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What to measure when measuring noise in
MRI
Santiago Aja-Fernández
UNIVERSIDAD DE VALLADOLID E. T. S. INGENIEROS DE TELECOMUNICACIÓN
Antwerpen 2013
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Noise in MRI
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Motivation:
• Many papers and methods to estimate noise out of MRI data.
• Noise estimation vs. SNR estimation• In single coil systems, variance of noise is a “good”
measure.• Complex systems: what are we really measuring? Is the
variance of noise still valid?
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Outline1. Noise in MR acquistions2. Basic Models
– Rician
– Non-central chi
3. More Complex Models– Correlated multiple coils
– Parallel MRI: SENSE and GRAPPA
4. The nc-chi example– Non-stationary noise
– Effective values
5. Other models
10. Conclusions
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1- Noise in MRI
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Scanner K-spaceX-space
(complex) magnitude
F-1 | . |
Signal acquisition (Single coil)
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K-spaceX-space
(complex)magnitude
F-1 | . |
Acquisition Noise (single coil)
Complex Gaussianσ2Κ
Complex Gaussianσ2n=σ2Κ /|Ω|
Ricianσ2n
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F-1
Signal acquisition (Multiple coil)
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F-1
Acquisition noise (Multiple coil)
Complex Gaussianσ2Κi
Complex Gaussianσ2i=σ2Κi /|Ω|
ρ12
σ2Κ2
σ2Κ3
σ2Κ4
σ21
σ22
σ23
σ24ρ2
3ρ34
ρ14
ρ12
ρ14
ρ34
ρ23
σ2Κ1
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Acquisition noise:
• Noise in receiving coils is complex Gaussian (assuming no post-processing)
• Noise in x-space related to noise in k-space• Final distribution will depend on the
reconstruction
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2- Basic Noise Models
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K-spaceX-space
(complex)magnitude
F-1 | . |
Rician Model
Complex Gaussianσ2Κ
Complex Gaussianσ2n=σ2Κ /|Ω|
Ricianσ2n
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Complex
Magnitude
Rician
Rayleigh
Rician Model
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RicianGaussian
σn Meaning of σn?
SNR=A / σn
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Non-central chi model
Complex Gaussianσ2i=σ2Κi /|Ω|
σ21
σ22
σ23
σ24
ρ12
ρ14
ρ34
ρ23
Particular case:
σ2i= σ2j = σ2nρij=0
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Non-central chi model
Complex Gaussianσ2n|
σ2n
σ2n
σ2n
σ2n
Sum of Squares
Non central chiL, σ2n|
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Non-central chi model
Non Central Chi
Central Chi
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Basic models:
• Rician: relation between σ2n and variance of noise in Gaussian complex data.
• Nc-chi: also relation between σ2n and Gaussian Variance.
• Nc-chi: many times, interesting parameter σ2n·L
EM(x)2=A(x)2+2L·σ2n
SNR=A(x)/L1/2·σn• Usually: equivalence between L·σ2n (nc-chi)
and σ2n (Rician).
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Example: Conventional approach
Rician
Noncentral-chi
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Example: LMMSE filter
Rician
Noncentral-chi
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3- More Complex Models
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Limitation of the nc-model:
Only valid if:• Same variance of noise in each coil• No correlation between coils• No acceleration• Reconstruction done with sum of squares
Real acquisitions.• Correlated, different variances• Accelerated• Reconstructed with different methods
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A- Effect of Correlations
σ21
σ22
σ23
σ24
ρ12
ρ14
ρ34
ρ23
=
221
22221
11221
LLL
L
L
σσσ
σσσσσσ
Σ
Sum of Squares
Nc-chi no longer valid!!!
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Nc-chi approximation if effective parameters are used
Relative errors in the PDF for central-chi approximation as a function of the correlation coefficient. A) Using effective parameters. B) Using the original parameters.
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B- Sampling of the k-space:
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In real acquisitions:
• Different variances and correlations → effective values and approximated PDF.
• Subsampling → modification of σ2i in x-space
• Reconstruction method → output may be Rician or an approximation of nc-chi
• The variance of noise (σ2i) becomes x-dependant → σ2i(x)
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Survey of statistical models for MRI
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4- Example: the non stationary nc-chi
approximation
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Nc-chi approximation
σ21
σ22
σ23
σ24
ρ12
ρ14
ρ34
ρ23
=
221
22221
11221
LLL
L
L
σσσ
σσσσσσ
Σ
Sum of Squares
Nc-chi approximation if effective parameters
are used
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Effective number of coils as a function of the coefficient of correlation. A) Absolute value. B) Relative Value.
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σeff(x) Leff(x)
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• Params. σeff(x) and Leff(x) both depend on x.
• Good news:
Leff(x)· σ2eff(x)= tr(Σ)=σ21+…+ σ2L=L·< σ2i >
• The product is a constant:
Leff(x)· σ2eff(x)=L·σ2n
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Implications:
• Equivalence between effective and real parameters
• Product: easy to estimate
Leff(x)· σ2eff(x)= L·σ2n=mode EML2(x)x / 2
• In some problems: only product needed:I2(x)= EML2(x)x - 2L·σ2n
• NOTE: If effective values are used for σ2eff(x), also for Leff(x)·
σ2eff(x)·L → Wrong!!!
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Implications:
• My point of view: σ2eff(x) and Leff(x) should be seen as a single parameter:
σ2L = Leff(x) · σ2eff(x)and therefore
σ2eff(x) = σ2L / Leff(x) • Some applications do need σ2eff(x)
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• Param. σ2eff(x) now depends on position.• The dependence can be bounded. SNR → 0
σ2B= σ2n(1+<ρ2>(L-1)) SNR → ∞
σ2S= σ2n(1+<ρ>(L-1)) Total:
σ2eff(x)=(1-φ(x)) σ2S + φ(x) σ2Bwith
φ(x)=(SNR2(x)+1)-1
X-dependant noise:
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σ2B
σ2S
Where is noise estimated?
What to estimate: σ2eff(x), σ2n,σ2B, σ2S…
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Implications:
• Estimation over the background → underestimation of noise.
• Use of a single value of σn → error is most areas.
• Noise is higher in the high SNR.• Main source of non-stationarity: correlation
between coils.• High correlation: lower effective coils and
higher noise.• Possible source of error: σ2eff(x)·L
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5- Other models
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SENSE: (non stationary Rician)
σ2R(x) x-dependant noise
σ2n = σ2K (r / |Ω|)
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σeff(x)
GRAPPA: nc-chi approx.
Leff(x) (σ2eff(x) Leff(x) )1/2
σ2n = σ2K / (r |Ω|)Product σ2eff(x)·Leff(x) is not a
constant
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6- Conclusions
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• Be sure what you need in your application.• Follow the whole reconstruction pipeline to
be sure which is your “original” noise.• Useful: simplified models to make process
easier.• Be sure how noise affects the different slides.
Conclusions:
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Questions?
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What to measure when measuring noise in
MRI
Santiago Aja-Fernández
UNIVERSIDAD DE VALLADOLID E. T. S. INGENIEROS DE TELECOMUNICACIÓN
Antwerpen 2013