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Analysis of denoising filters on MRI brain images

Article  in  International Journal of Imaging Systems and Technology · August 2017

DOI: 10.1002/ima.22225

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DOI: 10.1002/ima.22225

RESEARCH ARTICLE

Analysis of denoising filters on MRI brain images

Saritha Saladi | N. Amutha Prabha

School of Electrical Engineering, VIT

University, Vellore, India
Correspondence
Saritha Saladi, School of Electrical
Engineering, VIT University, Vellore,
India.
Email: saladi.saritha2014@vit.ac.in
Abstract
The magnetic resonance imaging (MRI) modality is an effective tool in the diagnosis
of the brain. These MR images are introduced with noise during acquisition which
reduces the image quality and limits the accuracy in diagnosis. Elimination of noise
in medical images is an important task in preprocessing and there exist different
methods to eliminate noise in medical images. In this article, different denoising algo-
rithms such as nonlocal means, principal component analysis, bilateral, and spatially
adaptive nonlocal means (SANLM) filters are studied to eliminate noise in MR.
Comparative analysis of these techniques have been with help of various metrics
such as signal-to-noise ratio, peak signal-to-noise ratio (PSNR), mean squared error,
root mean squared error, and structure similarity (SSIM). This comparative study
shows that the SANLM denoising filter gives the best performance in terms of better
PSNR and SSIM in visual interpretation. It also helps in clinical diagnosis of the
brain.

KEYWORDS
bilateral filter, denoising, MRI brain, NLM, PCA, SANLM

1 | INTRODUCTION images including linear filters and nonlinear filters. The

The major problem occurring in biomedical images is noise,
which affects the coherent nature of the images. This image
denoising is applicable to other fields such as astronomy and
forensic sciences to obtain the useful potential information.
Many researchers concentrate on different fields of magnetic
resonance imaging (MRI) brain images like preprocessing,
enhancement, segmentation,1 and feature extraction. In gen-
eral, the noise interfered may be either Gaussian or speckle
noise and the image capturing equipment itself incorporates
salt and pepper noise. This noise degrades the images and
leads to the incorrect diagnosis of the disease. Owing to this
coherent noise, it is more difficult to distinguish the adequate
details of the images during the diagnosis of the disease by a
human expert. Various denoising filters are used to remove
the noise and improve the image quality of computed tomog-
raphy images.2 Denoising methods are intended to eliminate
the noise from an image without losing the original attributes
of the image. Thus, denoising the noisy image has become
the imperative step in processing the medical MR images.
The number of denoising techniques has performed on MR
mean, median, and adaptive filters are linear methods and
nonlinear methods include anisotropic diffusion, bilateral,
wavelets, principal component analysis (PCA), nonlocal
means (NLM), and so forth.3
The linear filters cause the image to blur by suppressing
the fine details. The performance of these filters is not
acceptable because they blur the sharp edges, rescind lines,
and other details. To avoid these difficulties nonlinear filters
are used. The anisotropic diffusion filter is used to reduce
noise without removing the important details from the image
(edges, lines) which are significant for the elucidation.4 Bilat-
eral filtering is a nonlinear filter and noniterative method
which combines domain and range filters simultaneously.5
This technique is an alternative to wavelet thresholding
achieved by combining two Gaussian filters; first filter works
in spatial domain and the second in intensity domain.6
Wavelets challenges to remove noise by denoising the
noisy images, noise present in the signal while holding all
the signal characteristics irrespective of its frequency.7 The
wavelet filter for denoising the MR images is precisely
designed to lever the Rician noise.8 The main drawback of

Int. J. Imaging Syst. Technol. 2017;27:201–208. wileyonlinelibrary.com/journal/ima V

