Main Project Report 2017-18

TEXTURE FEATURE EXTRACTION AND CLASSIFICATION
OF NORMAL AND ALZHEIMER SUBJECTS USING MR

IMAGES
A Project Report submitted in partial fulfillment of the requirement
for the award of degree of
BACHELOR OF TECHNOLOGY
in
ELECTRONICS AND COMMUNICATION ENGINEERING
Submitted by
V. LAKSHMI SRUJANA A.RAJESH KUMAR

(14341A04H3) (15345A0426)
BALAJI MOHANTY
(15345A0425)
Under the Esteemed Guidance of
Supervisor
Dr. T. Prabhakar
Associate Professor, Dept. of ECE.
DEPARTMENT OF ELECTRONICS AND COMMUNICATION ENGINEERING
(Accredited by NBA, NAAC with ‘A’ Grade & ISO 9001:2008 Certified Institution)
GMR Nagar, Rajam – 532 127,

Andhra Pradesh, India
APRIL 2018
Department of Electronics and Communication Engineering
CERTIFICATE
This is to certify that the thesis entitled TEXTURE FEATURE EXTRACTION AND
CLASSIFICATION OF NORMAL AND ALZHEIMER SUBJECTS USING MR
IMAGES submitted by V. LAKSHMI SRUJANA, BALAJI MOHANTY, A. RAJESH
KUMAR, bearing Reg. No: 14341A04H3, Reg. No: 15345A0425, Reg. No: 15345A0426,
respectively have been carried out in partial fulfilment of the requirement for the award of
degree of Bachelor of Technology in Electronics and Communication Engineering of
GMRIT, Rajam affiliated to JNTUK, KAKINADA is a record of bonafide work carried out
by her under my guidance & supervision. The results embodied in this report have not been
submitted to any other University or Institute for the award of any degree.
Signature of Supervisor Signature of HOD
Dr. T. Prabhakar Dr. M. V. Nageswara Rao

Associate Professor, Professor & HOD,
Dept. of ECE, GMRIT. Dept. of ECE, GMRIT.
ii
ACKNOWLEDGEMENT
It gives us an immense pleasure to express deep sense of gratitude to my guide
Dr.T.Prabhakar, Associate Professor, Department of Electronics and Communication
Engineering of whole hearted and valuable guidance throughout the report. Without his
sustained and sincere effort, this report would not have taken this shape. He encouraged and
helped us to overcome various difficulties that we have faced at various stages of our project.
We would like to sincerely thank Dr. M. V. Nageswara Rao, HOD, Electronics and
Communication Engineering, for providing all the necessary facilities that led to the
successful completion of our project.
I would like to thank our respected Dr. M. Sekar, Dean-R&D Coordinator, providing
support and stimulating environment in which the project has been developed.
We would like to take this opportunity to thank our beloved Vice - Principal
Dr. J. Raja Murugadoss, for providing a great support to us in completing our project and
for giving us the opportunity of doing the project.
We would like to take this opportunity to thank our beloved Principal

Dr.C.L.V.R.S.V.Prasad, for providing all the necessary facilities and a great support to us in
completing the project.
We would like to thank all the faculty members and the non-teaching staff of the
Department of Electronics and Communication Engineering for their direct or indirect support
for helping us in completion of this project.
Finally, we would like to thank all of our friends and family members for their
continuous help and encouragement.
V. Lakshmi Srujana (14341A04H3)
Balaji Mohanty (15345A0425)
A. Rajesh Kumar (15345A0426)

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ABSTRACT
Alzheimer's Disease (AD) is a common form of dementia and logically a lethal

neurodegenerative disorder resulting in atrophy of brain region leads to ventricle enlargement
and whole brain shrinkage. It affects grey and white matter of the brain. Most of the times the
radiologist can misunderstand the disorder to be a normal ageing effect. MR imaging is an
essential tool for diagnosing Alzheimer's Disease (AD) because it can qualitatively measure
the atrophy of neuro-anatomical structures more easily. It is an indispensable non-invasive
imaging modality that reflects both the geometry and pathology of the brain. In this project, a
system is being introduced which automatically classifies the kind of neurodegenerative
disease. Basic image processing like preprocessing followed by feature extraction has been
done with input Magnetic Resonance Image (MRI). The T1 weighted Transversal view of
Normal and Alzheimer's images considered in this work. Feature extraction is a technique for
image characterization and also indexing and retrieval. The K-NN classification algorithm has
been used for testing and training the classifier. The classifier categorizes the image's which
are preceded by Gray Level Co-occurrence Matrix (GLCM). Some of the extracted texture
based features are able to differentiate the AD subjects from Normal with low standard
deviation of 0.01 to 0.02. Thus this study seems to be clinically useful. In order to evaluate the
proposed method, we have performed evaluations on the MRI acquiring from the OASIS
database. The proposed method yields an average testing accuracy of 74.73 % which indicates
that the proposed method can differentiate AD and Normal satisfactorily.
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TABLE OF CONTENTS
ACKNOWLEDGEMENTS iii
ABSTRACT iv
LIST OF TABLES vii
LIST OF FIGURES viii
LIST OF ABBREVIATIONS ix
1. INTRODUCTION 1
1.1. ALZHEIMER'S DISEASE (AD) 1
1.2. STATISTICS OF ALZHEIMER’S 3
1.3. HOW ALZHEIMER’S AFFECTS THE BRAIN 4
1.4. STAGES OF THE DISEASE 6
1.4.1. Early-stage Alzheimer’s 7
1.4.2. Middle-stage Alzheimer’s 7
1.4.3. Late-stage Alzheimer’s 7
1.5. DETECTION OF ALZHEIMER’S 7
1.6. BRAIN IMAGING OR NEUROIMAGING 8
1.7. MAGNETIC RESONANCE IMAGING 8
1.7.1. Working of MRI 10
1.8. WORK FLOW 11
1.9. BASIC MRI SCANS 12
1.9.1. Role of structural MRI in Alzheimer's disease 13
1.9.2. Reason for Choosing MRI 14
1.10. DIGITAL IMAGE PROCESSING 15
1.11. INTRODUCTION TO MATLAB 15
1.11.1. Images as Matrices 16
2. LITERATURE REVIEW 18
3. GLCM FEATURE EXTRACTION OF MR IMAGES 25
3.1. TEXTURE FEATURE 25
3.1.1. Texture Feature Extraction 25
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3.2. CO-OCCURRENCE MATRICES 26
3.3. GRAY LEVEL CO-OCCURRENCE MATRIX 26
3.3.1. Algorithm 27
3.4. HARALICK TEXTURE FEATURES 28
4. AD AND NORMAL MR IMAGE CLASSIFICATION 33
4.1. DIGITAL IMAGE CLASSIFICATION 33
4.1.1. Spectral differentiation 33
4.1.2. Radiometric differentiation 34
4.1.3. Spatial differentiation 34
4.1.4. Supervised classification 35
4.1.5. Unsupervised classification 35
4.2. K-NN CLASSIFICATION 37
4.2.1. How to choose the value of K 38
4.3. KNN PROS. AND CONS 38
5. RESULT AND DISCUSSION 40
5.1. GLCM FEATURE’S MEAN AND STANDARD DEVIATION 40
5.2. GLCM FEATURE’S OF NORMAL AND AD 41
5.3. PERFORMANCE OF K-NN CLASSIFIER 48
5.4. MATLAB OUTPUT 48
6. CONCLUSION 49
REFERENCE 50
vi
LISTOFTABLES
TABLE NO TITLE PAGE NO
5.1 GLCM Features Mean and SD 40
5.2 K-NN classification results 48
vii
LISTOF FIGURES
FIGURE NO TITLE PAGE NO
1.1 Plaques and tangles tend to spread through the cortex as Alzheimer's progresses. 5
1.2 Damaging of Neurons 6
1.3 MR imaging equipment 10
1.4 Flow chart 12
1.5 MRI image of AD 14
1.6 MRI image of NORMAL 14
5.1 Angular Second Moment of AD vs NORMAL 41
5.2 Contrast of AD vs NORMAL 42
5.3 Correlation of AD vs NORMAL 42
5.4 Variance of AD vs NORMAL 43
5.5 Inverse Difference of AD vs NORMAL 43
5.6 Sum Average of AD vs NORMAL 44
5.7 Sum Variance of AD vs NORMAL 44
5.8 Sum Entropy of AD vs NORMAL 45
5.9 Entropy of AD vs NORMAL 45
5.10 Difference Variance of AD vs NORMAL 46
5.11 Difference Entropy of AD vs NORMAL 46
5.12 Information Measure of Correlation I of AD vs NORMAL 47
5.13 Information Measure of Correlation II of AD vs NORMAL 47
5.14 Maximal Correlation Coefficient AD vs NORMAL 48
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LIST OF ABBREVIATIONS
AD : Alzheimer’s Disease.
TP : True Positive.
TN : True Negative.
FP : False Positive.
FN : False Negative.
N : Normal.
MMSE : Mini-Mental State Examination.
GRE : Gradient Echo.
GLCM : Gray Level Co-occurrence Matrix.
MRI : Magnetic Resonance Imaging.
K-NN : Kernal Nearest Neighbor.
CT : Computed Tomography.
MPRAGE : Magnetization Prepared Rapid Acquisition Gradient Echo.
PCA : Principal Component Analysis.
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Texture Feature Extraction and Classification of Alzheimer’s Disease and Normal using MR
images
CHAPTER – 1
INTRODUCTION
1.1 ALZHEIMER’S DISEASE

