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Vol. 2, No. 10, 2010
Denoising of Magnetic Resonance Images using
Wavelets- A Comparative Study
S Satheesh1 Dr.KVSVR Prasad2
1
Asst.Prof., Dept. of ECE, G Narayanamma Institute of Technology and Science, Hyderabad, , India
satheesh.s17@gmail.com
2
Prof. & Head Dept. of ECE, D.M.S.S.V.H. College of Engineering, Machilipatnam, India
3
Asst.prof., Dept. of ECE, G Narayanamma Institute of Technology and Science, Hyderabad, India
Abstract: Image denoising has become an essential exercise in
medical imaging especially the Magnetic Resonance Imaging
(MRI). As additive white Gaussian noise (AWGN) exhibits finest
grain property of noise, multi resolution analysis using wavelet
transform is gaining popularity. The aim of the work is to
compare the effectiveness of three wavelet based denoising
algorithms viz. Wiener filter, hard threshold and soft threshold
using MRI images in the presence of AWGN. Wiener filter
performs better visually and in terms of PSNR than the other
thresholding techniques.
Keywords: Denoising, Wavelet, MRI, Wiener filtering,
Threshold
1. Introduction
Image denoising is a procedure in digital image
processing aiming at the removal of noise, which may
corrupt an image during its acquisition or transmission,
while retaining its quality. Medical images obtained from
MRI are the most common tool for diagnosis in medical
field. These images are often affected by random noise
arising in the image acquisition process. The presence of
noise not only produces undesirable visual quality but also
lowers the visibility of low contrast objects. Noise removal is
essential in medical imaging applications in order to
enhance and recover anatomical details that may be hidden
in the data.
The wavelet transform has recently entered the arena of
image denoising and it has firmly established its stand as a
powerful denoising tool. There has been a fair amount of
research on filtering and wavelet coefficients thresholding
[8], because wavelets provide an appropriate basis for
separating noisy image from the original image. These
wavelet based methods mainly rely on thresholding the
discrete wavelet transform (DWT) coefficients, which have
been affected by AWGN.
There has been much research by Donoho & Johnstone [1,
2, 3] on finding thresholds, however few are specifically
designed for images. One of the most popular method
consists of thresholding the wavelet coefficient (using the
hard threshold or the soft threshold) as introduced by
Donoho.
Another denoising method in the wavelet domain consists of
Wiener filtering the wavelet coefficients. In this paper, the
performance of this method is done on a degraded image X
such that X=S+N where S is the original image and N is an
AWGN. The performance of three denoising techniques
(IJCNS) International Journal of Computer and Network Security,
P.Vasuda3
such as hard thresholding, soft thresholding and Wiener
filter is compared both visually and in the PSNR sense.
2. Wavelet Based Image Denoising
DWT has attracted more interest in image denoising [5].
The DWT can be interpreted as image decomposition in a
set of independent, spatially oriented frequency channels.
The image is passed through two complementary filters and
emerges as two images, Approximation and Details. This is
called Decomposition or Analysis. The components can be
assembled back into the original image without loss of
information. This process is called Reconstruction or
Synthesis. The mathematical manipulation, which implies
analysis and synthesis, is called DWT and inverse DWT.
For a 2D image, an N level decomposition can be performed
resulting in 3N+1 different frequency bands namely, LL,
LH, HL, HH.
Denoising algorithms that use the wavelet transform consist
of three steps:
• Calculate the wavelet transform of the noisy image
• Modify the noisy wavelet coefficients according to
some rule.
• Compute the inverse transform using the modified
coefficients.
2.1 Wiener Filter
In signal processing, the Wiener filter is a filter proposed
by Norbert Wiener during the 1940s.Its purpose is to reduce
the amount of noise present in a signal by comparison with
an estimation of the desired noiseless signal. The discrete-
time equivalent of Wiener's work was derived independently
by Kolmogorov in 1941. Hence the theory is often called the
Wiener-Kolmogorov filtering theory.
The inverse filtering is a restoration technique for
deconvolution, i.e., when the image is blurred by a known
lowpass filter, it is possible to recover the image by inverse
filtering or generalized inverse filtering. However, inverse
filtering is very sensitive to additive noise. The approach of
reducing one degradation at a time develops a restoration
algorithm for each type of degradation and simply combines
them. The Wiener filtering executes an optimal tradeoff
between inverse filtering and noise smoothing. It removes
the additive noise and inverts the blurring simultaneously.
