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Application of Neural Networks for Image Analysis of Magnetic

Resonance Imaging (MRI) in Multiple Sclerosis Patients

Diego F. Valero1, Camila Clavijo2, Oscar Avilés3, Rubén Hernández4

1,2,3
Mechatronics Department, Piloto University of Colombia
4
Biomedical Department, Nueva Granada Military University
1
diego-valero1, 2camila-clavijo, 3oscar-aviles{@upc.edu.co},
4
ruben.hernandez@unimilitar.edu.co

Abstract
In this article is explored the potential of the image analysis in the process of multiple
sclerosis diagnosis, through Machine Learning algorithms to build applications that
support the specialist during the identification stage. To accomplish this, a neuronal
network is trained with a database containing combined with both: multiple sclerosis
images as well as disease-free images; then a backpropagation algorithm is applied to
determine the optimal parameters to classify the new input data, according to its
characteristics..

Keywords: Image processing, multiple sclerosis, Machine Learning, backpropagation

algorithm, forward propagation algorithm, neural network, and diagnosis

1. Introduction
The study of the evolution processes of multiple sclerosis (MS) introduce an area of
interest at a research level. According to different definitions, such as the one that is
introduced in the New Manual Merck of General Medical Information, multiple sclerosis
can be interpreted as a disorder in which the areas of myelitis and nerve fibers are affected
such that, due the demyelinating of the nerves emerge multiple areas of scarring (sclerosis).
This generates a response or recurrent symptoms that take into consideration sensitive
aspects, motor and at a psychological level, which points towards potential research areas
of technological development according to the parameters that a therapist or health care
professional require. In the literature are found well-defined structures where the
technological immersion got to achieve significant advancements on the different stages of
the disease-progress. Namely, the review of such projects has resulted in the identification
of three major research fronts: the first group corresponds to those projects related to the
analysis of alterations in motor evolution in order to establish if there are characteristics
that lead to believe that a person has MS, which also has impact in the development of the
task of selecting the right sensors and technology to obtain the required information; the
second group, contains applications of physical structures such as exoskeletons or support
structures, so that the patients are required to manipulate them, this area have had some
promising developments as it will be shown below, and finally, the third area is
characterized by the research in the diagnosis stage to develop new technologies, which is
the main topic of this paper.
It is known that equilibrium disorders are common in MS patients, so it is useful to carry
out tests to evaluate this aspect as shown in figure 1. One of the techniques explored in [4],
takes into account the performance of some patients on a rotating platform with three
degrees of freedom (DOF), and the results are contrasted with the control group; from there
important data are extracted about the position of the foot as well as pressure centers to
characterize the postural relationships as shown in the figure 1. Now, with the relation of
postural adjustment and equilibrium is extracted the electromyographic activity data in the

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inferior train muscles and trunk, to record changes at the pressure points and run their
respective analysis as presented in [6]. For example, with this is possible to take into
account the proposal in article [11], where a method is worked out to get characteristics
from the position to determine whether the signals obtained show an abnormal behavior or
not, such that it could result in an indicator to support the diagnosis of MS; then, it is
possible to collect information where images can be processed and characterized to be
compared with certain criteria of normal control patterns.

Figure 1. Pressure platforms to detect equilibrium disorders [4].

As can be seen in figure 2, the incursion at a mechatronics level to integrate various
areas of engineering in the data analysis are based in the requirement of normalization and
extraction of features by pretreating the measurement of the sensors, this output lead to the
decision-making process according with the predetermined classification. Therefore an
essential attribute in said incursion is related to the problem of determine the most suitable
sensors and other components to transform the data observed into a computer-level
program, to carry the reconstruction of series of images that allow the characterization as
expressed in [11].

Figure 2. Extraction of data features [11].

In addition, it is possible to consider the feasibility of employing commercial software
to the recollection, documentation and information management, or to establish whether it
would be more appropriate to design a new piece of software that fits the design
specifications for the application desired; this last option is not the usual case. While the
above applications cover a wide range of important fields of research where the engineering
developments have had an impact in relation to the evolution control of MS in patients, it
has also been found two other well-documented large areas of concern, related to the
communication by means of a human-machine interface, and the areas that employ
exoskeletons or other robots for assistance of rehabilitation.
As for the human-machine interface concerns, it has become common to find
applications that capture signals through electroencephalography, and after generating an
appropriate characterization, the actions are determined in accordance with the goal of the
application as shown on one side in figure 3. Afterwards, though there signals [9] seeks to
determine the characteristics that allow the optimization of the processed data, to allow
communication channels that do not require any conventional motion such as: muscle
movement or eye tracking in patients with motor restrictions due any kind of physical

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disorder. In the same way, there is another kind of application that is booming, and relates
to the integration of virtual reality techniques to carry out trainings that are more engaging
for patients.