Alzheimer's is the most common form of dementia [1], a general term for loss of
memory and other intellectual abilities serious enough to interfere with daily life. Alzheimer's
disease accounts for 50 to 70 percent of dementia cases. It is not a normal part of aging,
although the greatest known risk factor is increasing age, and the majority of people with
Alzheimer's are 65 and older. But Alzheimer's is not just a disease of old age. Up to 5 percent
of people with the disease have early onset of Alzheimer's (also known as younger-onset),
which often appears when someone is in their 40’s or 50’s. Alzheimer's worsens over time. It
is a degenerative disease, where symptoms gradually worsen over a number of years. In its
early stages, memory loss is mild, but at a later stage, individuals lose the ability to carry on a
conversation and respond to their environment. The development of biomarker is necessary
for the early diagnosis of Alzheimer’s disease.[2] [1].
Conventional Biomarkers[10][12] to identify Alzheimer’s disease depend on the skill of
the doctor, the case history of the patient given to the doctor and the ability of the patient to
respond to the doctor. No single test can detect Alzheimer’s. The medical workup is designed
to evaluate overall health and identify any conditions that could affect the mind and how well
it works. Experts believe that a skilled physician can diagnose Alzheimer’s with more than 90
percent accuracy. The Alzheimer's Association [1] [8] believes that home screening tests
cannot and should not be used as a substitute for a thorough examination by a skilled doctor.
There is an established diagnostic criterion that physicians adhere to when diagnosing
someone for Alzheimer's disease. Although dementia screening tests do not claim to offer
100% accurate diagnosis, any test that is conducted may cause great psychological distress to
the test taker. Some of the other tests usually conducted by the doctors are reviewing medical
history, in which doctors interview the person being examined or family members to gather
information about the current and past illnesses; Mental status testing which gives the doctor a
Department of ECE, GMRIT 1

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general idea of whether the person is aware of his problem or he feels that nothing is wrong;
and he knows the date, time and where he is and can remember a short list of words and
follow instructions and do simple calculations etc.
The Mini-Mental State Examination (MMSE) is one of the tests most commonly used to
assess mental function. In the MMSE, a health professional asks the patient a series of
questions designed to test a range of everyday mental skills. The maximum MMSE score is
30 points. A score of 20 - 24 suggests mild dementia, 13 - 20 suggests moderate dementia,
and less than 12 indicates severe dementia. On an average, the MMSE score of a person with
Alzheimer’s declines by 2 - 4 points each year. All these tests require the patient’s
cooperation and the doctor’s skill. New imaging technologies have revolutionized the
understanding of the structure and function of the live brain. Currently, a standard medical
workup for Alzheimer’s disease often includes structural imaging with Magnetic Resonance
Image (MRI)[3] [9] or, less frequently, Computed Tomography (CT). These images are used
primarily to detect tumours, evidence of small or large strokes, and damage from severe head
trauma or a build up of fluid. Researchers do intensively try to find whether the use of MRI
and other imaging methods may be expanded to play a more direct role in diagnosing
Alzheimer’s. Many research findings have shown that the brains of people with Alzheimer’s
shrink significantly as the disease worsens. Research has also shown that shrinkage in specific
brain regions, particularly the hippocampus, may be an early sign of Alzheimer’s. The
hippocampus is a major component of the brains of humans and other mammals. It belongs to
the limbic system and plays important roles in long-term memory and spatial navigation.
However, scientists have not yet agreed upon standardized values that would establish the
significance of a specific amount of shrinkage in any person at a single point in time. Due to
the deposition of amyloid-beta and tau on the hippocampus of the AD patients, the texture
features can be utilized to identify the AD.
The research work undertaken is focused on developing a biomarker to detect the
Alzheimer’s disease from Hippocampus MRI texture features, which is automatic, accurate
and fast. [1]

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Dementia: Dementia is a general term for the loss of memory and other cognitive abilities
serious enough to interfere with daily life.
Alzheimer's has no current cure, but treatments for symptoms are available and research
continues. Although current Alzheimer's treatments cannot stop Alzheimer's from progressing,
they can temporarily slow the worsening of dementia symptoms and improve quality of life for
those with Alzheimer's and their caregivers. Today, there is a worldwide effort under way to find
better ways to treat the disease, delay its onset, and prevent it from developing. [1]
1.2 STATISTICS OF ALZHEIMER’S

Alzheimer's worsens over time. Alzheimer's is a progressive disease, where dementia
symptoms gradually worsen over a number of years. In its early stages, memory loss is mild, but
with late-stage Alzheimer's, individuals lose the ability to carry on a conversation and respond to
their environment. Alzheimer's is the sixth leading cause of death in the United States. Those
with Alzheimer's live an average of eight years after their symptoms become noticeable to
others, but survival can range from four to 20 years, depending on age and other health
conditions. It is estimated that there are currently about 18 million people worldwide with
Alzheimer’s disease. This figure is likely double by 2025 to 34 million (Ferri 2005). Much of
this increase will occur in developing countries, and will be due to aging. Currently, more than
50% of people with Alzheimer’s disease live in developing countries and by 2025, this will be
over 70%. Recent research in India suggests that the risk of Alzheimer’s disease is possibly
higher in urban than in rural areas. There is an accelerating worldwide effort under way to find
better ways to treat the disease, delay its onset, or prevent it from becoming serious. Early
diagnosis of AD patients is important because it allows early treatment with cholinesterase
inhibitors, which have been shown to delay institutionalization, improve or stabilize cognition
and behavioral symptoms. As therapeutic interventions become available, there is a need for
developing methodologies that will serve as an in vivo surrogate for these pathologic changes,
and thus, accurately identify those cognitively impaired individuals who are in the earliest stages
of Alzheimer’s disease. [1]

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1.3 HOW ALZHEIMER’S AFFECTS THE BRAIN

