processing hardi data to recover crossing fibers maxime descoteaux phd student advisor: rachid...
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Processing HARDI Data to Recover Crossing Fibers
Maxime DescoteauxPhD student
Advisor: Rachid Deriche
Odyssée Laboratory, INRIA/ENPC/ENS,INRIA Sophia-Antipolis, France
Plan of the talk
Introduction of HARDI data
Spherical Harmonics Estimation of HARDI
Q-Ball Imaging and ODF Estimation
Multi-Modal Fiber Tracking
Short and long association fibers in the right hemisphere
([Williams-etal97])
Brain white matter connections
Radiations of the corpus callosum ([Williams-etal97])
Cerebral Anatomy
Diffusion MRI: recalling the basics
• Brownian motion or average PDF of water molecules is along white matter fibers
• Signal attenuation proportional to average diffusion in a voxel
[Poupon, PhD thesis]
Classical DTI model
Diffusion profile : qTDqDiffusion MRI signal : S(q)
• Brownian motion P of water molecules can be described by a Gaussian diffusion process characterized by rank-2 tensor D (3x3 symmetric positive definite)
DTI-->
Principal direction of DTI
QuickTime™ and aYUV420 codec decompressor
are needed to see this picture.
• DTI fails in the presence of many principal directions of different fiber bundles within the same voxel
• Non-Gaussian diffusion process
Limitation of classical DTI
[Poupon, PhD thesis]True diffusion
profileDTI diffusion
profile
High Angular Resolution Diffusion Imaging (HARDI)
• N gradient directions • We want to recover fiber crossings
SolutionSolution: Process all discrete noisy samplings on the sphere using high order formulations
162 points 252 points
[Wedeen, Tuch et al 1999]
Our Contributions
1. New regularized spherical harmonic estimation of the HARDI signal
2. New approach for fast and analytical ODF reconstruction in Q-Ball Imaging
3. New multi-modal fiber tracking algorithm
Sketch of the approachData on the
sphere
Spherical harmonic
description of data
ODF
For l = 6,
C = [c1, c2 , …, c28]
ODF
Spherical Harmonic Estimation of the Signal
Description of discrete data on the sphere
Physically meaningful spherical harmonic basis
Regularization of the coefficients
Spherical harmonicsformulation
• Orthonormal basis for complex functions on the sphere
• Symmetric when order l is even• We define a real and symmetric modified
basis Yj such that the signal
[Descoteaux et al. MRM 56:2006]
Spherical Harmonics (SH) coefficients
• In matrix form, S = C*BS : discrete HARDI data 1 x NC : SH coefficients 1 x R = (1/2)(order + 1)(order + 2)
B : discrete SH, YjR x N(N diffusion gradients and R SH basis elements)
• Solve with least-square C = (BTB)-1BTS
[Brechbuhel-Gerig et al. 94]
Regularization with the Laplace-Beltrami ∆b
• Squared error between spherical function F and its smooth version on the sphere ∆bF
• SH obey the PDE
• We have,
Minimization & -regularization
• Minimize (CB - S)T(CB - S) + CTLC
=>C = (BTB + L)-1 BTS
• Find best with L-curve method• Intuitively, is a penalty for having higher order
terms in the modified SH series=> higher order terms only included when needed
Effect of regularization
= 0
With Laplace-Beltrami regularization
[Descoteaux et al., MRM 06]
Fast Analytical ODF Estimation
Q-Ball Imaging
Funk-Hecke Theorem
Fiber detection
Q-Ball Imaging (QBI) [Tuch; MRM04]
• ODF can be computed directly from the HARDI signal over a single ball
• Integral over the perpendicular equator = Funk-Radon Transform
[Tuch; MRM04]~= ODF
ODF ->
Illustration of the Funk-Radon Transform (FRT)
Diffusion Signal
FRT->
ODF
Funk-Hecke Theorem
[Funk 1916, Hecke 1918]
Recalling Funk-Radon integral
Funk-Hecke ! Problem: Delta function is discontinuous at 0 !