C 2017 Wiley Periodicals, Inc. | 201
202 | SARITHA
this filtering method is that any small structures that are simi-
lar in size to the noise are also eliminated.9Whereas PCA
offers an efficient and simple way to analyze multivariate
statistical distribution to reduce optimal dimensionality, it
aids as one of the best approaches to produce statistic sam-
ples.10,11 It functions as an effective technique to perform a
linear mapping with maximal variance and minimal mean
squared error (MSE).12
Among these solutions, the NLM filter is gained with an
increasing attractiveness due to its outstanding performance
and verified for Gaussian, additive, and multiplicative
noise.13 It not only eradicates noise from the input image in
an effective way but also preserves fine details. The main
idea is to exploit the natural redundancy in the input image
to restore better image quality. The MR images are tainted
by random noise which appears during the process of analy-
sis. This leads to the difficulty in extracting the features and
segmenting the brain images.14 The significant property of a
good denoising method is to provide the noise free images
along with preserving nature of the edges.
The evaluation of denoising methods is compared in terms
of peak signal-to-noise ratio (PSNR), MSE, signal-to-noise
ratio (SNR), root mean squared error (RMSE), and structure
similarity (SSIM) values. Image denoising methods provide
better image quality by improving the visibility of fine details,
which in turn helps in clinical diagnosis of the disease to
obtain the accurate information. Different denoising MRI fil-
ters are discussed and compared with different metrics. This
helps in future processing like segmentation, registration and
classification used for computer aided diagnosis.15 This article
is organized as follows: PCA, NLM, bilateral, PCA-NLM,
and SANLM denoising filters are described in Section 2. Per-
formance metrics used in evaluation are described in Section
3. Comparative analysis of results is presented in Section 4
and concluded in Section 5.
2 | METHODS AND MATERIALS
2.1 | Principal component analysis
PCA is a statistical method which takes a large number of
interconnected variables and transmutes this data into a
smaller number of uncorrelated variables while recollecting
highest amount of dissimilarity. These uncorrelated varia-
bles are termed as principal components and this method
recognizes the outlines in data and assigns the emphasized
resemblances and variances. PCA is used as the most dom-
inant tool for analyzing data.16 PCA-based denoising
method calculates the locally fitted base and transmutes the
image.17 PCA is applied directly on the MR images to
eliminate the noise and visual artifacts occur in the noisy
images.18
AND AMUTHA PRABHA
2.2 | Bilateral filter
Bilateral filter is well-defined as a weighted mean of adjoin-
ing pixels/voxels that is analogous to Gaussian convolution.
The use of this filter is grown-up promptly and it is used in
applications such as image denoising and image enhance-
ment.6 It is an efficient method to smooth the MR images
while preserving their disjoints and to separate the image
structures of different regions. Bilateral filtering is a method
to smooth the images while preserving the edges. The bilat-
eral filter considers the modification in values of the neigh-
bors to preserve edges while smoothing.19
2.3 | Nonlocal means
NLM method uses an innovative idea in removing the noise
from the images. It averages the similar pixels/voxels in the
image based on the intensity distance to regain the single
pixel/voxel value. Estimation of each individual pixel/voxel
is based on the weighted mean of all pixels/voxels in the MR
image. These weights are ascertained based on the compari-
son of the pixels/voxels.13 The NLM is a robust method for
removing the noise, but limits the performance on wide
applications with high computational loads. Owing to this
drawback, NLM lacks the efficiency for larger noise remov-
als in the image.
2.4 | Principal component analysis–nonlocal
means
PCA-NLM method computes neighborhood resemblances
once the PCA projection is done. This method works on the
hypothesis that the image contains a widespread volume of
self-similarity. It performs best when compared with the
other denoising methods in edge preserving and in enhancing
the visual appearance of the denoised MR image. This
amendment to the NLM filter results in better accuracy and
the computational performance is improved.20 This PCA-
NLM method is compared with wavelets and conventional
PCA and acquires better results.21
2.5 | Spatially adaptive nonlocal means
SANLM filter improves the eminence of the image. SANLM
deals with the noise level, spaciously erratic within the MR
image.22 It can be estimated locally by processing data with
static or spaciously erratic noise fields in fully automatic
manner. Several adaptive filtering techniques are used to
improve the quality of magnitude MR images. The idea of
spatially distributed noise fields has specific augmentation to
more interest and demands closer attention.22
SARITHA AND AMUTHA PRABHA | 203