The brain has 100 billion nerve cells (neurons). Each nerve cell connects with many
others to form communication networks. Groups of nerve cells have special jobs. Some are
involved in thinking, learning and remembering. Others help us see, hear and smell. To do
their work, brain cells operate like tiny factories. They receive supplies, generate energy,
construct equipment and get rid of waste. Cells also process and store information and
communicate with other cells. Keeping everything running requires coordination as well as
large amounts of fuel and oxygen.
Scientists believe Alzheimer's disease prevents parts of a cell's factory from running well.
They are not sure where the trouble starts. But just like a real factory, backups and
breakdowns in one system cause problems in other areas. As damage spreads, cells lose their
ability to do their jobs and, eventually die, causing irreversible changes in the brain. The
changes that take place in the brain begin at the microscopic level long before the first signs
of memory loss. The brain has 100 billion nerve cells (neurons). Each nerve cell connects too
many others to form communication networks. In addition to nerve cells, the brain includes
cells specialized to support and nourish other cells. Groups of nerve cells have special jobs.
Some are involved in thinking, learning and memory. Others help us see, hear, smell and tell
our muscles when to move. Brain cells operate like tiny factories. They receive supplies,
generate energy, construct equipment and get rid of waste. Cells also process and store
information and communicate with other cells. Keeping everything running requires
coordination as well as large amounts of fuel and oxygen. Scientists believe Alzheimer’s
disease prevents parts of a cell’s factory from running well. They are not sure where the
trouble starts. But just like a real factory, backups and breakdowns in one system cause
problems in other areas. As damage spreads, cells lose their ability to do their jobs and,
eventually, die.
The brains of individuals with Alzheimer’s have an abundance of plaques and tangles.
Plaques are deposits of a protein fragment called beta-amyloid that builds up in the spaces
between nerve cells. Tangles are twisted fibers of another protein called tau that builds up
inside cells. Though autopsy studies show that most people develop some plaques and tangles
as they age, those with Alzheimer’s tend to develop far more and in a predictable pattern,

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beginning in the areas important for memory before spreading to other regions. Scientists do
not know exactly what role plaques and tangles play in Alzheimer’s disease. Most experts
believe that they disable or block communication among nerve cells and disrupt processes the
cells need to survive. The destruction and death of nerve cells causes memory failure,
personality changes, problems in carrying out daily activities and other symptoms of
Alzheimer’s disease. Two abnormal structures called plaques and tangles are prime suspects
in damaging and killing nerve cells. Plaques are deposits of a protein fragment called beta-
amyloid (BAY-tuh AM-uh-loyd) that build up in the spaces between nerve cells. Tangles are
twisted fibers of another protein called tau (rhymes with “wow”) that build up inside cells.
Though autopsy studies show that most people develop some plaques and tangles as they age,
those with Alzheimer’s tend to develop far more and in a predictable pattern, beginning in the
areas important for memory before spreading to other regions.
Fig 1.1 Plaques and tangles tend to spread through the cortex as Alzheimer's progresses.
Scientists do not know exactly what role plaques and tangles play in Alzheimer's disease.
As shown in fig 1.1 plaques and tangles spread throughout the brain. Most experts believe
they somehow play a critical role in blocking communication among nerve cells and
disrupting processes that cells need to survive. It's the destruction and death of nerve cells that
causes memory failure, personality changes, problems carrying out daily activities and other
symptoms of Alzheimer's disease. [1]

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Fig 1.2 Damaging of Neurons
1.4 STAGES OF THE DISEASE
Different types of dementia are associated with particular types of brain cell damage in
particular regions of the brain. For example, in Alzheimer's disease, high levels of certain
proteins inside and outside brain cells make it hard for brain cells to stay healthy as shown in
fig 1.2 the neurons get damaged. The brain region called the hippocampus is the center of
learning and memory in the brain, and the brain cells in this region are often the first to be
damaged. That's why memory loss is often one of the earliest symptoms of Alzheimer's.
While most changes in the brain that cause dementia are permanent and worsen over time,
thinking and memory problems caused by the following conditions may improve when the
condition is treated or addressed:
1) Depression
2) Medication side effects
3) Excess use of alcohol
4) Thyroid problems
5) Vitamin deficiencies
Alzheimer’s disease typically progresses slowly in three general stages: early, middle and
late (sometimes referred to as mild, moderate and severe in a medical context). Since

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Alzheimer’s affects people in different ways, each person may experience symptoms or
progress through the stages differently.
1.4.1 Early-stage Alzheimer’s

In the early stage of Alzheimer’s, a person may function independently. He or she may
still drive, work and be part of social activities. Despite this, the person may feel as if he or
she is having memory lapses, such as forgetting familiar words or the location of everyday
objects. Friends, family or others close to the individual begin to notice difficulties. During a
detailed medical interview, doctors may be able to detect problems in memory or
concentration.
1.4.2 Middle-stage Alzheimer’s

Middle-stage Alzheimer’s is typically the longest stage and can last for many years. As
the disease progresses, the person with Alzheimer’s will require a greater level of care. You
may notice the person with Alzheimer’s confusing words,
getting frustrated or angry, or acting in unexpected ways, such as refusing to bathe. Damage
to nerve cells in the brain can make it difficult to express thoughts and perform routine tasks.
1.4.3 Late-stage Alzheimer’s

In the final stage of the disease, individuals lose the ability to respond to their
environment, carry on a conversation and, eventually, control movement. They may still say
words or phrases, but communicating pain becomes difficult. As memory and cognitive skills
worsen, significant personality changes may occur and extensive help with daily activities
may be required.
1.5 DETECTION OF ALZHEIMER’S

Several potential biomarkers are being studied for their ability to indicate early stages of
Alzheimer’s disease (An example of biomarker is fasting blood glucose level (blood sugar)
level, which indicate the presence of diabetes). Examples being studied include beta-amyloid

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and tau levels in cerebrospinal fluid and brain changes detectable by imaging. Recent research
suggests that these indicators may change at different stages of the disease process.
1.6 BRAIN IMAGING OR NEUROIMAGING

Neuroimaging is among the most promising area of research focused on early detection.
Today, a standard workup for Alzheimer’s disease often includes structural imaging with
magnetic resonance imaging (MRI) or computed tomography imaging (CT). These tests are
currently used chiefly to rule out other conditions that may cause symptoms similar to
Alzheimer’s but require different treatment. Structural imaging provides information about
the shape, position or volume of brain tissue. Structural techniques include magnetic
resonance imaging (MRI) and Computed tomography (CT).
1.7 MAGNETIC RESONANCE IMAGING

Magnetic Resonance imaging (MRI) is a medical imaging technique that permits the
detailed visualization of internal anatomical structures in living human subjects. In today's
clinical settings, MR has become a standard diagnostic tool, and the increased availability of
imaging techniques permit the routine scanning of patients to detect a variety of tumor,
lesions and abnormalities in a non-invasive way . MRI has proved to have sensitivity perhaps
times greater than that of Computerized Tomography (CT) in detecting MS lesions. The most
common MR technique used for diagnostic studies is based on the magnetic resonance of
hydrogen nuclei. Since water is by far the most common source of hydrogen nuclei in living
tissue, it is likely that the water content of tissue produces most of the signal seen on the
scans. The body is largely composed of water molecules. Each water molecule has two
hydrogen nuclei or protons. When a person is inside the powerful magnetic field of the
scanner, the magnetic moments of some of these protons become aligned with the direction of
the field. A radio frequency transmitter is briefly turned on, producing a further varying
electromagnetic field. The photons of this field have just the right energy, known as the
resonance frequency, to be absorbed and flip the spin of the aligned protons in the body. The
frequency at which the protons resonate depends on the strength of the applied magnetic field.
After the field is turned off, those protons which absorbed energy revert back to the original