Funk-Hecke formula
Solving the FR integral:Trick using a delta sequence
=>
Delta sequence
• Fast: speed-up factor of 15 with classical QBI• Validated against ground truth and classical QBI
[Descoteaux et al. ISBI 06 & HBM 06]
Final Analytical ODF expression in SH coefficients
Biological phantom
T1-weigthed Diffusion tensors
[Campbell et al.NeuroImage 05]
Corpus callosum - corona radiata - superior longitudinal fasciculus
FA map + diffusion tensors ODF + maxima
Multi-Modal Fiber Tracking
Extract ODF maxima
Extension to streamline FACT
Streamline Tracking
• FACT: FFiber AAssignment by CContinuous TTracking• Follow principal eigenvector of diffusion tensor• Stop if FA < thresh and if curving angle >
typically thresh = 0.15 and = 45 degrees)
• Limited and incorrect in regions of fiber crossing• Used in many clinical applications
[Mori et al, 1999Conturo et al, 1999,Basser et al 2000]
Limitations of DTI-FACT
Classical DTIPrincipal tensor direction
HARDIODF maxima
DTI-FACT Tracking
start->
DTI-FACT + ODF maxima
start->
Principal ODF FACT Tracking
start->
Multi-Modal ODF FACT
start->
DTI-FACT Tracking
start->
Principal ODF FACT Tracking
start->
Multi-Modal ODF FACT
start->
DTI-FACT Tracking
start->
start->
DTI-FACT Tracking
start->
<-start
Lower FA thresh
start->
start->
Very low FAthreshold
Principal ODF FACT Tracking
start->
start->
Multi-modal FACT Tracking
start->
start->
SummarySignal S on the
sphere
Spherical harmonic
description of S
ODF Fiber directionsMulti-Modal
tracking
Contributions & advantages
1) Regularized spherical harmonic (SH) description of the signal
2) Analytical ODF reconstruction• Solution for all directions in a single step• Faster than classical QBI by a factor 15
3) SH description has powerful properties• Easy solution to : Laplace-Beltrami smoothing, inner
products, integrals on the sphere• Application for sharpening, deconvolution, etc…
Contributions & advantages
4) Tracking using ODF maxima = Generalized FACT algorithm
=> Overcomes limitations of FACT from DTI1. Principal ODF direction
• Does not follow wrong directions in regions of crossing
2. Multi-modal ODF FACT• Can deal with fanning, branching and crossing
fibers
Perspectives
• Multi-modal tracking in the human brain• Tracking with geometrical information from locally
supporting neighborhoods• Local curvature and torsion information• Better label sub-voxel configurations like bottleneck,
fanning, merging, branching, crossing
• Consider the full diffusion ODF in the tracking and segmentation• Probabilistic tracking from full ODF
[Savadjiev & Siddiqi et al. MedIA 06], [Campbell & Siddiqi et al. ISBI 06]
BrainVISA/Anatomist
• Odyssée Tools Available• ODF Estimation, GFA Estimation• Odyssée Visualization• + more ODF and DTI applications…
• http://brainvisa.info/
• Used by:• CMRR, University of Minnesota, USA• Hopital Pitié-Salpétrière, Paris
QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.
Thank you!
Thanks to collaborators:C. Lenglet, M. La Gorce, E. Angelino, S. Fitzgibbons, P. Savadjiev, J. Campbell, B. Pike, K. Siddiqi, A. Andanwer
Key references:-Descoteaux et al, ADC Estimation and Applications, MRM 56, 2006.-Descoteaux et al, A Fast and Robust ODF Estimation Algorithm in Q-Ball
Imaging, ISBI 2006. -http://www-sop.inria.fr/odyssee/team/Maxime.Descoteaux/index.en.html
-Ozarslan et al., Generalized tensor imaging and analytical relationships between diffusion tensor and HARDI, MRM 2003.