3 | PERFORMANCE METRICS closeness of the two images x and y in terms of mean lumi-
nance (lx and ly ).
The performances of different filters are evaluated using dif- Contrast is the difference in color that makes an object
ferent performance metrics such as MSE, PSNR, RMSE, distinguishes the image representation. In visual perception,
SNR, and SSIM. Different perceptual quality assessments contrast is determined by the difference in the color and
are clearly explained for two-dimensional images with differ- brightness of the object and other objects within the same
ent evaluation metrics.23 field of view. The term c(x,y) is the contrast comparison
function, measures the contrasts in the images x and y are
how close to each other in terms of standard deviations
3.1 | MSE and PSNR (rx and ry ).
MSE and PSNR are the two quality measures used in the Structure provides the structural information in an
evaluation of the performance on images.24 The MSE image is defined as the attributes that represent the structure
between the original image and noisy image is defined as of objects in the scene, independent of the average luminance
and contrast. The term s(x,y) is the structure comparison
1 NX X
21 M 21
function, measures the correlation coefficient between the
MSE5 ½xði; jÞ2yði; jÞ2 (1)
N
M i50 j50 images x and y in terms of covariance(rxy ).
where x(i,j) is the original image, y(i,j) is the noisy image, SSIMðx; yÞ5½lðx; yÞa3½cðx; yÞb3½sðx; yÞg (6)
and N,M are the number of rows and columns in the image. where,
The PSNR is given as
  2lx ly 1C1
MAX2 lðx; yÞ5 (7)
PSNR510log10 (2) l2x 1l2y 1C1
MSE
2rx ry 1C2
where MAX-255, small MSE value means lesser the error, cðx; yÞ5 (8)
r2x 1r2y 1C2
results in high PSNR. Acceptable PSNR range is 30–50 dB.
rxy 1C 3
sðx; yÞ5 (9)
rx ry 1C3
3.2 | Root mean squared error
where lx is the local mean of x, ly is the local mean of y, rx
RMSE is defined as is the standard deviation of x, ry is the standard deviation of
pffiffiffiffiffiffiffiffiffiffi y, and rxy is the cross-covariance of x, y for the image. There-
RMSE5 MSE (3)
  fore, a 5 b 5 g 5 1 and C1 5ðL3K1 Þ2 andC2 5ðL3K2 Þ2 ,
MAX
PSNR520log10 (4) where L is the dynamic range of the pixel values (255 for 8-
RMSE bit grayscale images), C1 is a very small constant at K1  1,
C2 is non-negative constant at K2  1 and C3 5 C2=2.
The similarity index is simplified to
3.3 | Signal-to-Noise Ratio   
2lx ly 1C1 2rxy 1C2
SNR is defined as the ratio of the noisy image to that of the SSIMðx; yÞ5   (10)
difference between the original image and noisy image. l2x 1l2y 1C1 r2x 1r2y 1 C2
PN21 PM21 2
i50 j50 yði; jÞ
SNR5 PN21 PM21 2
(5)
i50 j50 ½xði; jÞ2yði; jÞ
3.5 | Analytical relationship between PSNR
and SSIM
3.4 | Structure similarity The analytical relationship between PSNR and SSIM is men-
SSIM is based on the multiplication of three terms, the lumi- tioned.25 First we obtain the relation between SSIM and
nance, the contrast, and the structural terms.24 MSE, and then we relate SSIM to PSNR. Equation 1 is
Luminance is the amount of energy an observer per- rewritten as
ceives from the light source. It is also defined as the product X
N X
21 M 21
of the illumination and the reflectance an object being NM
MSEðx; yÞ5 ½xði; jÞ2yði; jÞ2
i50 j50
observed in the image. But the structures of the objects in
the scene are independent of the illumination. The term l (x, by defining lX is the mean values of x and lY is the mean
y) is the luminance comparison function, measures the value of y. We derive
204 | SARITHA AND AMUTHA PRABHA