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lower-energy spin down state. Now a hydrogen dipole has two spins, 1 high spin and 1 low.
In low spin both dipole and field are in parallel direction and in high spin case it is anti-
parallel. They release the difference in energy as a photon, and the released photons are
detected by the scanner as an electromagnetic signal, similar to radio waves. As a result of
conservation of energy, the resonant frequency also dictates the frequency of the released
photons. The photons released when the field is removed have energy and therefore a
frequency which depends on the energy absorbed while the field was active. It is this
relationship between field-strength and frequency that allows the use of nuclear magnetic
resonance for imaging. An image can be constructed because the protons in different tissues
return to their equilibrium state at different rates, which is a difference that can be detected.
Five different tissue variables — spin density, T1 and T2 relaxation times and flow and
spectral shifts can be used to construct images. By changing the parameters on the scanner,
this effect is used to create contrast between different types of body tissue or between other
properties, as in fMRI and diffusion MRI. The 3D position from which photons were released
is learned by applying additional fields during the scan. This is done by passing electric
currents through specially-wound solenoids, known as gradient coils. These fields make the
magnetic field strength vary depending on the position within the patient, which in turn makes
the frequency of released photons dependent on their original position in a predictable
manner, and the original locations can be mathematically recovered from the resulting signal
by the use of inverse Fourier transform. Contrast agents may be injected intravenously to
enhance the appearance of blood vessels, tumours or inflammation. Contrast agents may also
be directly injected into a joint in the case of arthrograms, MRI images of joints. Unlike CT,
MRI uses no ionizing radiation and is generally a very safe procedure. Nonetheless the strong
magnetic fields and radio pulses can affect metal implants, including cochlear implants and
cardiac pacemakers. In the case of cochlear implants, the US FDA has approved some
implants for MRI compatibility. In the case of cardiac pacemakers, the results can sometimes
be lethal, so patients with such implants are generally not eligible for MRI. MRI is used to
image every part of the body, and is particularly useful for tissues with many hydrogen nuclei
and little density contrast, such as the brain, muscle, connective tissue and most tumours. An
advantage of MRI is its ability to produce images in axial, coronal, sagittal and multiple

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oblique planes with equal ease. MRI scans give the best soft tissue contrast of all the imaging
modalities. With advances in scanning speed and spatial resolution, and improvements in
computer 3D algorithms and hardware, MRI has become an important tool in neuroradiology.
1.7.1 Working of MRI

MRIs employ powerful magnets which produce a strong magnetic field that forces
protons in the body to align with that field. When a radiofrequency current is then pulsed
through the patient, the protons are stimulated, and spin out of equilibrium, straining against
the pull of the magnetic field. When the radiofrequency field is turned off, the MRI sensors
are able to detect the energy released as the protons realign with the magnetic field. The time
it takes for the protons to realign with the magnetic field, as well as the amount of energy
released, changes depending on the environment and the chemical nature of the molecules.
Physicians are able to tell the difference between various types of tissues based on these
magnetic properties. To obtain an MRI image, a patient is placed inside a large magnet and
must remain very still during the imaging process in order not to blur the image. Contrast
agents (often containing the element Gadolinium) may be given to a patient intravenously
before or during the MRI to increase the speed at which protons realign with the magnetic
field. The faster the protons realign, the brighter the image. MRI equipment is shown in fig
1.3.
Fig 1.3 MR Imaging Equipment.

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MRI scanners are particularly well suited to image the non-bony parts or soft tissues of
the body. They differ from computed tomography (CT), in that they do not use the damaging
ionizing radiation of x-rays. The brain, spinal cord and nerves, as well as muscles, ligaments,
and tendons are seen much more clearly with MRI than with regular x-rays and CT; for this
reason MRI is often used to image knee and shoulder injuries. In the brain, MRI can
differentiate between white matter and grey matter and can also be used to diagnose
aneurysms and tumors. Because MRI does not use x-rays or other radiation, it is the imaging
modality of choice when frequent imaging is required for diagnosis or therapy, especially in
the brain. However, MRI is more expensive than x-ray imaging or CT scanning. One kind of
specialized MRI is functional Magnetic Resonance Imaging (fMRI.) This is used to observe
brain structures and determine which areas of the brain “activate” (consume more oxygen)
during various cognitive tasks. It is used to advance the understanding of brain organization
and offers a potential new standard for assessing neurological status and neurosurgical risk.
1.8 WORK FLOW
As shown in fig 1.4 the input images are MR images and the image properties are:
File type: .GIF,

Dimensions: 176 x 208.
We used AD and Normal MR images of each 30. Then we extracted the 14 texture
features of each image using GLCM texture extraction algorithm. Then we used K-NN
classifier for characterizing AD and NORMAL MRI images. We fed the 14 features of 30 AD
images and 30 NORMAL images to classifier as test sets and training sets. These are taken by
classifier as 14 x 30 matrix. The K-NN classifier calculates the distance function using these
features and classify the AD and NORMAL on the basis of this distance value.

images
Input MRI image
GLCM Feature
Extraction
Extracted Features
fed to k-NN
Training the input MRI

images based on the
extracted GLCM features
Testing the given

MRI image
Performance
evaluation
Fig 1.4 Flow chart
1.9 BASIC MRI SCANS

T1-weighted MRI - T1-weighted scans are a standard basic scan, in particular
differentiating fat from water - with water darker and fat brighter use a gradient echo (GRE)
sequence, with short TE and short TR. This is one of the basic types of MR contrast and is a

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commonly run clinical scan. The T1 weighting can be increased (improving contrast) with
the use of an inversion pulse as in an MPRAGE sequence. Due to the short repetition time
(TR) this scan can be run very fast allowing the collection of high resolution 3D datasets. A
T1 reducing gadolinium contrast agent is also commonly used, with a T1 scan being
collected before and after administration of contrast agent to compare the difference. In the
brain T1- weighted scans provide good gray matter/white matter contrast; in other words, T1-
weighted images highlight fat deposition. T2-weighted MRI - T2-weighted scans are another
basic type. Like the T1- weighted scan, fat is differentiated from water - but in this case fat
shows darker, and water lighter. For example, in the case of cerebral and spinal study, the
CSF (cerebrospinal fluid) will be lighter in T2-weighted images. These scans are therefore
particularly well suited to imaging edema, with long TE and long TR. Because the spin echo
sequence is less susceptible to inhomogeneities in the magnetic field, these images have long
been a clinical workhorse. Proton Density weighted MRI- Spin density, also called proton
density, weighted scans try to have no contrast from either T2 or T1 decay, the only signal
change coming from differences in the amount of available spins (hydrogen nuclei in water).
It uses a spin echo or sometimes a gradient echo sequence, with short TE and long TR.
1.9.1 Role of structural MRI in Alzheimer's disease

Alzheimer's disease (AD) is a multifaceted disease in which cumulative pathological
brain insults result in progressive cognitive decline that ultimately leads to dementia. Amyloid
plaques, neurofibrillary tangles (NFTs), neurodegeneration, and inflammation are the well-
established pathological hallmarks of AD. A plausible model for the development of AD
posits that amyloid deposition occurs early in the process but by itself does not directly cause
clinical symptoms. Neuronal and synaptic losses appear to be key determinants of cognitive
impairment in AD. If neuronal loss leads to cerebral atrophy (as is likely), then it can be
expected that cognitive decline and atrophy will be closely associated. On the basis of this
evidence, it has been hypothesized that AD pathological cascade is a two-stage process in
which amyloidosis and neuronal pathology (tauopathy, neuronal injury, and
neurodegeneration) are largely sequential rather than simultaneous processes. There is also
sufficient literature to support the fact that atrophy of the brain structures or

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neurodegeneration is the most proximate substrate of cognitive impairment in AD. Owing to

the close relationship between neurodegeneration and cognition, atrophy measured on
structural magnetic resonance imaging (sMRI) is a powerful AD biomarker. MR images of
AD and NORMAL brain are shown in fig 1.5 & fig 1.6 respectively.
Fig 1.5 MRI of AD Brain Fig 1.6 MRI of NORMAL Brain
1.9.2 Reason for Choosing MRI

1. Non invasive.
2. Highest soft tissue contrast.
3. To obtain cross-sectional images on any plane without repositioning the patient.
4. No ionizing radiation involved with MRI.
5. Possible to obtain vascular images without using any vascular contrast or any
invasive approach.
6. MR Spectroscopy allows analyzing the biochemical properties and metabolic
activities of the tissues.

