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MICCAI 2010 Tutorial Proposal (submitted and under review)
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== From MICCAI Algorithms to Clinical Translational Tools: The NA-MIC Platform ==
 
== From MICCAI Algorithms to Clinical Translational Tools: The NA-MIC Platform ==
 
   
 
   
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'''Outline:''' [http://www.miccai2010.org/ MICCAI] offers a window on the technological breakthroughs in medical image computing, computer assisted interventions and surgical robotics that will allow for revolutionary progress in clinical care. A critical step to maximize the long-term positive impact of MICCAI algorithms is to foster their deployment, validation and concrete use by the clinical research community for whom they were developed.
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The objective of the tutorial is to introduce the challenges inherent in delivering advanced medical imaging technologies (image processing, analysis and interventional capabilities) to end users for clinical translational research and to present solutions available in the National Alliance for Medical Image Computing (NA-MIC) open-source software toolkit.  The day begins with an overview of the software components of the NA-MIC kit, followed by multiple example applications in current use for clinical research, with a final optional hands-on tutorial session that guides participants through the process of building, testing and deploying an exemplar algorithm using the NA-MIC open-source software toolkit.
  
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Through concrete examples drawn from the translational research efforts of NA-MIC, this tutorial provides insights on practical approaches for bridging the gap between the scientific advances made by the biomedical imaging community and their widespread use in the clinical research community. By the end of the day course participants will know how to use the NA-MIC kit to facilitate greater use of their own algorithms by clinical end users.
  
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'''Outline:''' MICCAI offers a window on the technological breakthroughs in medical image computing, computer assisted interventions and surgical robotics that will allow for revolutionary progress in clinical care. A critical step to maximize the long-term positive impact of MICCAI algorithms is to foster their deployment, validation and concrete use by the clinical research community for whom they were developed.
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== Organizers ==
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The objective of the tutorial is to introduce the challenges inherent in delivering advanced medical imaging technologies (image processing, analysis and interventional capabilities) to end users for clinical translational research and to present solutions available in the National Alliance for Medical Image Computing (NA-MIC) open-source software toolkit.  The day begins with an overview of the software components of the NA-MIC kit, followed by multiple example applications in current use for clinical research, with a final optional hands-on tutorial session that guides participants through the process of building, testing and deploying an exemplar algorithm using the NA-MIC open-source software toolkit.
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*Ron Kikinis, M.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School
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By the end of the day course participants will know how to use the NA-MIC kit to facilitate greater use of their own algorithms by clinical end users.
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*Guido Gerig, Ph.D., The Scientific Computing and Imaging Institute (SCI), University of Utah
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*Sonia Pujol, Ph.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School
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*Martin Styner, Ph.D., Neuro Image Research and Analysis Laboratory, University of North Carolina
  
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== Tutorial Faculty ==
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== Logistics ==
  
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The tutorial will be held on Monday September 20, 2010 '''from 8:30 am to 6:00 pm in room 402A on the L4 level''' at the China National Convention Center (CNCC), No.7 Tianchen East Road, Chaoyang District, Beijing, China.
  
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*Ron Kikinis, M.D.
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To register for the tutorial, please visit the [http://www.miccai2010.org/ MICCAI 2010 ] website.
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*Guido Gerig, Ph.D.
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== Tutorial format ==
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*Killian Pohl, Ph.D.
 
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*Steve Pieper, Ph.D.
 
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*Noby Hata, Ph.D.
 
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*Dinggang Shen, Ph.D.
 
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*Stephan Aylward, Ph.D.
 
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*Sonia Pujol, Ph.D.
 
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*Xiaodong Tao, Ph.D.
 
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*Martin Styner, Ph.D.
 
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*Sylvain Jaume, Ph.D.?
 
  
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== Workshops academic objectives and justification of relevance to MICCAI ==
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The tutorial consists of lectures and an optional instructor-led hands-on session with the participants programming on their own laptop computers. A technical training staff will be providing one-to-one assistance as needed.
  
