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. Pipeline development for VCFS (Marek Kubicki BWH)
  4. Prostate Robotics (Junichi Tokuda BWH)
  5. 2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images (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 to UCLA (Haiying Liu BWH)
  13. Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying Liu BWH)
  14. Segmentation of thalamic nuclei from DTI (Ion-Florin Talos BWH)
  15. Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev BWH)
  16. Fluid mechanics tractography and visualization (Nathan Hageman UCLA)
  17. DWI/DTI QC and Preparation Tool: DTIPrep (Zhexing Liu UNC)
  18. DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman UCLA)
  19. EPI Correction in Slicer3 (Ran Tao Utah)
  20. FastMarching for brain tumor segmentation (Andrey Fedorov BWH)
  21. EM Segment (Sylvain Jaume MIT, Nicolas Rannou BWH)
  22. Meningioma growth simulation (Andrey Fedorov BWH)
  23. Automatic brain MRI processing pipeline (Marcel Prastawa Utah)
  24. HAMMER Registration (Guorong Wu UNC)
  25. Spherical Mesh Diffeomorphic Demons Registration (Luis Ibanez Kitware)
  26. BSpline Registration in Slicer3 (Samuel Gerber Utah)
  27. 4D Imaging (Perfusion, Cardiac, etc.) (Junichi Tokuda BWH)
  28. MRSI Module (Bjoern Menze MIT)
  29. Gated 4D ultrasound reconstruction for Slicer3 (Danielle Pace Robarts Institute)
  30. Integration of stereo video into Slicer3 (Mehdi Esteghamatian Robarts Institute)
  31. multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego Cantor Robarts Institute)
  32. Using ITK in python (Steve Pieper BWH)
  33. Taking advantage of multicore machines & clusters with python (Julien de Siebenthal BWH)
  34. Deferring heavy computational tasks with Slicer python (Julien de Siebenthal BWH)
  35. Accelerating python with cython: application to stochastic tractography (Julien de Siebenthal BWH)
  36. VTK 3d Widgets in Slicer3 (Nicole Aucoin BWH)
  37. Updates to Slicer3 Colors module (Nicole Aucoin BWH)
  38. Plug-in 3D Viewer based on XIP (Lining Yang Siemens Research)
  39. Slicer3 Informatics Workflow Design & XNAT updates for Slicer (Wendy Plesniak BWH)
  40. Registration reproducibility in Slicer3 (Andrey Fedorov BWH)
  41. The Vascular Modeling Toolkit in 3D Slicer (Daniel Haehn BWH)
  42. Extension of the Command Line XML Syntax/Interface (Bennett Landman)
  43. XNAT user interface improvements for NA-MIC (Dan Marcus WUSTL)
  44. XNAT File System with FUSE (Dan Marcus WUSTL)
  45. XNAT integration into Harvard Catalyst i2b2 framework (Yong Harvard)
  46. GWE-XNAT Integration (Marco Ruiz UCSD)
  47. Slicer 3 registration (Andrew Rausch)
  48. Transrectal Prostate Biopsy (Andras Lasso Queen's)
  49. 3D GRASE (Scott Hoge BWH)
  50. Atlas to CT Registration in Trigeminal Neuralgia (Marta Peroni PoliMI, Maria Francesca Spadea UMG, Greg Sharp MGH)
  51. Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients (Doug Terry, Marek Kubicki BWH)
  52. Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer (Jayender Jagadeesan BWH)

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.

Attendee List

If you plan to attend, please add your name here.