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1.10 DIGITAL IMAGE PROCESSING

An image may be defined as a two-dimensional function, f(x, y), where x and y are
spatial (plane) coordinates, and the amplitude of f at any pair of coordinates (x, y) is called the
intensity or gray level of the image at that point. When x, y, and the amplitude values of f are
all finite, discrete quantities, we call the image a digital image. The field of digital image
processing refers to processing digital images by means of a digital computer. Note that a
digital image is composed of a finite number of elements, each of which has a particular
location and value. These elements are referred to as picture elements, image elements, pels
and pixels. Pixel is the term most widely used to denote the elements of a digital image.
Vision is the most advanced of our senses, so it is not surprising that images play the
single most important role in human perception. However, unlike humans, who are limited to
the visual band of the electromagnetic (EM) spectrum, imaging machines cover almost the
entire EM spectrum, ranging from gamma to radio waves. They can operate on images
generated by sources that humans are not accustomed to associating with images. These
include ultrasound, electron microscopy, and computer-generated images. Thus, digital image
processing encompasses a wide and varied field of applications.[14]
1.11 INTRODUCTION TO MATLAB
The name MATLAB stands for MATrix LABoratory. MATLAB was written
originally to provide easy access to matrix software developed by the LINPACK (linear
system package) and EISPACK (Eigen system package) projects. MATLAB is a high-
performance language for technical computing. It integrates computation, visualization, and
programming environment. Furthermore, MATLAB is a modern programming language
environment: it has sophisticated data structures, contains built-in editing and debugging
tools, and supports object-oriented programming. These factors make MATLAB an excellent
tool for teaching and research.

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MATLAB is being used as a platform for laboratory exercises and the problems
classes in the Image Processing half of the Computer Graphics and Image Processing course
unit. This handout describes the MATLAB development environment you will be using, you
are expected to have read it and be familiar with it before attempting the Laboratory and
Coursework Assignments.
MATLAB is a data analysis and visualization tool designed to make matrix
manipulation as simple as possible. In addition, it has powerful graphics capabilities and its
own programming language. The basic MATLAB distribution can be expanded by adding a
range of toolboxes, the one relevant to this course is the image-processing toolbox (IPT). The
basic distribution and all of the currently available toolboxes are available in the labs. The
basic distribution plus any installed toolboxes will provide a large selection of functions,
invoked via a command line interface.
MATLAB’s basic data structure is the matrix. In MATLAB a single variable is a 1 x 1
matrix, a string is a 1 x n matrix of chars. An image is an n x m matrix of pixels. A raw image
will take up a lot of storage space. Methods have been defined to compress the image by
coding redundant data in a more efficient fashion, or by discarding the perceptually less
significant information. MATLAB supports reading all of the common image formats. Image
coding is not addressed in this course unit. [23]
1.11.1 Images as Matrices

The coordinate system lead to the following representation for a digitized image:
The right side of this equation is a digital image by definition. Each element of this
array is called an image element, picture element, pixel, or pel. The terms image and pixel are
used throughout the rest of our discussions to denote a digital image and its elements.

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A digital image can be represented as a MATLAB matrix:
where f(1, 1) =f(0,0) (note the use of a monospace font to denote MATLAB quantities).
Clearly, the two representations are identical, except for the shift in origin. The notation f(p,
q) denotes the element located in row p and column q. For example, f(6, 2) is the element in
the sixth row and second column of matrix f. Typically, we use the letters M and N,
respectively, to denote the number of rows and columns in a matrix. A 1×N matrix is called a
row vector, whereas an M×1 matrix is called a column vector. A 1×1 matrix is a scalar.
Matrices in MATLAB are stored in variables with names such as A, a, RGB,
real_array, and so on. Variables must begin with a letter and contain only letters, numerals,
and underscores. As noted in the previous paragraph, all MATLAB quantities in this book are
written using monospace characters. We use conventional Roman, italic notation, such as
f(x,y), for mathematical expressions.

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CHAPTER – 2
LITERATURE REVIEW
Clinical criteria for the diagnosis of Alzheimer’s disease include insidious onset and
progressive impairment of memory and other cognitive functions. There are no motor,
sensory, or coordination deficits early in the disease. The diagnosis cannot be determined by
laboratory tests. These tests are important primarily in identifying other possible causes of
dementia that must be excluded before the diagnosis of Alzheimer’s disease may be made
with confidence. Neuropsychological tests provide confirmatory evidence of the diagnosis of
dementia and help to assess the course and response to therapy. The criteria proposed are
intended to serve as a guide for the diagnosis of probable, possible, and definite Alzheimer’s
disease; these criteria will be revised as more definitive information becomes available. [25]
The Open Access Series of Imaging Studies is a series of magnetic resonance imaging
data sets that is publicly available for study and analysis. The initial data set consists of a
cross-sectional collection of 416 subjects aged 18 to 96 years. One hundred of the included
subjects older than 60 years have been clinically diagnosed with very mild to moderate
Alzheimer’s disease. The subjects are all right-handed and include both men and women. For
each subject, three or four individual T1-weighted magnetic resonance imaging scans
obtained in single imaging sessions are included. Multiple within-session acquisitions provide
extremely high contrast-to-noise ratio, making the data amenable to a wide range of analytic
approaches including automated computational analysis. Additionally, a reliability data set is
included containing 20 subjects without dementia imaged on a subsequent visit within 90 days
of their initial session. Automated calculation of whole-brain volume and estimated total
intracranial volume are presented to demonstrate use of the data for measuring differences
associated with normal aging and Alzheimer’s disease. [8].

images
Alzheimer’s disease (AD), is a degenerative disease which leads to memory loss and
problems with thinking and behaviour.AD is a type of dementia which accounts for an
estimated 60% to 80% of cases. Accurate diagnosis depends on the identification of
discriminative features of AD. Recently, different feature extraction methods are used for the
classification of AD. In this paper, we proposed a classification framework to select features,
which are extracted using Gray-Level Co-occurrence Matrix (GLCM) method to distinguish
between the AD and the Normal Control (NC). In order to evaluate the proposed method, we
have performed evaluations on the MRI acquiring from the OASIS database. The proposed
method yields an average testing accuracy of 75.71% which indicates that the proposed
method can differentiate AD and NC satisfactorily. [3].
Grey Level Co-occurrence Matrices (GLCM) are one of the earliest techniques used for
image texture analysis. In this paper we defined a new feature called trace extracted from the
GLCM and its implications in texture analysis are discussed in the context of Content Based
Image Retrieval (CBIR). The theoretical extension of GLCM to n-dimensional gray scale
images are also discussed. The results indicate that trace features outperform Haralick features
when applied to CBIR. [5].
The nearest neighbor decision rule assigns to an unclassified sample point the
classification of the nearest of the nearest of a set of previously classified points. This rule is
independent of the underlying joint distribution on the sample points and their classifications,
and hence the probability of error R of such a rule must be at least as great as the Bayes
probability of error R*--the minimum probability of error over all decision rules taking
underlying probability structure into account. However, in a large sample analysis, we will
show in the M-category case that R* ≤ R ≤ R*(2 - MR*/ (M-1)), where these bounds are the
tightest possible, for all suitably smooth underlying distributions. Thus for any number of
categories, the probability of error of the nearest neighbor rule is bounded above by twice the
Bayes probability of error. In this sense, it may be said that half the classification information
in an iu6uite sample set is contained iu the nearest neighbor. [22]