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Vol. 2, No. 10, 2010
The Wiener filtering is optimal in terms of the mean When using the Haar wavelet transform the steps for
square error. In other words, it minimizes the overall mean implementing denoising using the Wiener filter technique is
square error in the process of inverse filtering and noise as follows:
smoothing. The Wiener filtering is a linear estimation of the i. Apply the Haar wavelet transform to the original image

{ } {y }
original image. The approach is based on a stochastic 2
framework [6, 7]. ii. qi , j is computed by convolving i, j with a
2.1.1 Wiener Filter in the Wavelet Domain kernel of size 9.
In the model we assume that the wavelet coefficients are iii. The Wiener filter is then applied using the formula
conditionally independent Gaussian random variables. The max(qi , j − σ n2 , 0)
noise is also modeled as stationary independent zero-mean sˆ = yi , j = aˆi , j yi , j
qi , j
Gaussian variable. Let us consider an image corrupted by a
zero-mean Gaussian noise. The coefficients of the noisy iv. Apply the inverse Haar wavelet transform.
image in the wavelet domain are given by [4].
yi, j = si, j + ni , j (1) 2.2 Soft Thresholding
Where yi , j represent the coefficients of the noisy image in In soft thresholding, the wavelet coefficients with
magnitudes smaller than the threshold are set to zero, but
the wavelet domain, si , j represent the coefficients of the the retained coefficients are also shrunk towards zero by the
amount of the threshold value in order to decrease the effect
undegraded image, ni , j represent the coefficients of the
of noise assumed to corrupt all the wavelet coefficients. Soft
noise. thresholding shrinks the coefficients above the threshold in
Without loss of generality, we can assume that absolute value.
the E { yi2, j } ’s can be determined by averaging the squared When using the Haar wavelet transform, the steps for
implementing denoising using the soft thresholding
values of yi , j in a window centered at (i, j). This technique is as follows:
information can be expressed as • Apply the Haar wavelet transform to the original
R R image
Qi , j = ∑ ∑y
k =− R l =− R
2
i − k , j −1 • Apply the soft thresholding on the wavelet
(2) coefficients y(i, j )
M = (2R + 1)2
(3)
 y − T if y(i , j ) ≥ T
Qi , j 
qi , j = s$ (i, j ) =  y + T if y(i , j ) ≤ −T
M  0
(4)  otherwise
As a result, the coefficients of the Wiener filter can be (9)
expressed as T = σ 2 log ( n )
(10)
qi , j − σ n2 Where y(i, j ) is the standard deviation of the noise, n is
ai, j =
qi , j the number of wavelet coefficients, sˆ(i, j ) are the de-
(5) noised wavelet coefficients, and T is the universal
Restricting the values to only positive values, the numerator threshold and the variance is estimated using MAD
of the equation (4) takes the form max ( qi , j − σ n2 , 0 ) and so method.
sˆi , j = max ( a i , j , 0 ) yi , j • Apply the inverse haar wavelet transform.
(6) 2.3 Hard Thresholding
Where sˆi , j is the best linear estimate of the signal
In hard thresholding, the wavelet coefficients with greater
component si , j magnitudes than the threshold are retained unmodified as
The noise variance is estimated using the mean absolute they are thought to comprise the informative part of data,
deviation (MAD) method and is given by while the rest of the coefficients are considered to represent
2 noise and set to zero. However, it is reasonable to assume
 mad 
var iance =   (7) that coefficients are not purely either noise or informative
 0.6745  but mixtures of those.
mad ( ( wi )i ) = median (( w ) )
i i
The denoising method described in the previous
subsection (soft thresolding) can be carried out using the
(8) hard threshold instead of the soft threshold on the wavelet
wi represents the wavelet coefficients. coefficients in (ii).
The hard thresholding formula is given as
194 (IJCNS) International Journal of Computer and Network Security,
Vol. 2, No. 10, 2010
pretty well in the smooth regions but performs poorly along
f y(i , j ) ≥ T the edges.
 y(i, j )
sˆ(i, j ) = 
0 if y(i, j ) < T The comparison of PSNR of the three wavelet filters for
(11) different MRI images are tabulated in Table1 and is
observed that the Wiener filter gives better values compared
3. Results and Discussion to soft and hard thresholding for different noise variances
(σ ) such as 15, 20, 25, 30.