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The emergence of increasingly sophisticated mathematical models, image analysis and visualization tools that have followed the rapid development of new medical imaging technologies has led to a better understanding of organ functions in human health and disease.
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== Tutorial Faculty ==
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For the past five years, the National Alliance for Medical Image Computing (NA-MIC), one of the seven National Centers for Biomedical Computing (NCBC), part of the NIH Roadmap for medical research, has focused its efforts on the conversion of scientific advances from the biomedical imaging community into an open-source toolkit, so as to improve the availability and deployment of advanced software tools on a national scale.
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*Ron Kikinis, M.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School
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*Sonia Pujol, Ph.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School
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*Noby Hata, Ph.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School
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*Guido Gerig, Ph.D.,The Scientific Computing and Imaging Institute (SCI), University of Utah
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*Killian Pohl, Ph.D., Section for Biomedical Image Analysis, University of Pennsylvania
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*Dinggang Shen, Ph.D., Radiology and BRIC, University of North Carolina School of Medicine
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*Martin Styner, Ph.D., Neuro Image Research and Analysis Laboratory, University of North Carolina
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*Stephan Aylward, Ph.D., Kitware, Inc.
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*Xiaodong Tao, Ph.D., Visualization & Computer Vision, GE Research
  
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The NA-MIC toolkit is a set of open-source software packages for medical image computing, which includes 3D Slicer, VTK, ITK, CMake, CTest and BatchMake. 3D Slicer is an end-user application for image analysis and an open-source environment for software development. This deployment platform has been envisioned and designed as a modular software tool that is both easy to use for clinical researchers and easy to extend for programmers.
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== Tutorial Agenda ==
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*8:45 am - 9:00 am: Introduction and goals of the workshop (Sonia Pujol)
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*9:00 am - 9:15 am: [[media:Kikinis-NA-MIC-2010-09-20.ppt|Overview of the National Alliance for Medical Image Computing (NA-MIC)]] (Ron Kikinis)
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*9:15 am - 9:45 am: [[media:NAMIC_Programming_Environment_MICCAI2010_SoniaPujol.pdf‎  | NA-MIC Programming Environment]] (Sonia Pujol)
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*9:45 am - 10:15 am: [https://na-mic.org/w/images/1/15/NAMIC_Testing_MICCAI2010_XiaodongTao.pdf  ‘Hardening’ your software with the NA-MIC kit, regression tests and dashboard ](Stephen Aylward/Xiaodong Tao)
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*10:15 am - 10:30 am: Morning Tea/Coffee Break
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*10:30 am - 11:00 am: [[media:BuildingBridgesBetweenSoftwarePlatforms_MICCAI2010_SoniaPujol.pdf‎ | Building bridges between complementary medical image analysis platforms (e.g. Freesurfer, BRAINS2, HAMMER) ]](Sonia Pujol)
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*11:00 am - 11:30 am: [[media:Kikinis-How to work with NA-MIC-2010-09-20.ppt|How to participate in NA-MIC: collaboration grants, user and developer community (Kikinis)]]
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*11:30 am - 12:00 pm: Exemplar Clinical Research Applications: Image-Guided Therapy (Hata)
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*12:00 pm - 1:00 pm: Lunch
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*1:00 pm - 3:00 pm: Exemplar Clinical Research Applications 
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**1:00 pm - 1:30 pm: Image Registration (Dinggang Shen)
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**1:30 pm - 2:00 pm: Image Segmentation: [[media:MICCAI10-Tutorial-Pohl.pdf | EM Segmenter]] (Kilian Pohl) and Automatic Brain Segmentation  [[media:NAMIC-ABC-MICCAI2010b.pdf‎ | ABC (Guido Gerig) ]]
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**2:00 pm - 2:30 pm: [[media:2010_09_CortThick-NAMIC-MICCAI.pdf‎ | Cortical Thickness Measurements (Martin Styner) ]]
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**2:30 pm - 3:00 pm: Diffusion Tensor Imaging (Sonia Pujol, Guido Gerig [[media:DTI_NAMIC-MICCAI2010.pdf | Gerig-Slides]])
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*3:00 pm - 3:30 pm: Afternoon Tea/Coffee Break
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*3:30 pm - 3:45 pm: [[media:Kikinis-Slicer Community-2010-09-20.ppt|Other examples from the community]] (Ron Kikinis)
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*3:45 pm - 5:30 pm: Optional Hands-on Session: [[media:ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf‎ | Interfacing your MICCAI algorithm with the NA-MIC open-source toolkit: the ‘Hello Python’ tutorial ]](Sonia Pujol)
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*5:30 pm - 6:00 pm: Open Discussion and one-on-one consultations for individual projects
  
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This tutorial educates participants on the most common obstacles to translating their novel image analysis and computer assisted interventions into clinical research practice and provides open source, freely available solutions to these problems.  Multiple examples of clinical research projects that have been recently completed or that are underway are provided to illustrate these issues and solutions.  The final optional session is a Hands-On tutorial on how to integrate the NA-MIC toolkit with a third party executable program.
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== Preparation for the tutorial ==
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The course uses an exemplar program and pre-computed training MRI datasets. The workshop is intended for scientists and engineers of the medical image analysis community. Pre-requisites include C++ and ITK programming experience.
 