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A preliminary study for mapping sea ice patterns (texture) with 100-m ERS-1 synthetic
aperture radar (SAR) imagery is presented in the paper. We used gray-level co-occurrence
matrices (GLCM) to quantitatively evaluate textural parameters and representations and to
determine which parameter values and representations are best for mapping sea ice texture.
We conducted experiments on the quantization levels of the image and the displacement and
orientation values of the GLCM by examining the effects textural descriptors such as entropy
have in the representation of different sea ice textures. We showed that a complete gray-level
representation of the image is not necessary for texture mapping, an eight-level quantization
representation is undesirable for textural representation, and the displacement factor in texture
measurements is more important than orientation. In addition, we developed three GLCM
implementations and evaluated them by a supervised Bayesian classifier on sea ice textural
contexts. This experiment concludes that the best GLCM implementation in representing sea
ice texture is one that utilizes a range of displacement values such that both microtextures and
macrotextures of sea ice can be adequately captured. These findings define the quantization,
displacement, and orientation values that are the best for SAR sea ice texture analysis using
GLCM. [6].
Early detection of Alzheimer's Disease (AD) is important so that preventative measures

can be taken. Current techniques for detecting AD rely on cognitive impairment testing which
unfortunately does not yield accurate diagnoses until the patient has progressed beyond a
moderate AD. In this project, we develop a new approach based on mathematical and image
processing techniques for better classification of AD. The most popular current technique
analyzes MRI scans using properties of diffeomorphism which generates a mapping from one
MRI to another. Since MRIs are very high dimensional vector spaces, the existing technique
reduces it to three dimensions and then clusters the images according to presence or lack of
AD. However, reducing a high dimensional vector space to three dimensions compromises
the information in the data and thus results in some loss of accuracy. We propose to reduce
the high dimensional MRI image vector space to 150 dimensions using Principal Component
Analysis. In order to categorize the reduced dimensions from PCA for progression of AD, we
employ a multiclass neural network. The neural network is trained initially on 230 diagnosed

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MRIs obtained from OASIS MRI database. We then test our trained neural network on the
entire set of 457 MRIs provided by OASIS dataset to confirm the accuracy of diagnosis by
our system. Our results produce nearly 90% accuracy in AD diagnosis and classification. [10].
The different feature extraction techniques for lesion identification in Dynamic Contrast
Enhancement - Magnetic Resonance Imaging (DCE - MRI) of Breast is discussed in the
paper. In DCE- MRI, kinetic feature extraction is a popular radiological approach used by
Radiologists. However, extracting more features like entropy, homogeneity, heterogeneity,
and statistical features of the region of interests would enhance the accuracy of lesion
diagnosis, especially in ‘not sure' (plateau) cases. This paper discuss about a survey of
different feature extraction techniques such as structural, statistical, modelbased and
transform based methods. The paper also advocates a comparative study of feature extraction
using statistical and intensity time kinetic curve methods. These two features are employed in
understanding the prominence of malignancy in the lesion.
Ventricle enlargement is a useful structural biomarker for the diagnosis of Alzheimer’s

Disease (AD). This devastating neurodegenerative disorder results in progression of dementia.
Although AD results in the passive increment of ventricle volume, there exists a large overlap
in the volume measurements of AD and normal subjects. Hence, shape based analysis of
ventricle dilation is appropriate to detect the subtle morphological changes among these two
groups. In this work, segmentation of ventricle in Alzheimer MR images is employed using
level set method and anisotropic based diffusion filtering. Images considered for this study are
pre-processed using filters. Anisotropic based diffusion filtering is employed to extract the
edge map. This filtering performs region specific smoothing process using the diffusion
coefficient as a function of image gradient. Filtered images are subjected to level set method
which employs an improved diffusion rate equation for the level set evolution. Geometric
features are extracted from the segmented ventricles. Results show that the diffusion filter
could extract edge map with sharp region boundaries. The modified level set method is able to
extract the morphological changes in ventricles. The observed morphological changes are
distinct for normal and AD subjects (p < 0.0001). It is also observed that the sizes of ventricle

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in the AD subjects are noticeably enlarged when compared to normal subjects. Features
obtained from the segmented ventricles are also clearly distinct and demonstrate the
differences in the AD subjects. As ventricle volume and its morphometry are significant
biomarkers, this study seems to be clinically relevant. [21].
Texture is one of the important characteristics used in identifying objects or regions of

interest in an image, whether the image be a photomicrograph, an aerial photograph, or a
satellite image. This paper describes some easily computable textural features based on gray-
tone spatial dependancies, and illustrates their application in category-identification tasks of
three different kinds of image data: photomicrographs of five kinds of sandstones, 1:20 000
panchromatic aerial photographs of eight land-use categories, and Earth Resources
Technology Satellite (ERTS) multispecial imagery containing seven land-use categories. We
use two kinds of decision rules: one for which the decision regions are convex polyhedra (a
piecewise linear decision rule), and one for which the decision regions are rectangular
parallelpipeds (a min-max decision rule). In each experiment the data set was divided into two
parts, a training set and a test set. Test set identification accuracy is 89 percent for the
photomicrographs, 82 percent for the aerial photographic imagery, and 83 percent for the
satellite imagery. These results indicate that the easily computable textural features probably
have a general applicability for a wide variety of image-classification applications. [4].
The Open Access Series of Imaging Studies is a series of magnetic resonance imaging
data sets that is publicly available for study and analysis. The initial data set consists of a
cross-sectional collection of 416 subjects aged 18 to 96 years. One hundred of the included
subjects older than 60 years have been clinically diagnosed with very mild to moderate
Alzheimer’s disease. The subjects are all right-handed and include both men and women. For
each subject, three or four individual T1-weighted magnetic resonance imaging scans
obtained in single imaging sessions are included. Multiple within-session acquisitions provide
extremely high contrast-to-noise ratio, making the data amenable to a wide range of analytic
approaches including automated computational analysis. Additionally, a reliability data set is

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included containing 20 subjects without dementia imaged on a subsequent visit within 90 days
of their initial session. Automated calculation of whole-brain volume and estimated total
intracranial volume are presented to demonstrate use of the data for measuring differences
associated with normal aging and Alzheimer’s disease. [2].
The classification of the brain MRI is an important task. In this paper, the automatic
approach to the classification of brain tumor into malignant Vs. benign and low grade Vs.
high grade glioma is present. This method employs GLCM technique to extract the texture
features from images and stored as a feature vector. The extracted features were classified
using supervised SVM and KNN algorithm. The proposed system is applied on the 251
images (85 malignant and 166 benign) of clinical database and 80 images (50 low grade
glioma and 30 high grade glioma) of brats 2012 training database. The accuracy of the
proposed system is 96% and 86% for SVM and KNN respectively for clinical database and
85% and 72.50% for SVM and KNN respectively for Brats database. [14].
A novel method for detecting the onset of Alzheimer’s disease (AD) from Magnetic
Resonance Imaging (MRI) scans is presented in the paper. It uses a combination of three
different machine learning algorithms in order to get improved results and is based on a three-
class classification problem. The three classes for classification considered in this study are
normal, very mild AD and mild and moderate AD subjects. The machine learning algorithms
used are: the Extreme Learning Machine (ELM) for classification, with its performance
optimized by a Particle Swarm Optimization (PSO) and a Genetic algorithm (GA) used for
feature selection. A Voxel-Based Morphometry (VBM) approach is used for feature
extraction from the MRI images and GA is used to reduce the high dimensional features
needed for classification. The GA-ELM-PSO classifier yields an average training accuracy of
94.57% and a testing accuracy of 87.23%, averaged across the three classes, over ten random
trials. The results clearly indicate that the proposed approach can differentiate between very

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mild AD and normal cases more accurately, indicating its usefulness in detecting the onset of
AD. [15].

