Data interoperability of DTI-TK for DTI analysis A …...A typical DTI analysis pipeline for group...

Data interoperability of DTI-TK for DTI analysis&

A preview of ITK-SNAP 2.0

Gary Hui Zhang, Paul A Yushkevich, and James C Gee

Penn Image Computing & Science Laboratory (PICSL)Department of Radiology, University of Pennsylvania

Copyright © 2009 Gary Hui Zhang

Sunday, June 21, 2009

Data interoperability of DTI-TK for DTI analysis



A typical DTI analysis pipeline for a single subject

Tensor reconstruction

Diffusion-Weighed Images

Diffusion-Tensor Images

Fiber Tractography

White Matter (WM) Tracts

Feature Computation

Measures of WM Tracts







Fiber Tractography


Feature Computation


e1







Fiber Tractography


Feature Computation




A typical DTI analysis pipeline for group studies

subject 1




Fiber Tractography


Feature Computation


subject 2




Fiber Tractography


Feature Computation


subject n




Fiber Tractography


Feature Computation


Population studies Spatial Normalization



How do existing DTI tools support DTI analysis?

each subject




Fiber Tractography


Feature Computation


Spatial Normalization




each subject




Fiber Tractography


Feature Computation



CaminoLargest collection of tensor reconstruction algorithms & HARDI




each subject




Fiber Tractography


Feature Computation




FSLProbabilistic tractography &Tract-based spatial statistics (TBSS)




each subject




Fiber Tractography


Feature Computation





DTIStudioInteractive deterministic tractography &Tract-specific ROI analysis




each subject




Fiber Tractography


Feature Computation





DTIStudioInteractive deterministic tractography &Tract-specific ROI analysis

DTI-TKDTI spatial normalization + atlas construction & Tract-specific analysis



DTI ToolKit: A Spatial Normalization and Atlas Construction Toolkit

Optimized for Examining White Matter Morphometry Using DTI Data.

Control Population

Subject 1

Subject 2

Subject 3

Subject 4

Disease Population

Subject 1

Subject 2

Subject 3

Subject 4

Atlas

Control Population

Subject 1

Subject 2

Subject 3

Subject 4

Disease Population

Subject 1

Subject 2

Subject 3

Subject 4

More discriminatingimage features

Better Registration

Closest to the average ofthe populations in shape and features

!

"

Spatial normalization and atlas construction White matter morphometry

whole-brain

tract-specific

T1 DTI

?

?

Tensor-based registration leverages rich

discriminating features afforded by DTI !

Population-specific white matter

atlas with shape-averaging"

Hui Zhang, Paul A Yushkevich, and James C Gee

Penn Image Computing and Science Laboratory (PICSL), University of Pennsylvania

Summary of Key Features:

• Open standard-based file IO support: NIfTI format for scalar, vector

and tensor image volumes

• Tool chains for manipulating tensor image volumes: resampling,

smoothing, warping, registration and visualization

• Pipelines for White Matter Morphometry: spatial normalization and

atlas construction for population-based studies

• Built-in cluster-computing support via Sun Grid Engine

• Interoperability with other popular DTI tools: AFNI, Camino, FSL

• Interoperability with ITK-SNAP to support multi-modal segmentation

Coming soon:

• Interoperability with DTI Studio

• Tract-specific analysis [4]

Binaries for Linux and Mac OS X Available at http://www.nitrc.org/projects/dtitk

References:

[1] Zhang et al. Deformable registration of diffusion tensor MR images

with explicit orientation optimization.!Medical Image Analysis, 10(5):

764-785, October 2006.

[2] Zhang et al. Unbiased white matter atlas construction using

diffusion tensor images. In!MICCAI, volume 4792 of!LNCS, pages

211-218, October 2007.

[3] Zhang et al.. High-dimensional spatial normalization of diffusion

tensor images improves the detection of white matter differences in

amyotrophic lateral sclerosis.!IEEE Transactions on Medical Imaging,

26(11):1585-1597, November 2007.

[4] Yushkevich et al. Structure-specific statistical mapping of white

matter tracts. NeuroImage, 41(2):448-461, June 2008.

Acknowledgement:

The authors gratefully acknowledge the support from NIH via

the grants P30-NS045839, R01-EB006266, R01-DA022897,

R21-NS061111, K25-AG027785, R03-EB008200, and R03-

EB009321.


For download, visit http://www.nitrc.org/projects/dtitkSunday, June 21, 2009

http://www.nitrc.org/projects/dtitk

http://www.nitrc.org/projects/dtitk

DTI-TK Quick Look Plugin for Mac OSXAll Downloads

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206K

About DTI-TK Quick Look Plugin

This plugin uses the Mac OS X

Leopard’s built-in innovative Quick

Look framework to enable a quick

assessment of any 3-dimensional

image volume in the supported

medical image formats (NIfTI /

Analyze / FreeSurfer) directly from

the Finder. Using the Finder’s Cover

Flow mode, a large collection of

medical images can be browsed

through and quickly inspected just

as easy as flipping through your

photos. Furthermore, a large

number of images can be compared

side-by-side by selecting them

together in the Finder, then pressing

the space bar to bring up the Quick

Look preview mode.