Figure 3. Data acquisition and characterization by electroencephalography [15].

To continue, consider the design case and implementation of robots and exoskeletons to
rehabilitation purposes. In [1] is built an assistance robotic arm, to minimize the load on the
arm of the patient due gravitational effects while performing daily tasks, the signal of the
trajectories is compared to a default expected optimal trajectory to determine the motor
performance as shown in the figure 4. Then, a passive robotic arm is designed with weight
control and adjustable DOF (through a button or electromyography); after the activity is
performed both intention signals are obtained: to move forward and to move backwards.
Other approaches include robots that allow (from the position data obtained in therapy),
perform a supervised and enhanced process that adjusts the movement data of the robot
with a bank of programmed trajectories, for use as described in [5].

Figure 4. Rehabilitation through exoskeleton and human-machine interface [5].

In the literature there are different documented applications of engineering
developments that seek to aid the specialist in the diagnosis, and the patient for the treatment
of the disease. In the process of review, it was found that there are three major areas of
interest from the mechatronics perspective, and that those can act individually or altogether
to support at least one of the treatment courses of action. Those areas can be classified in
robotics and exoskeletons, sensorics and human-machine interface, and diagnostics.
Concerning to exoskeletons, there are some interactive structures for the person to
interact with, and it is directly related to the field of motor rehabilitation that has been
proven to be effective to delay the disease, taking into account postural aspects [6] and
motion planning [14], among others, there are key aspects to design or select the structure
to work with (as required by the therapist).
Likewise, the aforementioned for the case of sensorics and data collection process for
postural alterations through the pressure plates, or in the gait patterns as shown in [8], allow
to extract and spot characteristics that evolve in time and become more visible, represent a

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source of information not just for MS but for a wide range of other conditions. This
information is exposed on human-machine interfaces, or to directly generate responses
according with the readings of the sensors and the running program configurations.
Moreover, it is necessary to emphasize that one important aspect that is being displayed
here is the potential of technology in the diagnosis field by the techniques explored: image
analysis, sensors data characteristics identification, among others.
In this research area, the developments in terms of sensorics and robotics have played
an important role as can be appreciated so far. So, it is worth to highlight the relevance of
the usual tools focused on the diagnosis of the disease as an integral part of the overall
process to ensure the proper treatment if necessary. Thus, it is possible to mention the
benefits of employ a communication interface of the sort of brain-computer, where from
the signal classification, is workable to extract features that characterize this kind of
interaction by means of the distinction with controlled signals under the effect of different
algorithms that allow to group the data and determine the relationships between the
development of a task and its complexity [9] as shown in Figure 5. After that, the features
are normalized to enhance the computing efficiency of the architecture of the algorithm
applied such as Support Vector Machine (SVM), Naïve Bayes, Backpropagation,
linear/polynomial regression or Neural Network, to mention a few options.

Figure 5. Signal acquisition through the comparison between the task

development and rest state [9].

3. Materials and Methods

It has been found that the diagnosis of multiple sclerosis could fail at some point due
similarities in the symptoms with other health issues, this suggest an inconvenient respect
the result analysis and interpretation of the outcomes with the tools at hand; from this it can
be inferred that the specialist is exposed to slip into mistreating a patient. Namely, one of
the techniques that currently are employed to diagnose a patient consists in reviewing
images that show a brain-scan, where is possible to observe signs of interest such as the
white dot in Figure 6.

Figure 6. Brain scanner of a patient with MS.

