na-mic national alliance for medical image computing training core update sonia pujol – randy...

NA-MICNational Alliance for Medical Image Computing http://na-mic.org

Training Core Update

Sonia Pujol – Randy Gollub

NA-MIC Core 5

National Alliance for Medical Image Computing http://na-mic.org

Training Core Goals

• Training Material development– Facilitate cross discipline communication– Support deployment and dissemination of

NAMIC toolkit

•Strategy–Develop and test within NA-MIC community–Deploy to Scientific Community


Training Core Personnel

Faculty

Randy Gollub MD-PhD, PI Domain: Clinical Applications (MGH)

Ross Whitaker PhD Domain: Computer Science (Utah)

Guido Gerig PhD Domain: Medical Image Analysis (UNC)

Martha Shenton PhD Domain: Schizophrenia (BWH) with valuable help from her team, especially Sylvain Bouix

Post Doctoral Fellow

Sonia Pujol PhD Domain: Image Guided Therapy (BWH)

Training material development and teaching


Training Core Collaborators

Within NAMICSteve Pieper: Dissemination Core

Tina Kapur: Dissemination Core

Beyond NA-MICNicole Aucoin: Morphometry BIRN (BWH)

Kevin Teich: Morphometry BIRN (MGH)Marianna Jakob: Neuroimage Analysis Center (BWH)


Achievements in 2005

• Neuroanatomy for computer scientists

• Slicer 101: web-based training resources

• NA-MIC kit tutorials

• User Training Workshops


Neuroanatomy

• Fundamentals of neuroanatomy for computer scientists

NA-MIC programming weekMIT Cambridge, MA

June 27-July 1st, 2005

NA-MIC AHM 2006Jan.8, 2006


Neuroanatomy training AHM 2006


Slicer 101

Themes

Data

Tutorials

Installation instructions


Tutorials


NA-MIC Training kit

Our tutorials consist of – a goal describing the

learning outcome


NA-MIC Training kit

3D models of left and right hippocampi superimposed on

anatomical MR images

(NA-MIC Training 6)


learning outcome– an image of the

expected result


NA-MIC Training kit


learning outcome– an image of the

expected result– training datasets

Slicer DTI Sample data set acquisition protocol

(NA-MIC Training 4)


NA-MIC Training kit

Our tutorials consist of – a series of exercises

guiding the user

Saving a PNG image of the Viewer

(NA-MIC Training 7)


NA-MIC Training kit

Our tutorials consist of– a series of exercises

guiding the user– corresponding

descriptive solutions

Statistical distribution of the cortical thickness parameterized by the age of the population.

( NA-MIC Training 6)


NA-MIC Training kit

• More than 300 training slides


NA-MIC Training kit


• 400 MB of pre-computed datasets


NA-MIC Training kit


• 400 MB of pre-computed datasets

• NA-MIC communication format

2000 hits to Slicer 101 in 200 days


Workshops


NA-MIC Workshop Format

Input Data

Output Data

Data Processing

Training 1: Loading and Viewing Data

Training 7: Saving Data

Training 2..6: Slicer Modules


Training events organization

Announcement on NA-MIC wikiPreparation instructions

Registration closedRequirements reminder

Follow-up

WORKSHOPNA-MIC kit introduction

Hands-on sessions User feedback


NA-MIC Training Workshops

Training workshops were offered at

• Local universities within the NA-MIC community





• National meetings outside the NA-MIC community





• National meetings outside the NA-MIC community

• International Research conferences


Darmouth Hitchcock Medical Center Hanover, NH

Local universities within the NA-MIC community

41 participants



Athinoula Martinos Center for Biomedical Imaging, Charlestown, MA


41 participants

24 participants



Athinoula Martinos Center for Biomedical Imaging, Charlestown, MA

Surgical Planning Laboratory, Boston, MA


41 participants

24 participants

21 participants


Biomedical Informatics Research Network (BIRN) 2005 All Hands Meeting

San Diego, CA

National meetings outside the NA-MIC community

51 participants


International research conferences

Annual Meeting of the Association of University Radiologists (AUR 2005)Montreal, Canada

40 participants


Annual Meeting of the Association of University Radiologists (AUR 2005)Montreal, Canada

Annual Meeting of the Radiological Society of North America (RSNA 2005) Chicago, USA

International research conferences

40 participants

58 participants



Date May 26-27

Location Hanover, NH

Program

•Slicer Basics

•Registration

•fMRI and DTMRIhttp://www.na-mic.org/Wiki/index.php/Dissemination:Workshop_May_26-27_2005


Darmouth Medical Center May 26-27, 2005



Date September 16

Location Charlestown, MA

Program

•Slicer Basics

•FreeSurfer integration within Slicer (part 1)

•Saving data

http://www.na-mic.org/Wiki/index.php/Training:User_Workshop_MGH_Summer_2005


Martinos Center MGH Sept.16, 2005



Date September 30

Location Boston, MA

Program

•Slicer Basics

•FreeSurfer integration within Slicer (part 2)

•Saving Data

http://www.na-mic.org/Wiki/index.php/Training:User_Workshop_SPL_Fall_2005


Surgical Planning LabSept.30, 2005



Date October 20

Location San Diego, CA

Program

•Free Surfer Training

•Loading, Viewing and Saving data

•Slicer/FreeSurfer integration overview

http://www.na-mic.org/Wiki/index.php/Training:Workshop_Oct_20_2005


University of California San DiegoOct. 20, 2005


Geographical distribution of attendees

Dartmouth Hitchcock Medical Center, Hanover, NH

University of California Irvine

University of California San Diego

Biomedical Informatics Research Network Coordinating Center, San Diego

Mental Illness and Neuroscience Discovery, University of New Mexico

Massachusetts Institute of Technology, Cambridge MA

General Electrics, Niskayuna NY

Center for Addiction and Mental Healh

University of Toronto, Canada

Brigham and Women’s Hospital, Boston MA

Athinoula A. Martinos Center for

Biomedical Imaging, Charlestown, MA

Cornell University, Ithaca, NY

Georgia Institute of Technology, Atlanta, GA

Johns Hopkins University, Baltimore, MD



235 participants in 6 months


2006 Training Plan Highlights

• All day DTI Workshop• Tutorial Materials for new NA-MIC tools• Impact Assessment methods

Details at 8:30 AM tomorrow


Conclusion

• 2005 Achievements – Neuroanatomy for computer scientists – Slicer 101 page– NA-MIC kit tutorials– User Training Workshops

• 2006 Training Plans

• Questions/suggestions


Testimonials

« I really enjoyed the course and learned a lot. I think it had a nice mix of science and hands on. »

Trainee, Slicer Workshop at Darmouth« The course is a great one, well prepared and very informative. It was a bit surprising that

people learnt Slicer so quickly »Xiaodong, Slicer Workshop MGH

« Because the Slicer tutorials are all online, the need for note-taking or handouts was minimized and the workshop remained truly hands-on. »

Marisa, Slicer Workshop SPL« I am incredibly impressed with the 3D Slicer program and the training workshop. I very

much appreciate that this preeminent program is available and maintained for the MacIntosh. Further the 3D Slicer workshop was a delight well organized and well taught, with a knowledgeable and helpful staff. »

Monica, Slicer Workshop SPL« As someone who had neither worked with freesurfer or 3D slicer before I found the

workshop a clear, informative introduction to the capabilities and use of both packages. With the help of the online tutorials, I look forward to using the software in the near future.

David, Slicer Workshop in San Diego

na-mic national alliance for medical image computing training core update sonia pujol – randy...

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