What’s New in this Version

- Improved user feedback for failed

image preview

Company: university of pennsylvania

Version: 1.7.3

Post Date: June 8, 2009

License: Freeware

File Size: 206K

URL Type: Download

Download ID: 24493

206K

System Requirements

Mac OS X 10.5 or later

Download Details

DTI-TK Quick Look Plugin 1.7.3Recently Added to

Imaging & 3D

ViewIt 2.31

06/19/2009

3D Image Commander 1.05

06/19/2009

solidThinking 7.6

06/18/2009

Contenta Converter Premium

4.5

06/18/2009

OSG Composer CAD 1.0

06/18/2009

Vue Personal Learning Edition

7.5

06/17/2009

Microspot Interiors

Professional 4.1

06/17/2009

PhotoK 0304

06/17/2009

Goodies: Keynote Objects FX

1.0

06/17/2009

Toycamera AnalogColor 0.3

06/17/2009

Apple is providing links to these applications as a courtesy, and makes no representations regarding the applications or any information related thereto. Any questions, complaints or claims regarding

the applications must be directed to the appropriate software vendor.



DTI-TK Quick Look Plugin: Cover Flow Mode



DTI-TK Quick Look Plugin: Multi-Volume Preview



Data interoperability of diffusion tensor images

D =

!

"

Dxx Dyx Dzx

Dyx Dyy Dzy

Dzx Dzy Dzz

#

$

= !1e1eT

1 + !2e2eT

2 + !3e3eT

3




D =

!

"

Dxx Dyx Dzx

Dyx Dyy Dzy

Dzx Dzy Dzz

#

$

= !1e1eT

1 + !2e2eT

2 + !3e3eT

3

matrix representation




D =

!

"

Dxx Dyx Dzx

Dyx Dyy Dzy

Dzx Dzy Dzz

#

$

= !1e1eT

1 + !2e2eT

2 + !3e3eT

3


eigensystem representation




D =

!

"

Dxx Dyx Dzx

Dyx Dyy Dzy

Dzx Dzy Dzz

#

$

= !1e1eT

1 + !2e2eT

2 + !3e3eT

3

(Dxx, Dyx, Dyy, Dzx, Dzy, Dzz)DTI-TK This is the NIfTI Tensor standardlower triangular






D =

!

"

Dxx Dyx Dzx

Dyx Dyy Dzy

Dzx Dzy Dzz

#

$

= !1e1eT

1 + !2e2eT

2 + !3e3eT

3


Camino Dxx, Dyy, Dzz, Dyx, Dzx, Dzy

individual NIfTI scalar files






D =

!

"

Dxx Dyx Dzx

Dyx Dyy Dzy

Dzx Dzy Dzz

#

$

= !1e1eT

1 + !2e2eT

2 + !3e3eT

3




(Dxx, Dyx, Dzx, Dyy, Dzy, Dzz)FSL !1,!2,!3, e1, e2, e3 or upper triangularindividual NIfTI scalar or vector files






D =

!

"

Dxx Dyx Dzx

Dyx Dyy Dzy

Dzx Dzy Dzz

#

$

= !1e1eT

1 + !2e2eT

2 + !3e3eT

3




(Dxx, Dyx, Dzx, Dyy, Dzy, Dzz)FSL !1,!2,!3, e1, e2, e3 or upper triangularindividual NIfTI scalar or vector files



DTIStudio Dxx, Dyy, Dzz, Dyx, Dzx, Dzy

individual Analyze files for export

FA, e1

individual raw binary files for import



Data interoperability tools in DTI-TK




• Interoperability to Camino, FSL, and DTIStudio





• fully implemented, tested, and documented






• Benefits






• Benefits

• Make the core capability of DTI-TK accessible to users of major DTI tools






• Benefits


• Users can choose their favorite tools for tensor reconstruction






• Benefits



• Minimal adoption barrier for users with existing DTI analysis pipeline






• Benefits




• Access to new capability of DTI-TK, such as the tract-specific analysis.






• Benefits





• Improve the quality of DTI analysis within the neuroimaging community






• Benefits






• Users can now choose the best available tool for each component in their analysis pipeline






• Benefits






• Users can now choose the best available tool for each component in their analysis pipeline

• New techniques can be more easily compared to existing tools



A preview of ITK-SNAP 2.0



Overview of ITK-SNAP




• ITK-SNAP is a software application used to segment structures in 3D medical images. It provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation.





• Key enhancements implemented for version 2.0






• Full featured multi-session synchronized image navigation - enabling synchronized cursor, zoom and pan







• Full NIfTI support - enabling synchronized image navigation across multiple ITK-SNAP sessions even when images have oblique orientation








• Full featured multiple image overlay support - enabling multiple RGB or greyscale image overlay as well as greyscale to color mapping









• Enhanced support for manual segmentation via the new adaptive brush









• Enhanced support for manual segmentation via the new adaptive brush

• User experience enhancement, including redesigned user interface, native file chooser, and automatic check for update



ITK-SNAP 2.0 Preview Demo

For download, visit http://www.itksnap.org



http://www.itksnap.org

http://www.itksnap.org

Acknowledgement

• DTI-TK

• NIH grant: R03 EB009321

• DTI-TK user community

• ITK-SNAP

• NIH grant: R03 EB008200

• Prof. Guido Gerig, original SNAP developers at UNC

• ITK-SNAP user community

Thank you for your attention.



Data interoperability of DTI-TK for DTI analysis A …...A typical DTI analysis pipeline for group...

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