johns hopkins dti projects jonathan farrell bennett landman, hao huang, thomas ng man cheuk, susumu...
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Johns Hopkins DTI ProjectsJonathan Farrell
Bennett Landman, Hao Huang,
Thomas Ng Man Cheuk, Susumu Mori
2 Progress Report Slides
To Do List from 2005
• High SNR DTI Calibration Dataset @ 1.5T– Several studies wrap up & publish
– Original and coregistered data post
– Useful software post
• DTI Database of 61 Healthy Controls @ 1.5T– Original data post
– Coregistered and processed data post
• Image Distortion Correction for DTI– Study wrap up & publish
• Tractography Reproducibility– Study wrap up & publish
Progress Report in 2006
• High SNR DTI Calibration Dataset @ 1.5T– Several studies 2 papers submitted
– Original and coregistered data Posted
– Useful software 2 posted + 1 soon
• DTI Database of 61 Healthy Controls 1.5T– Original data Posted
– Coregistered and processed data soon
• Image Distortion Correction for DTI– Study under revision (round 2)
• Tractography Reproducibility– Study under revision (round 2)
Summary of Each Project
GoalResults
Endpoints
DTI Calibration Study: SNR
QUESTION: How does SNR affect DTI contrasts in vivo ?
TAKE HOME POINT: Provide methods to calibrate SNR across sites
ENDPOINT: Paper submitted September 2006
DTI Calibration Study: DW Scheme
QUESTION: Which diffusion weighting scheme should you use and why?
TAKE HOME POINT: Use a scheme with many directions ( ~ 30) to get uniform precision and accuracy at all
fiber orientations. BUT…Effect size is small (less than intra and inter scan variability)
ENDPOINT: Paper submitted October 2006
Multi-Site DTI Calibration Study
GOAL: Measure accuracy and precision of DTI contrasts at several imaging sites and scanners.
DATA COLLECTION SITES: Johns Hopkins Duke MGH University of Texas South Western
DETIALS: Will make DTI-contrast vs SNR curves Hopefully, the sites show similar behavior
Software: CATNAP
GOAL: To simplify and accelerate DTI &
anatomical data processing
HOW IT WORKS: Coregistration with FSL FLIRT Computes DTI gradient table Computes diffusion tensor and
DTI contrasts
DETIALS: Runs in MATLAB Philips data only (so far)
http://www.nbirn.net/downloads/
Software: DTI_gradient_table_creator
GOAL: Figure out the gradient
table for Philips DTI data
HOW IT WORKS: Takes scanner / imaging
options & parameters into account
Rules can be tricky !
DETIALS: MATLAB function JAVA applet (online)
http://www.nbirn.net/downloads/
Software: PARtoNRRD_Philips
GOAL: Create NRRD headers files for Philips DTI data .nhdr files contain all relevant DTI parameters
Resolution, FOV, Slices Gradient directions, b-value, coordinate space
Compatible with Slicer
HOW IT WORKS: Uses .par file (Philips text file) Uses DTI_gradient_table_creator_Philips_RelX
WHAT YOU NEED : .nhdr file and .rec (data file) Will be posted soon
http://www.nbirn.net/downloads/
GOAL: Distribute DTI data for 61 healthy controls
DTI Database of Healthy Controls
ISSUES: Data management, defacing and de-identification
ENDPOINT: Original data (posted), coregistered data (TBD), meta-data (TBD)
http://www.nbirn.net/downloads/
Tractography Reproducibility
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Intra-rater
Inter-raterAlmost perfect
Substantial
Moderate
Fair
GOAL: Test reproducibility of tractography Performed multi-site inter-rater tests for 11 major WM tracts.
RESULTS: Substantial reproducibility
was observed for the protocol developed under this project
ENDPOINT: Paper submitted and under
revision
Image Distortion Correction for DTI
a) Non distorted T1w image, b) DTI with distortion
c) Landmark-based LDDMM correction
d) Intensity –based SPM e) segmentation-based SPM.
f) The LDDMM method undistorts the image smoothly g) Guantifies the distortion by Jacobian. Although the segmentation-based SPM could correct the distortion (e), the transformation contains severe discontinuity (h), which may cause DTI calculation errors.
Paper is in preparation.Working on implementing other techniques (Song, others)