  
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We believe that building upon the latest open-source analysis tools will help scientists and engineers achieve new technological breakthroughs that will benefit the MICCAI community.
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In preparation for the optional hands-on session, please install the [http://www.slicer.org/pages/Special:SlicerDownloads Slicer3.6 release version] appropriate to the platform you'll be using, and the [[media:HelloPython.zip | HelloPython dataset]] Hardware minimum requirement: 2GB of main memory and graphics hardware acceleration with 256 MB of dedicated graphics memory (nvidia preferred).  
  
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[[media:MICCAI2010_T2tutorial_NAMIC_Draft_Tutorial_Notes.pdf| Draft Tutorial Notes]]
  
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== Tutorial format ==
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[[media:MICCAI2010_T2tutorial_NAMIC_flyer.pdf| Tutorial flyer]]
  
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The tutorial consists of lectures and an optional instructor-led hands-on session with the participants programming on their own laptop computers. A technical training staff will be providing one-to-one assistance as needed.
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Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]

Latest revision as of 18:27, 10 July 2017

Home < MICCAI 2010
Miccai2010logo.jpg
NAMIC.jpg Logo nac.gif NCIGTlogo.gif

From MICCAI Algorithms to Clinical Translational Tools: The NA-MIC Platform

Outline: MICCAI offers a window on the technological breakthroughs in medical image computing, computer assisted interventions and surgical robotics that will allow for revolutionary progress in clinical care. A critical step to maximize the long-term positive impact of MICCAI algorithms is to foster their deployment, validation and concrete use by the clinical research community for whom they were developed. The objective of the tutorial is to introduce the challenges inherent in delivering advanced medical imaging technologies (image processing, analysis and interventional capabilities) to end users for clinical translational research and to present solutions available in the National Alliance for Medical Image Computing (NA-MIC) open-source software toolkit. The day begins with an overview of the software components of the NA-MIC kit, followed by multiple example applications in current use for clinical research, with a final optional hands-on tutorial session that guides participants through the process of building, testing and deploying an exemplar algorithm using the NA-MIC open-source software toolkit.

Through concrete examples drawn from the translational research efforts of NA-MIC, this tutorial provides insights on practical approaches for bridging the gap between the scientific advances made by the biomedical imaging community and their widespread use in the clinical research community. By the end of the day course participants will know how to use the NA-MIC kit to facilitate greater use of their own algorithms by clinical end users.

Organizers

  • Ron Kikinis, M.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School
  • Guido Gerig, Ph.D., The Scientific Computing and Imaging Institute (SCI), University of Utah
  • Sonia Pujol, Ph.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School
  • Martin Styner, Ph.D., Neuro Image Research and Analysis Laboratory, University of North Carolina

Logistics

The tutorial will be held on Monday September 20, 2010 from 8:30 am to 6:00 pm in room 402A on the L4 level at the China National Convention Center (CNCC), No.7 Tianchen East Road, Chaoyang District, Beijing, China.

To register for the tutorial, please visit the MICCAI 2010 website.

Tutorial format

The tutorial consists of lectures and an optional instructor-led hands-on session with the participants programming on their own laptop computers. A technical training staff will be providing one-to-one assistance as needed.

Tutorial Faculty

  • Ron Kikinis, M.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School
  • Sonia Pujol, Ph.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School
  • Noby Hata, Ph.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School
  • Guido Gerig, Ph.D.,The Scientific Computing and Imaging Institute (SCI), University of Utah
  • Killian Pohl, Ph.D., Section for Biomedical Image Analysis, University of Pennsylvania
  • Dinggang Shen, Ph.D., Radiology and BRIC, University of North Carolina School of Medicine
  • Martin Styner, Ph.D., Neuro Image Research and Analysis Laboratory, University of North Carolina
  • Stephan Aylward, Ph.D., Kitware, Inc.
  • Xiaodong Tao, Ph.D., Visualization & Computer Vision, GE Research

Tutorial Agenda

Preparation for the tutorial

In preparation for the optional hands-on session, please install the Slicer3.6 release version appropriate to the platform you'll be using, and the HelloPython dataset Hardware minimum requirement: 2GB of main memory and graphics hardware acceleration with 256 MB of dedicated graphics memory (nvidia preferred).

Draft Tutorial Notes

Tutorial flyer

Back to NA-MIC Events

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