-Tuch, Q-Ball Imaging, MRM 52, 2004
Principal direction of DTI
Spherical Harmonics
• SH
• SH PDE
• Real• Modified basis
Trick to solve the FR integral
• Use a delta sequence n approximation of the delta function in the integral• Many candidates: Gaussian of decreasing
variance
• Important property
n is a delta sequence
=>
1)
2)
3)
Nice trick!
=>
Funk-Hecke Theorem
• Key Observation:• Any continuous function f on [-1,1] can be extended to
a continous function on the unit sphere g(x,u) = f(xTu), where x, u are unit vectors
• Funk-Hecke thm relates the inner product of any spherical harmonic and the projection onto the unit sphere of any function f conitnuous on [-1,1]
• Funk-Radon Transform
• True ODF
Funk-Radon ~= ODF
(WLOG, assume u is on the z-axis)
J0(2z)
z = 1 z = 1000
[Tuch; MRM04]
Synthetic Data Experiment
• Multi-Gaussian model for input signal
• Exact ODF
Field of Synthetic Data
90 crossing
b = 1500SNR 15order 6
55 crossingb = 3000
ODF evaluation
Tuch reconstruction vsAnalytic reconstruction
Tuch ODFs Analytic ODFs
Difference: 0.0356 +- 0.0145Percentage difference: 3.60% +- 1.44%
[INRIA-McGill]
Human Brain
Tuch ODFs Analytic ODFs
Difference: 0.0319 +- 0.0104Percentage difference: 3.19% +- 1.04%
[INRIA-McGill]
Time Complexity
• Input HARDI data |x|,|y|,|z|,N• Tuch ODF reconstruction:
O(|x||y||z| N k)
(8N) : interpolation point
k := (8N) • Analytic ODF reconstruction
O(|x||y||z| N R)
R := SH elements in basis
Time Complexity Comparison
• Tuch ODF reconstruction:• N = 90, k = 48 -> rat data set
= 100, k = 51 -> human brain= 321, k = 90 -> cat data set
• Our ODF reconstruction:• Order = 4, 6, 8 -> m = 15, 28, 45
=> Speed up factor of ~3
Time complexity experiment
• Tuch -> O(XYZNk)• Our analytic QBI -> O(XYZNR)
• Factor ~15 speed up
Estimation of the ADC
Characterize multi-fiber diffusion
High order anisotropy measuresanisotropy measures
Apparent Diffusion Coefficient
ADC profile : D(g) = gTDgDiffusion MRI signal : S(g)
In the HARDI literature…
2 class of high order ADC fitting algorithms:
1) Spherical harmonic (SH) series[Frank 2002, Alexander et al 2002, Chen et al 2004]
2) High order diffusion tensor (HODT)[Ozarslan et al 2003, Liu et al 2005]
High order diffusion tensor (HODT) generalization
Rank l = 2 3x3
D = [ Dxx Dyy Dzz Dxy Dxz Dyz ]
Rank l = 4 3x3x3x3
D = [ Dxxxx Dyyyy Dzzzz Dxxxy Dxxxz Dyzzz Dyyyz Dzzzx Dzzzy Dxyyy Dxzzz Dzyyy Dxxyy Dxxzz Dyyzz ]
Tensor generalization of ADC
• Generalization of the ADC,
rank-2 D(g) = gTDg
rank-l
Independent elementsDk of the tensor
General tensor
[Ozarslan et al., mrm 2003]
Summary of algorithm
High OrderDiffusion Tensor
(HODT)
SphericalHarmonic (SH)
Series
Modified SH basis Yj
C = (BTB + L)-1BTX
Least-squares with-regularization
D = M-1C
M transformation
HODT Dfrom linear-regression
[Descoteaux et al. MRM 56:2006]
3 synthetic fiber crossing