastien Barre Kitware
Luis Ibanez Kitware
Daniel Blezek Mayo
Yong Gao MGH
Randy Gollub MGH
Rui Li MGH
Greg Sharp MGH
Robert Yaffe MGH - Mon
Sylvain Jaume MIT
Bjoern Menze MIT
Jeremy Bockholt MRN (NAMIC Lupus DBP)
Mark Scully MRN (NAMIC Lupus DBP) Tue-Th
Joe Stam NVIDIA (Wed & Thurs)
Kimberly Powell NVIDIA (Wed)
Marta Peroni Politecnico di Milano
Andras Lasso Queen's (NAMIC DBP)
Yanling Liu SAIC/NCI-Frederick
Melanie Grebe Siemens Corporate Research
Lining Yang Siemens Corporate Research
Harish Doddi Stanford University
Marco Ruiz UCSD
Nathan Hageman UCLA
Hans Johnson U Iowa
Vincent Magnotta U Iowa
Jeffrey Yager U Iowa
Manasi Ramachandran U Iowa
Dave Welch U Iowa
Andrzej Przybyszewski UMass Med (Mon)
James Balter U Michigan
Dan McShan U Michigan
Zhou Shen U Michigan
Beatriz Paniagua UNC
Minjeong Kim UNC
Zhexing Liu UNC
Clement Vachet UNC (NAMIC DBP)
Guorong Wu UNC
Samuel Gerber SCI, Utah
Ran Tao SCI, Utah
Marcel Prastawa SCI, Utah
Ross Whitaker SCI, Utah
Curtis Rueden UW-Madison
Dan Marcus WUSTL
Misha Milchenko WUSTL
Kevin Archie WUSTL
Tim Olsen WUSTL
Mehdi Esteghamatian Robarts Research Inst. / Western Ontario
Diego Cantor Robarts Research Inst. / Western Ontario
Danielle Pace Robarts Research Inst. / Western Ontario
Vidya Rajagopalan VA Tech
Gregory Fischer WPI
Dominique Belhachemi Yale U (Tu & Wed)
Alark Joshi Yale U (Tu & Wed)
Xenios Papademetris Yale U (Tu & Wed)
Dustin Scheinost Yale U (Tu & Wed)
Michelle Borkin Harvard SEAS (Mon only)
Renxin Chu BWH (NCIGT) (Mon, Tue)
Ben Schwartz BWH (NCIGT) (Mon, Tue)

Testing Sortable Tables

demo
9
12
11

convert from excel to mediawiki markup: http://area23.brightbyte.de/csv2wp.php

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