training core update sonia pujol, phd randy gollub, md, phd harvard medical school

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

Training Core Update

Sonia Pujol, PhDRandy Gollub, MD, PhDHarvard Medical School

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

NA-MIC outreach activities at international conferences


Radiologists• NA-MIC Workshop for

Radiology residents, Brigham & Women’s Hospital, Boston, MA


Radiologists• NA-MIC Workshop for

Radiology residents, Brigham & Women’s Hospital, Boston, MA

• Hands-on training on 3D visualization of the Anatomy


Radiologists

• Task-oriented course on the liver segmentsRSNA 2009, Chicago, IL


Radiologists

• Task-oriented course on the liver segmentsRSNA 2009, Chicago, IL

• Course score on the RSNA evaluation form: 4.13/5.00


Neurosurgeons

•Hands-on training workshop in Image-Guided Therapy for neurosurgeons

•IBMISPS 2009 conference, Boston, MA

A. Golby, N. Hata, H. Liu A. Golby, N. Hata, H. Liu


Autism Researchers

• NA-MIC presentation at the annual meeting of the International Society for Autism Research

IMFAR 2009, Chicago, IL

““Use of the Slicer3 toolkit to produce Use of the Slicer3 toolkit to produce regional cortical thickness regional cortical thickness

measurements of pediatric MRI measurements of pediatric MRI data “ data “

Heather Cody et al., IMFAR 2009Heather Cody et al., IMFAR 2009

H.Cody


Orthopedic Surgeons

• 3D Visualization Workshop for Image-guided Therapy applications in Orthopedic Surgery

• Annual Meeting of the International Society for Computer Assisted Orthopaedic Surgery (CAOS 2009), Boston MA


Neuroscientists• ‘Mapping the Brain with

Diffusion Tensor Imaging’

One-day NA-MIC Workshopon DTI Analysis

• Annual Meeting of the Society for Neuroscience, SFN 2009, Chicago IL


Integration with CTSAs

• New partnership with the NIH NCRR funded Clinical Translational Science Awards (CTSAs) national Imaging Working Group




• Greatly expands the end-user community exposure to the NA-MIC kit




• Greatly expands the end-user community exposure to the NA-MIC kit

• Provides critical clinically relevant driving forces for new developments


Joint Workshop on Imaging Biomarkers

• Workshop on Quantitative Medical Imaging for Clinical Research and Practice -RSNA 2009, Chicago, IL





• More than 100 attendees


New PET/CT Fusion Module

PET/Fusion Module Programming

&Tutorial: Wendy Plesniak, Ph.D.

Special Thanks to Kathryn Hayes


Harvard Catalyst (CTSC)

• Jointly sponsored Slicer workshops delivered on a regular basis.


Harvard Catalyst (CTSC)

• Jointly sponsored Slicer workshops delivered on a regular basis.

• 1-hour hands-on training sessions on medical image analysis at Harvard Medical School


Tutorial Contests• Winter Project Week

2009, Salt Lake City• Summer Project Week

2009, Boston• Winter Project Week

2010, Salt Lake City

17 new additions of tutorials and training datasets to the NA-MIC Compendium


NA-MIC Compendium

NA-MIC Training Compendium &

Workshops


NA-MIC Compendium

1595 tutorial slides on 27 different

topics in medical image analysis


NA-MIC outreach activities

2005-2009:

More than 900 scientists and clinicians trained by NA-MIC at national and

international venues

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

DTI Tractography Validation Update

Sonia Pujol, Ph.D.Harvard Medical School


DTI Validation Challenge

• Comparison of DTI tractography algorithms in the absence of ground truth


DTI Validation Challenge

• Comparison of DTI tractography algorithms in the absence of ground truth

• Evaluation of different DTI tractography approaches in the absence of common platform


Tractography errors

Optic radiation

Courtesy of Dr. JJ Lemaire

Optic chiasm


Step1: Implementation of the Validation Framework

GTRACTIowa

University

StreamlineBWH, Harvard

Volumetric ConnectivitySCI, Utah

Fiber Tracking SCI, Utah

3D Slicer


Step 2: Implementation of the Validation Pipeline

Warfield SK, Zou KH, Wells WM. Simultaneous Truth and Performance Level Estimation (STAPLE): An algorithm for the Validation of Image Segmentation. IEEE Trans Med Imaging. 23(7):903-21.


Step 3: Evaluation of the Validation Method

•Evaluation of the accuracy and precision of the validation framework in synthetic data experiments.

STAPLE estimate tractography performances are accurate


Experiment 1: STAPLE Analysis applied to DTI

• Preliminary results on three different fascicles showed differences in sensitivity among algorithms.

Internal Capsule

A1: Fiber TrackingA2: 3DSlicerA3: GTractA4: Volumetric Connectivity


Abstract Presented at ISMRM 2009

Preliminary results on the use of STAPLE for evaluating DT-MRI tractography in the

absence of ground truth

S.Pujol, C-F Westin, R.Whitaker, G.Gerig, T.Fletcher, V.Magnotta, S.Bouix, R.Kikinis, W.Wells III, R.Gollub.

ISMRM 2009, Apr.18-24 2009,Honolulu, Hi


STAPLE Analysis applied to DTI

• Preliminary results showed differences in sensitivity among algorithms


STAPLE Analysis applied to DTI

• Preliminary results showed differences in sensitivity among algorithms

• Question: What is the statistical significance of the differences observed ?


Experiment 2: Statistical Analysis

25 DWI datasets


Experiment 2: Statistical Analysis

• The statistical analysis showed significant differences in sensitivity among 3D segmentations of the Arcuate Fasciculus by different algorithms

Arcuate Fasciculus

A1: Fast MarchingA2: GTractA3: StreamlineA4: Stochastic


Abstract presented at MICCAI 2009 DMFC Workshop

Towards Validation of DTI Tractography: Statistical Analysis of the Differences

Observed Among Tractography Algorithms

S.Pujol, V.Magnotta, J.De Siebenthal, M.Kubicki, K.Hayes, C-F.Westin, JJ.Lemaire, R.Kikinis, R.L. Gollub, W.Wells

III .

MICCAI 2009, Sept. 20-24,London, UK


DTI Validation Milestones• Implementation of the validation

framework• Evaluation of the validation

framework• Preliminary DTI Tractography

validation experiments • Statistical Analysis of the

differences observed among algorithms


DTI Validation Update

training core update sonia pujol, phd randy gollub, md, phd harvard medical school

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