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CHAPTER - 3
GLCM FEATURE EXTRACTION OF MR IMAGES
3.1 TEXTURE FEATURE

An image texture is a set of metrics calculated in image processing designed to quantify
the perceived texture of an image. Image texture gives us information about the spatial
arrangement of color or intensities in an image or selected region of an image. Image textures
can be artificially created or found in natural scenes captured in an image. Image textures are
one way that can be used to help in segmentation or classification of images. For more
accurate segmentation the most useful features are spatial frequency and an average grey
level. To analyze an image texture in computer graphics, there are two ways to approach the
issue: Structured Approach and Statistical Approach.
3.1.1 Texture Feature Extraction

Feature extraction involves reducing the amount of resources required to describe a large
set of data. When performing analysis of complex data one of the major problems stems from
the number of variables involved. Analysis with a large number of variables generally
requires a large amount of memory and computation power, also it may cause
a classification algorithm to over fit to training samples and generalize poorly to new samples.
Feature extraction is a general term for methods of constructing combinations of the variables
to get around these problems while still describing the data with sufficient accuracy. Many
machine learning practitioners believe that properly optimized feature extraction is the key to
effective model construction. [4]

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3.2 CO-OCCURRENCE MATRICES

The co-occurrence matrix captures numerical features of a texture using spatial relations
of similar gray tones. Numerical features computed from the co-occurrence matrix can be
used to represent, compare, and classify textures. [18]
3.3 GRAY LEVEL CO-OCCURRENCE MATRIX

The Gray Level Co-occurrence Matrix (GLCM) and associated texture feature
calculations are image analysis techniques. Given an image composed of pixels each with an
intensity (a specific gray level), the GLCM is a tabulation of how often different combinations
of gray levels co-occur in an image or image section. Texture feature calculations use the
contents of the GLCM to give a measure of the variation in intensity (a.k.a. image texture) at
the pixel of interest. Echo view offers a GLCM Texture Feature operator that produces a
virtual variable which represents a specified texture calculation on a single beam
echogram.[18]

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3.3.1 Algorithm
The virtual variable is created in the following way (using the settings on the GLCM
Texture page of the Variable properties dialog box identified in bold):
1. Quantize the image data. Each sample on the echogram is treated as a single image pixel
and the value of the sample is the intensity of that pixel. These intensities are then further
quantized into a specified number of discrete gray levels as specified under Quantization.
2. Create the GLCM. It will be a square matrix N x N in size where N is the Number of
levels specified under Quantization. The matrix is created as follows:
a. Let s be the sample under consideration for the calculation.
b. Let W be the set of samples surrounding sample s which fall within a window centered
upon sample s of the size specified under Window Size.
c. Considering only the samples in the set W, define each element i,j of the GLCM as the
number of times two samples of intensities i and j occur in specified Spatial relationship
(where i and j are intensities between 0 and Number of levels-1).
The sum of all the elements i, j of the GLCM will be the total number of times the
specified spatial relationship occurs in W.
d. Make the GLCM symmetric:
i. Make a transposed copy of the GLCM
ii. Add this copy to the GLCM itself.
This produces a symmetric matrix in which the relationship i to j is indistinguishable for
the relationship j to i (for any two intensities i and j). As a consequence the sum of all the
elements i, j of the GLCM will now be twice the total number of times the specified
spatial relationship occurs in W (once where the sample with intensity i is the reference
sample and once where the sample with intensity j is the reference sample), and for any
given i, the sum of all the elements i, j with the given i will be the total number of times a
sample of intensity i appears in the specified spatial relationship with another sample.
e. Normalize the GLCM:
i. Divide each element by the sum of all elements.

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The elements of the GLCM may now be considered probabilities of finding the
relationship i, j (or j, i) in W.
3. Calculate the selected Feature. This calculation uses only the values in the GLCM. See:
1) Angular Second Moment
2) Contrast
3) Correlation
4) Variance
5) Inverse Difference Moment
6) Sum Average
7) Sum Variance
8) Sum Entropy
9) Entropy
10) Difference Variance
11) Difference Entropy
12) Information Measure of Correlation I
13) Information Measure of Correlation II
14) Maximal Correlation Coefficient
4. The samples in the resulting virtual variable are replaced by the value of this calculated
feature. These 14 features are called Haralick Texture Features.
3.4 HARALICK TEXTURE FEATURES

Haralick’s texture features were calculated using the kharalick() function of the
cytometry tool box. The basis for these features is the gray-level co-occurrence matrix (G).
This matrix is square with dimension Ng, where Ng is the number of gray levels in the image.
Element [i,j] of the matrix is generated by counting the number of times a pixel with value i is
adjacent to a pixel with value j and then dividing the entire matrix by the total number of such
comparisons made. Each entry is therefore considered to be the probability that a pixel with
value i will be found adjacent to a pixel of value j. [7]

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G= ………………………………………. Eq (3.1)
Haralick then described 14 statistics that can be calculated from the co-occurrence matrix
with the intent of describing the texture of the image:
1. Angular second moment:

Angular second moment (ASM) feature is a measure of the uniformity of local gray scale
distribution. When pixels are very similar, the ASM value will be large. Energy is derived
from the ASM.
Angular second moment = …………………………… Eq (3.2)
Where p(i,j) = (i,j)th entry in a normalized gray-tone spatial-dependence matrix
2. Contrast:
Contrast measures the quantity of local changes in an image. It reflects the sensitivity of
the textures in relation to changes in the intensity. It returns the measure of intensity contrast
between a pixel and its neighbourhood. Contrast is 0 for a constant image. It is the amount of
local variation present in an image. If the amount of local variation is large, the contrast
feature also has consistently higher values comparatively. If the gray scale difference occurs
continually, the texture becomes coarse and the contrast becomes large. The texture becomes
acute if the contrast has a small value.
Contrast = ………. Eq (3.3)
3. Correlation:
This feature measures how correlated a pixel is to its neighbourhood. It shows the linear
dependency of gray level values in the co-occurrence matrix. Feature values range from -1 to
1, these extremes indicating perfect negative and positive correlation respectively.

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Correlation = ………………………………….. Eq (3.4)
Where ux, uy, σx and σy are means and standard deviations of px and py, the partial
probability density functions.
4. Entropy:
Entropy is the randomness or the degree of disorder present in the image. The value of
entropy is the largest when all elements of the co-occurrence matrix are the same and small
when elements are unequal.
Entropy = - ………………………………. Eq (3.5)
5. Inverse difference moment:
It is also called as Homogeneity. Homogeneity measures the similarity of pixels and how
close the distribution of elements in the GLCM is to the diagonal of GLCM. A diagonal gray
level co-occurrence matrix gives homogeneity of 1. It becomes large if local textures only
have minimal changes. As homogeneity increases, the contrast, typically, decreases.
Inverse difference moment = ………………… Eq (3.6)
6. Variance:
Variance is normally used to find how each pixel varies from the neighbouring pixel (or
centre pixel) and is used in classify into different regions.
Variance = ………………………………… Eq (3.7)
7. Sum average:
It is sum of averages of px+y ,the probability of co-occurance matrix coordinates

summing to x+y.
Sum average = ………………………… Eq (3.8)
Px+y(k) =

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i+j = k, k=2,3,4.......2Ng.
8. Sum variance:
Sum variance = ………………………… Eq (3.9)
Where f8 is the sum entropy.
9. Sum entropy:
Sum entropy = - …………………… Eq (3.10)
10. Difference Variance:
It is the variance of px-y, the probability of co-occurance matrix coordinates summing to

x-y.
Difference variance = …………………………………… Eq (3.11)
Px-y(k) = ,
|i-j| = k, k=0,1,2,.......Ng-1.
11. Difference Entropy:
It is the entropy of px-y
Difference Entropy = - …….………………. Eq (3.12)
12. Measure of Correlation I :
....………………………………………… Eq (3.13)
Where HX and HY are entropies of px and py.

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HXY =
HXY1 =
13. Measure of Correlation II:

…………………………………………… Eq (3.14)
Where HXY2 =
14. Max. Correlation Coefficient:

Square root of second largest eigen value of Q.
Where Q(i,j) = ……………………………………. Eq (3.14)

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CHAPTER - 4
AD & NORMAL MR IMAGE CLASSIFICATION
4.1 DIGITAL IMAGE CLASSIFICATION
Digital image classification uses the quantitative spectral information contained in an

image, which is related to the composition or condition of the target surface. Image analysis
can be performed on multispectral as well as hyperspectral imagery. It requires an
understanding of the way materials and objects of interest on the earth’s surface absorb,
reflect, and emit radiation in the visible, near-infrared, and thermal portions of the
electromagnetic spectrum. In order to make use of image analysis results in a GIS
environment, source image should be orthorectified so that the final image analysis product,
whatever its format, can be overlaid with other imagery, terrain data, and other geographic
data layers. Classification results are initially in raster format, but they may be generalized to
polygons with further processing. There are several core principles of image analysis that
pertain specifically to the extraction of information and features from remotely sensed data.
4.1.1 Spectral differentiation
Spectral differentiation is based on the principle that objects of different composition or

condition appear as different colors in a multispectral or hyperspectral image. For example, a
newly planted cornfield has a distinct color when compared to a field of mature plants, and
yet another color when the field has been harvested. Corn has a distinct color as compared to
wheat; healthy plants are a different color than pest-infested or drought-impacted plants. The
use of spectral signature, or color, to distinguish types of ground cover or objects is called
spectral differentiation.

