Software Packages for DTI/DWI QC and Analysis

Software Packages for DTI/DWI QC and Analysis

UNC Styner Group &

Utah Gerig Group

April 2014

Disclaimer

I don’t talk about MINC software

But

I discuss open-source/open-platform software freely available to the scientific community

& linked to MINC via Vladimirs itk file format conversion tools (nifty, nrrd, meta, gipl, etc.)

Alexander Leemans (Alexander@isi.uu.nl)

http://www.samsi.info/workshop/summer-2013-neuroimaging-data-analysis-june-4-14-2013

Alexander Leemans (Alexander@isi.uu.nl)

Hi Alex, I have been collecting “advanced DTI data”. Can you help me with the analysis?*

* Read: “Can you do the analysis for me?”

Alexander Leemans (Alexander@isi.uu.nl)

Alexander Leemans (Alexander@isi.uu.nl)

Alexander Leemans (Alexander@isi.uu.nl) Tournier J.-D. et al, Magn Reson Med (2011)

Our Approach • Assume that there is always a QC problem: Hardware, scanning

sequence, coils, export, protocol violation, table vibrations, subject motion, FOV errors, DICOM conversion, problems with analysis software.

• To develop and disseminate (open-source, open-platform) advanced QC software for quantitative analysis of image quality and for image correction.

• To publish papers associated with QC tools and methods → to raise awareness and inform.

• To develop guidelines for researchers and clinical users on how best to correct data for artifacts.

• Rules to become standard: No journal article on DWI use should be accepted unless researchers prove that there is rigorous QC testing and quantitative evidence that reported results are not a confounding factor of artifacts.

National Alliance for Medical Image Computing http://na-mic.org Slide 9

Diffusion Artifacts

Diffusion images are sensitive to a number of artifacts

• Motion

• Eddy-current distortions

• Noise/SNR issues

• Vibrational artifacts

• Venetian blind artifacts

• “unknown”…

Bad DWI’s are removed/corrected

Need tools that go beyond eyeballing

ACE-IBIS infant study, >1200 DWI (25 directions, >50 slices)

• Oguz, M. Farzinfar, J. Matsui, F. Budin, Z. Liu, G. Gerig, H.J. Johnson, M.A. Styner. “DTIPrep: Quality Control of

Diffusion-Weighted Images,” In Frontiers in Neuroinformatics, Vol. 8, No. 4, 2014. DOI: 10.3389/fninf.2014.00004

• PDF: http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00004/full

• Instruction manuals, Slicer and NITRC downloads: http://www.na-mic.org/Wiki/index.php/SPIE_2013_DTI_Workshop

M. Styner et al., UNC Chapel Hill & Gerig et al., Utah group.

National Alliance for Medical Image Computing http://na-mic.org Slide 15

QC Result

• Loads QC’ed DWI

when finished

• Detailed reporting

• Directions after

motion correction

• Reasons for

exclusion

Assume there is always Motion

Average and standard deviation of the percentage of motion-corrupted gradient directions as a function of thresholding on the estimated rotation angle in degrees (left) and the estimated translation magnitude in mm (right) for three human phantoms scanned twice at four clinical sites. Boxplots: Overall statistics of estimated motion parameters.

24 multi-site DWI scans of human phantom

Alexander Leemans (Alexander@isi.uu.nl)

“Subject motion”

Leemans A. & Jones D.K., Magn Reson Med (2009)

Alexander Leemans (Alexander@isi.uu.nl)

“Corrected for subject motion”

Leemans A. & Jones D.K., Magn Reson Med (2009)

Motion correction by DTIprep

Motion correction by DTIprep

Testing the Testing: S. Elhabian and G. Gerig, Utah

QA analysis of ODF construction (anisotropy of the dominant fiber), dipy analysis package.

Stripes seem bug in dipy analysis SW. QA analysis of ODF construction (reprogrammed). QC needs COMMUNITY EFFORT!