X
N X
21 M 21 X X
N 21 M 21      
2 1 1 1 1 aðx; yÞ3MSE1bðx; yÞ
½xði; jÞ2yði; jÞ2 5 xij 2lx 2 yij 2ly 1 lx 2ly 5 5 (18)
i50 j50 i50 j50
SSIM lðx; yÞ cðx; yÞ sðx; yÞ lðx; yÞsðx; yÞ
X
N X
21 M 21   X
N X
21 M 21 From Equation 2,
5 ½ðxij 2lx Þ2 yij 2ly  2 1 ðlx 2ly Þ2  
i50 J50 i50 j50 MAX2
PSNR510log10
X
N X
21 M 21   MSE
12 ½ðxij 2lx Þ2 yij 2ly ðlx 2ly Þ
i50 j50 MSE5 MAX2 3e2PSNR3lnð10Þ=10 (19)
(12) We show the relationship between SSIM and PSNR
Let us consider, from the equations:

X
N X
21 M 21    
1 aðx; yÞ3MAX2 3e2PSNR3lnð10Þ=10 1bðx; yÞ
xij 2lx 2 yij 2ly
2 5 (20)
A5 SSIM lðx; yÞsðx; yÞ
i50 J50  
X M21
X Let us assume that C2  max rx ; ry and C3 
N21 2  
B5 lx 2ly max rx ; ry , we obtain
i50 j50
1
X X
21 M 21  aðx; yÞ5
N   
  2rx ry
C52 xij 2lx 2 yij 2ly lx 2ly (13)
 2
i50 j50 2rxy 2 lx 2ly
bðx; yÞ5
Then, 2rx ry
rxy
X
N X
21 M 21 sðx; yÞ5
MN3MSEðx; yÞ5 ½xði; jÞ2yði; jÞ2 5 A1B1C rx ry
i50 j50
Substitute aðx; yÞ; bðx; yÞ and s(x,y) in expression,
(14)
2rxy 2ðlx 2ly Þ
2

Simplifying Equations 11, 12, and 13 yields 1

1
2rx ry 3MAX2 3e2PSNR3lnð10Þ=10 1 2rx ry
5 r
   2 SSIM lðx; yÞ rx xyry
A5NM r2x 1r2y 22rxy ; B5NM lx 2ly ; C50 (15)  2
1 MAX2 3e2PSNR3lnð10Þ=10 12rxy 2 lx 2ly
5 (21)
where rx is the standard deviation of the image x, ry is the SSIM 2rxy lðx; yÞ
standard deviation of the image y, rxy is the covariance
Rewriting the equation in terms of PSNR as,
between x and y. Finally from Equations 14 and 15, we
derive 2rxy lðx; yÞ  2
MAX2 3e2PSNR3lnð10Þ=10 5 22rxy 1 lx 2ly
SSIM
 2  
MSE5r2x 1r2y 22rxy 1 lx 2ly (16) 2PSNR3lnð10Þ=10 1 2rxy lðx; yÞ  2
e 5 22rxy 1 lx 2ly
MAX2 SSIM
From SSIM, consider term contrast, cðx; yÞ5 r2 1r
x y 2
2 1C is
2r r 1C
 2 !
x y 2
2rxy lðx; yÞ 2rxy 1 lx 2ly
rewritten based on the MSE (Equation 16): PSNR5210log10 2
MAX2 SSIM MAX2
1 r2x 1r2y 1C2  
5 2 2rxy ðlðx; yÞ2SSIMÞ lx 2ly 2
cðx; yÞ rx 1r2y 1C2 PSNR5210log10 1
MAX2 SSIM MAX
 2
1 MSE 2rxy 2 lx 2ly 1C2 (22)
5 1
cðx; yÞ 2rx ry 1C2 2rx ry 1C2 (17) Let the luminance of the image lðx; yÞ51 and, assume
5aðx; yÞ3MSE1bðx; yÞ mean of the image x is equal to mean of the image y
where, (lx 5ly ). Then the PSNR is written as
 
1 2rxy ð12SSIMÞ
aðx; yÞ5 ; PSNR5210log10 (23)
2rx ry 1C2 MAX2 SSIM
 2 Now PSNR is written as
2rxy 2 lx 2ly 1C2
bðx; yÞ5    
2rx ry 1C2 2rxy 12SSIM
PSNR5210log10 210log
From the above expressions, SSIM is written as MAX2 SSIM
SARITHA AND AMUTHA PRABHA | 205