In this section, simulation results are presented which is
performed on the four MRI images i.e. Brain, Knee, Spine
Abdomen. White Gaussian noise is added to the MRI Table 1: Comparison of PSNR of different wavelet filters
images and denoised with the methods described previously. for different MRI images corrupted by AWGN
The performance of the three techniques is compared
using PSNR , which is defined as
255 2
PSNR = 10log10
MSE Peak Signal to Noise Ratio in dB(PSNR)
Image Noise
(12)
(σ )
Where MSE denotes the mean square error for two
Hard Soft Wiener
m × n images l (i , j ) & k(i, j ) where one of the images is
Thresholding Thresholding Filter
considered a noisy approximation of the other and is given
15 25.441 26.946 27.692
as
2
Brain 20 22.936 25.065 25.615
1 m−1 n −1
MSE = ∑∑ [l (i, j ) − k(i, j )]
mn i =0 j = 0
25
30
21.031
19.452
23.507
22.181
23.957
22.577
(13) 15 25.219 26.231 26.803
From the simulation results it has been observed that the Knee 20 22.810 24.542 24.977
Wiener filter outperforms both thresholding methods 25 20.924 23.087 23.457
visually and in terms of PSNR. More details were lost with 30 19.357 21.836 22.170
the thresholding methods especially for the hard threshold 15 25.093 26.069 26.561
Spine 20 22.753 24.458 24.812
wherein the background was not well denoised. If the
25 20.869 23.073 23.359
Wiener filter could be thought as another thresholding
30 19.348 21.871 22.126
function, it will perform better as its shape is smoother than 15 25.402 27.135 27.656
the hard and soft thresholds. Abdomen 20 22.917 25.227 25.614
This can be clearly seen from Figure1 and Figure2 that the 25 21.011 23.660 23.981
background of the denoised images with Wiener filter 30 19.436 22.324 22.622
appears smoother. The Wiener filter removes the noise

Figure1. Denoising of Brain MRI image for variance=20 (a) Original image (b)Noisy image (c)Denoised image with hard
threshold (d) Denoised image with soft threshold (e) Denoised image with Wiener filter

(a) (b) (c) (d) (e)

Figure2. Denoising of Spine MRI image for variance=30 (a) Original image (b)Noisy image (c)Denoised image with hard
threshold (d) Denoised image with soft threshold (e) Denoised image with Wiener filter
 (IJCNS) International Journal of Computer and Network Security, 195
4. Conclusions
The paper presents a comparative analysis of three image
denoising techniques using wavelet transforms. The analysis
of all the experimental results demonstrates that Wiener
filter surpasses other methods that have been discussed.
There are a couple of areas which would like to be improved
on. One area is in improving the denoising along the edges
as the Wiener method did not perform so well along the
edges. Another area of improvement would be to develop a
better optimality criterion as the MSE is not always the best
optimality criterion.
Acknowledgements
We wish to express our sincere thanks to Dr. K. Jitender
Reddy, Consultant Radiologist, Dept. of Radiology &
Imaging Sciences, Apollo Health City, Hyderabad for
providing us with different MRI image datasets.
References
[1] DonohoD.L and. Johnstone I.M “Ideal spatial
adaptation via wavelet shrinkage” Biometrica, Vol.
81, pp. 425-455,1994
[2] Donoho D.L “De-noising by soft-thresholding” IEEE
Transactions on Information Theory, Volume: 41,
Issue: 3, Pages: 613 – 627, May 1995
[3] Donoho, D.L “Wavelet Shrinkage and W.V.D.: A 10-
minute Tour; (David L. Donoho's website)
[4] Kazubek, M “Wavelet domain image denoising by
thresholding and Wiener filtering” IEEE Signal
Processing Letters, Volume: 10, Issue: 11, Nov. 2003
[5] Kother Mohideen S, Dr. Arumuga Perumal. S , Dr.
Mohammed Sathik M “Image Denoising using Discrete
Wavelet Transform”, International Journal of Computer
Science and Network Security, Vol.8, No.1, January
2008.
[6] Lakhwinder Kaur , Savita Gupta , R.C. Chauhan
“Image Denoising using Wavelet Thresholding” Third
Conference on Computer Vision, Graphics and Image
Processing, India, Dec 16-18, 2002
[7] Nevine Jacob and Aline Martin “Image Denoising in
the Wavelet domain using Wiener filtering”, December
17, 2004.
[8] Zhong, S, Cherkassky V “Image Denoising using
Wavelet Thresholding and Model Selection” Image
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Vol. 2, No. 10, 2010
Author’s Profile
S.Satheesh received the B.Tech degree in
Electronics and Communication
Engineering from VRSEC (ANU,
Vijayawada, India) in 2001, and the M.E
(ECE) degree in Communication
Engineering specialization from CBIT
(OU, Hyderabad, India) in 2005.He is
currently pursuing the Ph.D. degree under
the guidance of Dr. KVSVR Prasad at
Jawaharlal Nehru Technological
University Hyderabad, India. He is the member of ISTE, IAENG
and IACSIT. His research interests are in the area of Medical
Image Processing and Signal Processing.
Dr. KVSVR Prasad obtained B Sc.
Degree in 1963 from Andhra University,
B.E (Telecommunication Engineering) in
1967 and M.E (ECE) Microwave
Engineering specialization in 1977 from
Osmania University. He received the
Ph.D. in 1985 from IIT Kharagpur in strip
and micro strip transmission lines. He
published six papers in IEEE Transactions
in MTT, Antenna and Propagation and
EMI/EMC and three papers in National
Conferences. He is fellow of IETE (life member). He worked in
various capacities in the Department of ECE, Osmania University,
Hyderabad. Presently he is working as professor and head,
Department of ECE, D.M.S.S.V.H. college of engineering,
Machilipatnam, India.
P.Vasuda received B.Tech degree from
G.Narayanamma Institute of Technology
and Science, Hyderabad, India in
Electronics and Communication
Engineering in the year 2007.Currently
she is pursuing her M.Tech degree from
G.Narayanamma Institute of Technology
and Science, Hyderabad, India in Digital
Electronics and Communication
Engineering. Her area of interest includes
Image Processing and Digital Communications.