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Now, by making use of methods such as image analysis with artificial intelligence
algorithms, is obtained a powerful tool to recognize the presence of factors that enable an
appropriate classification of patients, according to the architecture being tested. Based on
this, it is carried out a review of the characteristics in different MRIs of MS patients to get
the indicators of the disease, and from there improve the way that the algorithm spot those
signs with Machine Learning in the modality of supervised learning.
An image can be defined as a representation of elements in the visible spectrum on a
plane; it is common to find analogic images such as a painting, and digital images like a
photograph depending on the capturing tool. However, an image obtained by digital means,
like a camera, can be understood as an n-dimensional array where each element of the
matrix is a number that represents the sensed color-wave, and interpreted according with
standard values as the RGB scale (Red-Green-Blue), ranging from zero (black) to two
hundred and fifty-five (white), where the intermediate values represent different colors in
the visible spectrum.
In general, an image that contains aspects of interest for the diagnosis of MS can be
obtained through methods of Magnetic Resonance Imaging (MRI) or computerized
tomography (CT), among others. To understand the process of conversion the data from the
machine to an image, it is worth highlighting that an MRI is a non-invasive technique that
is useful to map the human brain function [2]; this is, a magnetically active nucleus (usually
hydrogen by its abundance in the body), absorbs energy and returns it in form of a frequency
to a coil where the data serve to reconstruct the area that has been mapped, by means of the
variations of the frequencies obtained [2] [10], as shown in figure 7.

Figure 7. Gradient coil to magnetic resonance [2].

In summary, a magnetic resonance imaging is a digital reconstruction that is made of
specific parts of the physiology by means of the interpretation of the readings of the gradient
coil frequency variations in a magnetic field. In figure 8 is shown an example of a scan of
the brain through MRI technique.

Figure 8. Brain image through an MRI.

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From the previous definitions is established that to perform an MRI, some powerful
magnets are required as well as radio waves and a processor to handle the obtained
information. By knowing this, it becomes relevant to note that the protocol to detect MS
according to [7] consider the analysis of:

• Sequences found in the resonance: (T1, T2, T2 Flear, diffusion, sagittal T1, coronal
T2, degrading echo and T1 millimeter sequence.)
• The axial sequence that is evaluated synchronously between T1 and T2.
• Injuries of perpendicular diameter to the midline sagittal in peri-ventricular
location to the midline. These are found in the cortical transition of substance gray
and white.

To know, there are several kinds of injuries that can be found in a magnetic resonance,
like infratentorial or juxtacortical, among others; this provides information about the
approximate onset time of the disease. In this document it will be carried out the analysis
and development of algorithms, based on the in juxtacortical injuries in FLAIR sequence,
considering the criteria presented by McDonald for the diagnostics of multiple sclerosis in
[7]. For this process it is taken into account that the blood oxygenation, measured
throughout the BOLD effect (based on the brain blood flow, neuronal metabolism, and the
magnetic properties of hemoglobin) has to be high enough, because if the blood is
deoxygenated. reduces the intensity of the resonant signal. From there the results are
presented as a paradigm in blocks, which indicate the activation zone of the brain [3].
A. Image Processing and Neural Networks
As noted earlier in this article, the image processing allows to obtain characteristics of
MS discernible from images that result useful to elucidate the probabilities of a patient
being in any stage of the disease, by making a comparison with recorded cases in the
database. Moving towards, in figure 9 is shown the evolution of the disease in two states
for a patient with MS: in (a) is visible an early phase and in (b) is the advanced phase. As
it can be seen, the progression of the disease generates a notorious alteration in the presented
images; then, it is possible to obtain a general visualization of the process to establish the
changes by merging both images: figure 9 (c).

(a) (b) (c)

Figure 9. (a) Early stage of MS, (b) Advanced stage of MS, (c) General view of the
alteration between stages
The proposed algorithm for image processing is structured starting from the Gaussian
filter, this filter is a convolution in which is sought to soften the images. This is known as
salt and pepper procedure, since it adds a series of black and white dots pseudo-randomly
in the image, analogous to the idea of spreading salt and pepper over a plane: the patterns
in which these dots are located tend to merge with a well-defined distribution. After this
process, the noise is eliminated through a low-pass filter that attenuates the high frequencies

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of the image so that the overall array is softened [13]. The Gaussian filter works spatially,
so that it affects the pixels following a normal distribution according to equation 1:

1 −𝑥 2+𝑦2 2
𝐺(𝑥, 𝑦) = 𝑒 2𝜎 (1)
2𝜋𝜎
The forward propagation model is based in the backpropagation algorithm in machine
learning, it is required to first apply the forward propagation to establish some weights for the
different units in the defined layers to generate the classification, and then with the backpropagation
rectify the weights to get a precise and accurate model based on the predefined architecture. This
forward propagation result in the error or cost function, then it is moved towards the synchronization
of values per unit in the network to work out the proper outputs, note that the supervised model
requires to generate an array with the predefined output classes, corresponding to the row input image
in the training dataset.
In concordance with this, the first thing to do is determine the activation function to get
the cost function. So, it is required an equation that turns the inputs into binary values to
work with, in this paper the equation employed to do so is the sigmoid in equation 2.