FIGURE 1 (a) Original MR image. (b) Noisy image (noise deviation 5 5)

FIGURE 2 Denoised images: (a) PCA, (b) NLM, (c) bilateral filter, (d) PCA-NLM, and (e) SANLM

   
MAX2 SSIM images lack the visual interpretation and leading to incorrect
PSNR510log10 110log (24) diagnosis of the disease by the clinician.
2rxy 12SSIM
The different performances metrics are used for evaluate
From these expressions, we can conclude the analytical and compared for noisy and denoised images in terms of
relation between PSNR and SSIM. PSNR, SNR, MSE, RMSE, and SSIM. In Table 1, the com-
parison of different denoising methods on noisy images for
4 | RESULTS AND DISCUSSIONS different measures is tabulated. These results are clearly in
the indicate that the SANLM method produces better results
A comparative analysis of the SANLM method with the con- in terms of all metrics that are compared with the other
denoising filters. Table 2 is clearly indicating that the
ventional denoising methods (PCA, NLM, bilateral filter,
and PCA-NLM) is implemented. MR image datasets of mul-
tiple sclerosis are acquired form many subjects of different T A BL E 1 Comparison of different denoising methods on noisy
age groups [http://www.medinfo.cs.ucy.ac.cy/]. These data- images for different measures
sets are then subjected to noise and a comparative analysis of
the existing methods is done to remove the noise. Figure 1 Filters Bilateral PCA-
measures PCA NLM filter NLM SANLM
shows the original image and the noisy image. Figure 2
shows the visual interpretation of the obtained denoised out- PSNR 34.3214 34.1687 35.4512 36.3270 37.2451
put MRI brain images. SNR 9.2783 9.1895 9.1727 9.2974 9.4543
The comparative analysis of PCA, NLM, bilateral, PCA-
NLM, and SANLM filters is performed with different noise MSE 9.5582 9.5734 9.5806 9.2145 9.0214
deviations r510; 15; 20, and 25. The PSNR and SSIM RMSE 3.0916 3.0941 3.0953 3.0355 3.0035
values of the noisy and denoised images are decreased and
SSIM 0.8849 0.8851 0.8878 0.8941 0.9014
the MSE and RMSE values are improved. The resultant
206 | SARITHA AND AMUTHA PRABHA

T A BL E 2 Comparison of different denoising methods on denoised

images for different measures

Filters Bilateral PCA-

measures PCA NLM filter NLM SANLM

PSNR 41.2317 42.2083 42.6807 42.7771 43.0942

SNR 13.4979 13.3142 13.2764 13.8742 14.4954

MSE 3.9202 3.9414 3.5352 3.4576 3.2141

RMSE 1.9799 1.9241 1.8802 1.8595 1.7928 F I G U R E 4 Comparison of SNR for different denoising filters.
[Color figure can be viewed at wileyonlinelibrary.com]
SSIM 0.9472 0.9486 0.9567 0.9597 0.9701