System’s Approach: Elhabian et al., submitted

3D Slicer (NA-MIC, R. Kikinis)

DWI software: Instruction manuals, Slicer and NITRC downloads:

http://www.na-mic.org/Wiki/index.php/SPIE_2013_DTI_Workshop

Details: Frontiers paper: DOI: 10.3389/fninf.2013.00051

www.slicer.org

UNC-Utah DTI Fiber Analysis • Analysis of DTI properties along the fiber

• Many years of methods & tool development

• Allows for localized analysis with high sensitivity

A.R. Verde, F. Budin, , G. Gerig, M. Styner. “UNC-Utah NA-MIC framework for DTI fiber tract analysis,” In Frontiers in Neuroinformatics, (7)51, Jan, 2014. DOI: 10.3389/fninf.2013.00051

I: DTI atlas building Combined v06-v12-v24 DTI atlas, Clement Vachet, Utah) (September: 978 data points, ACE-IBIS project)

Concept: S. Joshi, B. Davis, M Jomier, G. Gerig. “Unbiased Diffeomorphic Atlas Construction for Computational Anatomy,” In Neuroimage, Vol. 23 Suppl. 1, pp. S151--S160. 2004.

II: Tractography in Atlas Space: Use your favorite algorithm

Example Utah DS study: Tractography in atlas space of 17 healthy controls, language related tracts (unpublished)

• DSIstudio • 3D Slicer • DTIstudio • MINC tools • UNCTrack • dpy toolbox • Etc.

III: Tract Parametrization

Corouge et al. Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis. Medical Image Analysis 2006.

IIIb Tract Modeling: FiberViewer Light

FIberViewerLight: http://www.nitrc.org/projects/fvlight/

IV: Mapping tract back to original space

V: Statistics: Functional Data Analysis (FDA) on Fiber Bundles

Hongbin Gu: Longitudinal modeling with covariates

Hongtu Zhu: FMVCM

multiple diffusion properties along major white matter fiber bundles and their association with a set of covariates

V: Example: Tract diffusion development versus age

X. Geng, S. Gouttard, A. Sharma, H. Gu, M. Styner, W. Lin, G. Gerig, J.H. Gilmore. “Quantitative Tract-Based White Matter Development from Birth to Age Two Years,” In NeuroImage, pp. 1-44. March, 2012. DOI: 10.1016/j.neuroimage.2012.03.057

History:

• 2000/2001: SNAP Prototype: Student semester projects UNC Chapel Hill, G. Gerig

• 2003: NLM funding to port to ITK (Paul Yushkevich, U-Penn)

• 2004: itk-SNAP released, Linux, Windows and MacOS

• 2007: NIBIB R03 (Yushkevich), itk-SNAP 2.x

• 2012-14: NIBIB R01 (Yushkevich/Gerig) Multimodal itk-SNAP

Functionality:

• 3D level-set segmentation with step-by-step user-guidance for complex pipeline, open-source, open-platform

• Full 3D interactive editing in 2D and 3D.

• http://www.itksnap.org

MRIWatcher

MRIWatcher: ITK SW for quick

viewing of large #3D datasets,

with coupled zoom/scroll,

overlays, info: Quick QC,

reviewing, comparison.

MriWatcher: http://www.nitrc.org/projects/mriwatcher/

ABC: Atlas Based Classification Fully automatic, atlas-moderated segmentation pipeline • Stand-alone (http://www.nitrc.org/projects/abc) software system,

former EMS, so far applied to over 5000 brain MRI • Slicer plugin module (Utah: Prastawa, Gerig) • Flexible use of probabilistic atlases (infants, adults, monkeys) • Deformable registration of probabilistic atlas (fluid multimod.) • Multi-modal co-registration, arbitrary #channels • Includes pre-filtering, brain stripping, and bias-correction • Output: Posterior probabilities, binary label maps

Other tools: (collab. with M. Styner, UNC)

All tools come with comprehensive tutorials

http://www.ia.unc.edu/dev/download/index.htm