  1. Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
  2. Clare Tempany, BWH (NCIGT)
  3. Tina Kapur, BWH (NA-MIC, NCIGT)
  4. Steve Pieper, Isomics Inc
  5. Jim Miller, GE Research
  6. Xiaodong Tao, GE Research
  7. Randy Gollub, MGH
  8. Nicole Aucoin, BWH (NA-MIC) (Attending Tuesday-Friday)
  9. Dan Marcus, WUSTL
  10. Junichi Tokuda, BWH (NCIGT)
  11. Alex Gouaillard, Harvard Systems Biology
  12. Arnaud Gelas, Harvard Systems Biology
  13. Kishore Mosanliganti, Harvard Systems Biology
  14. Lydie Souhait, Harvard Systems Biology
  15. Luis Ibanez, Kitware Inc (Attending: Monday/Tuesday/Wednesday)
  16. Vincent Magnotta, UIowa
  17. Hans Johnson, UIowa
  18. Xenios Papademetris, Yale
  19. Gregory S. Fischer, WPI (Mon, Tue, Wed)
  20. Daniel Blezek, Mayo (Tue-Fri)
  21. Danielle Pace, Robarts Research Institute / UWO
  22. Clement Vachet, UNC-Chapel Hill
  23. Dave Welch, UIowa
  24. Demian Wassermann, Odyssée lab, INRIA, France
  25. Manasi Ramachandran, UIowa
  26. Greg Sharp, MGH
  27. Rui Li, MGH
  28. Mehdi Esteghamatian, Robarts Research Institute / UWO
  29. Misha Milchenko, WUSTL
  30. Kevin Archie, WUSTL
  31. Tim Olsen, WUSTL
  32. Wendy Plesniak BWH (NAC)
  33. Haiying Liu BWH (NCIGT)
  34. Curtis Lisle, KnowledgeVis / Isomics
  35. Diego Cantor, Robarts Research Institute / UWO
  36. Daniel Haehn, BWH
  37. Nicolas Rannou, BWH
  38. Sylvain Jaume, MIT
  39. Alex Yarmarkovich, Isomics
  40. Marco Ruiz, UCSD
  41. Andriy Fedorov, BWH (NA-MIC)
  42. Harish Doddi, Stanford University
  43. Scott Hoge, BWH (NCIGT)
  44. Vandana Mohan, Georgia Tech
  45. Ivan Kolosev, Georgia Tech
  46. Behnood Gholami, Georgia Tech
  47. James Balter, U Michigan
  48. Dan McShan, U Michigan
  49. Zhou Shen, U Michigan
  50. Maria Francesca Spadea, Italy
  51. Lining Yang, Siemens Corporate Research
  52. Beatriz Paniagua, UNC-Chapel Hill
  53. Bennett Landman, Johns Hopkins University
  54. Snehashis Roy, Johns Hopkins University
  55. Marta Peroni, Politecnico di Milano
  56. Sebastien Barre, Kitware, Inc.
  57. Samuel Gerber, SCI University of Utah
  58. Ran Tao, SCI University of Utah
  59. Marcel Prastawa, SCI University of Utah
  60. Katie Hayes, BWH (NA-MIC)
  61. Sonia Pujol, BWH (NA-MIC)
  62. Andras Lasso, Queen's University
  63. Yong Gao, MGH
  64. Minjeong Kim, UNC-Chapel Hill
  65. Guorong Wu, UNC-Chapel Hill
  66. Jeffrey Yager, UIowa
  67. Yanling Liu, SAIC/NCI-Frederick
  68. Ziv Yaniv, Georgetown
  69. Bjoern Menze, MIT
  70. Vidya Rajagopalan, Virginia Tech
  71. Sandy Wells, BWH (NAC, NCIGT)
  72. Lilla Zollei, MGH (NAC)
  73. Lauren O'Donnell, BWH
  74. Florin Talos, BWH (NAC)
  75. Nobuhiko Hata, BWH (NCIGT)
  76. Alark Joshi, Yale
  77. Yogesh Rathi, BWH
  78. Jimi Malcolm, BWH
  79. Dustin Scheinost, Yale
  80. Dominique Belhachemi, Yale
  81. Sam Song, JHU
  82. Nathan Cho, JHU
  83. Julien de Siebenthal, BWH
  84. Peter Savadjiev, BWH
  85. Carl-Fredrik Westin, BWH
  86. John Melonakos, AccelerEyes (Wed & Thu morning)
  87. Yi Gao, Georgia Tech
  88. Sylvain Bouix, BWH
  89. Zhexing Liu, UNC-CH
  90. Eric Melonakos, BWH
  91. Lei Qin, BWH
  92. Giovanna Danagoulian, BWH
  93. Andrew Rausch, BWH (Monday)
  94. Haytham Elhawary, BWH
  95. Jayender Jagadeesan, BWH
  96. Marek Kubicki, BWH
  97. Doug Terry, BWH
  98. Nathan Hageman, LONI (UCLA)
  99. Dana Peters, Beth Israel Deaconess
  100. Sun Woo Lee, BWH
  101. Melanie Grebe, Siemens Corporate Research
  102. Megumi Nakao, BWH/NAIST
  103. Moti Freiman, The Hebrew Univ. of Jerusalem
  104. Jack Blevins, Acoustic Med Systems
  105. Michael Halle, BWH
  106. Amanda Peters, Harvard SEAS
  107. Joe Stam, NVIDIA (Wednesday, Thursday)
  108. Petter Risholm, BWH (NCIGT)
  109. Kimberly Powell, NVIDIA (Wednesday)
  110. Padma Akella, BWH (NCIGT)
  111. Clif Burdette, Acousticmed (Mon, Tue, Wed)
  112. Mark Scully, MRN
  113. Jeremy Bockholt, MRN (tues-thurs)
  114. Curtis Rueden, UW-Madison
  115. Juhana Frosen, BWH (Tuesday)
  116. Andrzej Przybyszewski, UMass Medical School (Monday)
  117. Robert Yaffe, MGH
  118. Kenneth (Cal) Hisley, Des Moines University
  119. Ross Whitaker, University of Utah (Wed-Fri)

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
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