SANLM filter provides efficient and effective results com-

pared to other filters for the denoised images.
Figure 3 shows the graphical representation of PSNR
comparison between noisy and denoised MRI brain images.
NLM filters produce the least value for noisy image com-
pared to SANLM filter and its PSNR is improved by 9.00%.
PCA filters gives the least value for denoised image among
other filters and its PSNR is increased by 4.51%. With the
comparison of all filters, SANLM filter leads to the highest
PSNR for both noisy and denoised images on an average of F I G U R E 5 Comparison of MSE for different denoising filters.
6.27% and 20.7%, respectively. [Color figure can be viewed at wileyonlinelibrary.com]
Figure 4 explains the comparison of SNR between the
noisy and denoised MRI brain images; bilateral filter gives an average of about 2.40% and 6.11% as compared with
the lowest SNR in terms of both noisy and denoised images PCA, NLM, bilateral, and PCA-NLM denoising filters. The
improved by 3.06% and 9.18%. The highest SNR values are bilateral and PCA filters produce the highest value for a
given by the SANLM filter compared to other filters, the noisy image and denoised image, its RMSE is reduced by
SNR increased by a mean of 2.37% and 7.29% for both noisy 2.96% and 9.40%, respectively.
and denoised MR images. Figure 7 explains the comparison of SSIM between noisy
Figure 5 displays the comparison between noisy and and denoised MRI brains in which PCA filter yields the least
denoised images in terms of MSE, bilateral filters produces SSIM values in both images. The highest SSIM value is pro-
the highest value for noisy image compared to SANLM filter duced by the SANLM filter which is improved by 1.86%
and MSE is reduced by 5.83%. NLM filters give the maxi- and 2.41% for noisy and denoised MR images.
mum value for denoised image compared other filters and its The anisotropic diffusion, bilateral, and sparse represen-
MSE is decreased by 18.4%. SANLM filter leads the best tation methods are used for eliminating noise in MR images.5
results among other filters by an average of 4.79% and From the results, the anisotropic diffusion executes at lesser
13.1%. time and sparse representation executes at long time with
Figure 6 shows that SANLM filter yields better RMSE
value for both noisy and denoised images with a reduced by

F I G U R E 3 Comparison of PSNR for different denoising filters. F I G U R E 6 Comparison of RMSE for different denoising filters.
[Color figure can be viewed at wileyonlinelibrary.com] [Color figure can be viewed at wileyonlinelibrary.com]
SARITHA AND AMUTHA PRABHA
F I G U R E 7 Comparison of SSIM for different denoising filters.
[Color figure can be viewed at wileyonlinelibrary.com]
high PSNR and low PSNR values are obtained for bilateral
filters. The noise in MR images is eliminated using linear fil-
ters and wavelets for denoising.26 Among these linear filters,
wiener filter eliminates the noise with high PSNR but the
resolution of the images is enhanced by the wavelets by pre-
serving the edge and contour information. Study of denoising
filters is accomplished using linear filters such as adaptive,
mean, and median on T2-weighted MR images.27 This pro-
vides the best evaluation as salt and pepper noise is elimi-
nated by median filter and a speckle noise is reduced by
average filter.
The different MR images are denoised using various per-
formance metrics including picture quality scale and unique
quality index along with PSNR and RMSE.28 The hybrid
median, bilateral, wavelets, and independent component
analysis (ICA) filters are used in which ICA provides the
better result in removing salt and pepper noise and wavelets
works best for eliminating speckle noises. Various denoising
methods such a NLM, bilateral, and linear filters are used for
eliminating Rician noise in brain slices.29 The conclusion
from the obtained results indicates that images are blurred
and lacks the information while using linear filters. The
NLM and bilateral filters produce better performance in pre-
serving the edges. In this article, SANLM filter is imple-
mented that yields best performance by reducing noise to the
maximum extent which is measured in terms of PSNR and
SNR. This SANLM filter produces the better results when
compared to the conventional denoising methods in terms of
all performance metrices. The improvement is due to the
nature of eliminating the noise level, which is spaciously
erratic within the MR image along the noise fields.
5 | CONCLUSION
This article explores the implementation of various denoising
approaches verified with Gaussian noise on the MRI brain
images. Spatially adaptive NLM filter outperforms very effi-
ciently and effectively, compared to other conventional
denoising filters. This filter delivers better results with
| 207
improved PSNR of about 2.07% for denoised images. Bilat-
eral filters preforms least among other filters in noisy and
denoised MR images. The MSE and RMSE values are
reduced by a mean of 13.1% and 6.11% for denoised brain
images. The SNR and SSIM metrics are optimized by an
average of 7.20% and 2.32% for the denoised MR images.
From these results, it can be observed that variety of filters
work to eliminate noise in MR images. Depending on the
different types of noises and filtering methods are employed.
This analysis of denoising methods enhances the accurate-
ness of the MRI brain images for further processing such as
segmentation and feature extraction.
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How to cite this article: Saladi S, Amutha Prabha N.
Analysis of denoising filters on MRI brain images. Int.
J. Imaging Syst. Technol. 2017;27:201–208. https://doi.
org/10.1002/ima.22225