1
ℎ𝜃 (𝑥) = 𝑇𝑥
(2)
1 + 𝑒 −𝜃
Where 𝜃 is a vector that store the weights that correspond to each input, these values are
in constant change due the training iterations in every epoch. Because of it, the initialized
weights must be random and close to zero; this second characteristic has the goal to set the
gradient with the suitable conditions to find the global minimum or optimal values for the
neural network. One important step before implementing the computation, is add the bias
unit or unitary cell to each processing layer, this unit is not affected by the strings of units
in previous layers, so is said that the bias unit has no input strings, just output strings.
Proposition 1. Let 𝑋 be an array with the input values, 𝜃 a vector of n-dimensional weights, so
the values of the strings of the network are set depending on the value of each neuron in the
hidden layer j in the following scheme:
𝑎 = [(𝑏𝑖𝑎𝑠𝑢𝑛𝑖𝑡 ), 𝑋] (3)
𝑍=𝑎 𝜃1𝑇 → 𝑎𝑗 = sigm(𝑍) (4)
For each unit is obtained the corresponding cost function through the forward propagation.

Definition 1. Let ℎ𝜃 (𝑥) ∊ ℝ𝑘 where k is the output classification unit size, it is defined the cost
function for the neural network J as
𝑚 𝑙−1
𝐾 𝑠𝑙 𝑚
1 𝜆 2
𝐽 = ∑ (∑(𝑦𝑘𝑖 log (ℎ𝜃 (𝑥))𝑘 + (1 − 𝑦𝑘𝑖 )log (1 − ℎ𝜃 (𝑥))𝑘 )))) + ∑ ∑ ∑(θlji ) (5)
m 2
𝑘=1 𝑖=1
𝑖=1

Where m is the total number of samples, i corresponds to the i-th sample, j is the node
in l-layer, 𝑠𝑙 is the number of units in every layer (without the bias), 𝑦𝑘𝑖 is the value of
the i sample respect to k (note that this value only could be one or zero) and finally 𝜆
is a regularization parameter.
This model seeks to obtain the values of θ that minimize the cost function J and once
this function is implemented, it is generated an iterative cycle until the program finds the
global minimum (or an undesirable local minimum which does not optimize J). Since the
dimensions of the data are usually greater than 3, the overall visualization turns out to be
unviable, so it is necessary to look for an alternative way to project the data into a 3D-space
or 2D-plane and from there, plot the behavior of J so it becomes possible to be aware about
whether function found the global minimum (or at least a well-suited weights) or not. For

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example, by simplifying an ND-array into a 3D-projected surface is obtained something as

figure 10.

Figure 10. Data projection into a 3D surface to find the optimal 𝛉 to minimize J.
Where A represents a random starting point of the cost function and B is the objective
value or global minimum. Subsequently, through partial derivatives of the cost function
respect to the variable θ, is intended to move A to the position of B, as pointed out in
equation 6.
𝜕 (6)
𝐽(𝜃) → min 𝐽(𝜃)
𝜕𝜃 𝜃

Depending on the initialized values in the vectors of 𝜃, and the value of the
regularization constant (in case of work with a regularized model, usually denoted by 𝜆), it
will be proceeded to generate the partial derivatives of the cost function until the model
reaches the global minimum, which is where the values for 𝜃 are optimal. This step must
be done carefully because, as seen in figure 13, the system can fall into a local minimum or
even start at a maximum (global or local) and remain there, since at that point the derivatives
are equal to zero.
In general, according to the information provided by Professor Andrew Ng. regarding
Machine Learning, to train a neural network the following steps are required: randomly
initialize the weights of the function; implement forward propagation; implement the cost
function code; implement backpropagation for the partial derivatives (gradient) of J; verify
the values obtained with the numerical value of the gradient of J and finally use a method
of advanced optimization with backpropagation to minimize the parameters of 𝜃.
B. Application of the Algorithm
The effect of the procedure can be seen below. First, the original image is read in figure
11 (a). In the second place, the image is resized to make the processing compatible for the
entire database and to avoid incompatibilities in the computations. Then, with the size of
the images normalized, the system is programmed to perform the respective Gaussian filter
in two-steps: (a) add noise according to Gaussian distribution and (b) remove both: the
original noise in the image and the artificially added, in order to attenuate the effects due
high frequencies as shown in figure 11 (b).
After this, a mask runs through the image in order to make the binarization of the data
as shown in figure 12 (a) and (b), with the aim to allow the extraction of the best suited
features to produce an appropriate neural network to work with; the filtered image result
appears in figure 12 (c).

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Figure 11. (a) MRI of a patient with MS in an advanced phase; (b) Normalization of
the dimensions of the image to process.

Figure 15. (a) Image with Gaussian noise; (b) Filtered image; (c) Binarized image.
Hence, this binarized result represents one input of the neural network as appear in the
architecture shown in figure 16, where the forward and backpropagations are applied to
train the units of the network and generate the respective optimal value as set by the array
of classification. Once the network finds the appropriate weights, its created an array with
those values and then applied the analysis over new images, and the system gives as a
response a possible category, where the input image might belong: possible MS patient;
similar traces found; not MS traces detected.

Figure 16. General architecture of the Neural Network to run forward and
backpropagation.

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Note that for visualization purposes, figure 18 just show two hidden layers with nine
units each, plus the bias unit; six input images and three output classification classes. But
the implemented structure is set with a larger number of layers and units, also the input size
depends on the database.
After those parameters are set, the cost function computations take place as
explored in Definition 1., where the double sum simply adds up some regression cost
computed for each output unit, and the triple sum adds up the squared of all the θ present
in the neural network.
Proposition 2. Let a(f) denote the input to compute the next layer a(f+1) , considering
that for every hidden layer will be required to include the bias unit, and θ(g) denote the
weights of the strings; compute the forward propagation from the input layer, through
all hidden layers up to the output layer, with equation 7:
𝑎(𝑓+1) = 𝑠𝑖𝑔𝑚(𝑎(𝑓) 𝜃 (𝑓) ) (7)
Hence, with the forward propagation values arises an “error” 𝛿𝑗𝑙 of node j in layer l; to
find this value there is a vectorized implementation that takes the transpose of θ, times
the difference between the output unit in the layer and the output array, multiplied by
the gradient of the sigmoid in equation 7 (element-wise multiplication). Therefore, it is
required to run an algorithm from the output layer up to the input layer to set up these
proper weights, then run the backpropagation algorithm in equation 8.
(𝑓) (𝑓+1)
𝛿𝑗 = (𝜃 (𝑓) )𝑇 𝛿𝑗 .∗ 𝑔𝑟𝑎𝑑(𝑠𝑖𝑔𝑚(𝑎(𝑓−1) 𝜃 (𝑓−1) )) (9)

One way to get the gradient values and verify the performance of the neural network,
takes the value of a(f) and it multiplies it by the transpose of the array denoted by 𝛿 (𝑓+1)
since the algorithm runs from the output towards the input layer.
1
Δ(𝑓) = (𝛿 (𝑓+1) 𝑎(𝑓) ) (9)
𝑚
The previous statement corresponds with the vectorized implementation of the gradient,
which also requires to scale the output by the inverse of the total number of samples, as
shown in equation 9.
Finally, it is worth to implement some advanced optimization and check the numerical
values to guarantee the optimal performance of the neural network.
8. Conclusions
It can be observed that, by employing a mechanism that supports the specialist to
establish the features of the disease from image analysis, has a considerable effect when it
comes to improve the tools to establish reliable structures of information management, in
order to mitigate the risk of patients getting a misdiagnosis.
Also, and according to the analysis of the results obtained by the neural network, it is
concluded that the program allows to perform a filter of images with well-defined
characteristics, which serve to classify possible cases of MS, but it is required to increase
the database to enhance the neural network performance. Thus, this program represents the
first stage of a sufficiently robust application to elucidate the research case, if it is identified
as a necessity; so it is proposed a future work to be carried out by anyone who wants to
unify the tools into a process, that goes beyond any particular of the three major areas
mentioned in this paper.
In addition, it is validated here the potential of the use of technological support tools in
the processes of image analysis in the healthcare area, in order to support people. This is
clear after identifying the efficiency of the designed architecture and verify its performance

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with images that the system had never seen before. Similarly, it is concluded that because
of the area of application of this work, it is required a constant intervention to improve the
accuracy and precision of the system.

Acknowledgments
The research for this study was supported by Piloto University of Colombia and Nueva
Granada Military University.

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