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4.1.2 Radiometric differentiation
Radiometric differentiation is the detection of differences in brightness, which may in

certain cases be used to inform the image analyst as to the nature or condition of the remotely
sensed object.
4.1.3 Spatial differentiation
Spatial differentiation is related to the concept of spatial resolution. We may be able to

analyze the spectral content of a particular pixel or group of pixels in a digital image when
those pixels comprise a single homogeneous material or object. It is also important to
understand the potential for mixing of the spectral signatures of multiple objects into the
recorded spectral values for a single pixel. When designing an image analysis task, it is
important to consider the size of the objects to be discovered or studied compared to the
ground sample distance of the sensor.
The extraction of information from remotely sensed data is frequently accomplished

using statistical pattern recognition; land-use/land-cover classification is one of the most
frequently used analysis methods (Jensen, 2005). Land cover refers to the physical material
present on the earth’s surface; land use refers to the type of development and activities people
undertake in a particular location. The designation of “woodland” for a tree-covered area is a
land cover classification; the same woodland might be designated as “recreation area” in a
land use classification.
While certain aspects of digital image classification are completely automated, a human
image analyst must provide significant input. There are two basic approaches to classification,
supervised and unsupervised, and the type and amount of human interaction differs depending
on the approach chosen.

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4.1.4 Supervised classification
Supervised classification requires the image analyst to choose an appropriate

classification scheme, and then identifies training sites in the imagery that best represent each
class. A simple land cover classification scheme might consist of a small number of classes,
such as urban, water, wetlands, forest, grass/crops. Individual sites that fall into a single class
may have slightly different spectral characteristics; for example, the spectral signature of a
water body will depend on the amount of suspended sediment or plant material in the water.
Urban land cover signatures will vary based on the type of materials used; asphalt has a very
different spectral signature from concrete, wood, or glass.
The image analyst must select a sufficient number of training sites in each class to
represent the variation present within each class in the image. The classification algorithm
then uses spectral characteristics of the training sites to classify the remainder of the image.
Training sites developed in one scene may or may not be transferrable to an entire study area.
If ground conditions, lighting conditions, or atmospheric effects change from scene to
another, then training sites must be developed independently for each scene. Furthermore,
training sites may not be transferrable across time; in addition to the conditions noted above
that change over time as well as space, real changes in the land cover occurring at a training
site location over time will cause incorrect classification results in the second image. Accurate
supervised classification results depend entirely on the analyst’s ability to collect a sufficient
number of training sites and to recognize when training sites can or cannot be transferred from
one image to another.
4.1.5 Unsupervised classification
Unsupervised classification requires less input from the analyst before processing. The
classification algorithm searches and analyses the image, grouping pixels into clusters which
it deemed to be uniquely representative of the image content. After classification, the image

images
analyst must determine if these arbitrary classes have meaning in the context of the end-user
application. A significant amount of time may be spent trying to determine the physical
meaning of a class identified by the unsupervised algorithm. In addition, experimentation is
required to determine the optimal number of unique classes used for initialization of the
algorithm. Furthermore, there is no basis to believe that the classes discovered in one image
will be the same classes discovered in a second image. Time spent trying to optimize and
interpret the unsupervised results may far exceed the time an analyst would have spent
selecting training sites for supervised classification. Finally, because it is impossible to ensure
consistency in class identification from one image to the next, unsupervised classification is
not useful for change detection.
Classification schemes may be comprised of hard, discrete categories; in other words,

each pixel is assigned to one, and only one, class. Fuzzy classification schemes allow a
proportional assignment of multiple classes to pixels. The entire image scene may be
processed pixel-by-pixel, or the image may be decomposed into homogeneous image patches
for object-oriented classification. Measuring the accuracy of classification requires either
comparison with ground truth or comparison with an independent result. Errors of omission
are committed when an object is left out of its true class (a tree stand which is not classified as
forest, for example); errors of commission are committed when an object that does not belong
in a class is incorrectly included (in the example above, the tree stand is incorrectly classified
as a wetland).
TP : Defined as AD correctly classified as AD
TN : Defined as Normal correctly classified as Normal
FP : Defined as Normal incorrectly classified as AD
FN : Defined as AD incorrectly classified as Normal
Accuracy = …………………….. Eq (4.1)

images
Sensitivity = …………………………………….. Eq (4.2)
Specificity = ……………………………………. Eq (4.3)
4.2 K-NN CLASSIFICATION
It is the first algorithm we shall investigate which is most often used for classification,
although it can also be used for estimation and prediction. K-Nearest neighbor is an example
of instance-based learning, in which the training data set is stored, so that a classification for a
new unclassified record may be found simply by comparing it to the most similar records in
the training set. This method that has been used in many applications in areas such as data
mining, statistical pattern recognition, image processing. Successful applications include
recognition of handwriting, satellite image and EKG pattern. [19] [14]
The easiest way of doing this is to use K-nearest Neighbor:
 K-nearest neighbor algorithm (KNN) is part of supervised learning that has been used in
many applications in the field of data mining, statistical pattern recognition and many
others.
 KNN is a method for classifying objects based on closest training examples in the feature
space.
 An object is classified by a majority vote of its neighbors. K is always a positive integer.
The neighbors are taken from a set of objects for which the correct classification is
known.
 It is usual to use the Euclidean distance, though other distance measures such as the
Manhattean distance could in principle be used instead.

images
The algorithm on how to compute the K-nearest neighbors is as follows
1. Determine the parameter K = number of nearest neighbors beforehand. This value is all
up to us.
2. Calculate the distance between the query-instance and all the training samples. We can
use any distance algorithm.
Distance = Euclidian distance = …………………………… Eq (4.4)
3. Sort the distances for all the training samples and determine the nearest neighbor based
on the K-th minimum distance.
4. Since this is supervised learning, get all the Categories of your training data for the sorted
value which fall under K.
5. Use the majority of nearest neighbors as the prediction value.
4.2.1 How to choose the value of K

Choosing the number of nearest neighbors i.e. determining the value of k plays a
significant role in determining the efficacy of the model. Thus, selection of k will determine
how well the data can be utilized to generalize the results of the kNN algorithm. A large k
value has benefits which include reducing the variance due to the noisy data; the side effect
being developing a bias due to which the learner tends to ignore the smaller patterns which
may have useful insights. [22]
4.3 KNN PROS. AND CONS

Pros: The algorithm is highly unbiased in nature and makes no prior assumption of the
underlying data. Being simple and effective in nature, it is easy to implement and has gained
good popularity. [22]
Cons: Indeed it is simple but K-NN algorithm has drawn a lot of flake for being extremely
simple! If we take a deeper look, this doesn’t create a model since there’s no abstraction
process involved. Yes, the training process is really fast as the data is stored verbatim (hence
lazy learner) but the prediction time is pretty high with useful insights missing at times.

images
Therefore, building this algorithm requires time to be invested in data preparation (especially
treating the missing data and categorical features) to obtain a robust model.

images
CHAPTER 5
RESULTS and DISCUSSION
This project gives the analysis of GLCM texture feature extraction and classification
algorithm and it is tested on 60 MRI pictures of which 30 tests are observed to be Normal and
30 are AD. The GLCM texture features are extracted from the Normal and AD images.
In this project, we utilized brain MR images of 133 Normal people and 30 AD patients.
Entire brain T1-weighted 3D MPRAGE- Magnetization-prepared Rapid Acquisition Gradient
Echo data set were acquired using Siemens 1.5T Vision scanner in a single imaging session.
In this project utilized axial view for testing the proposed method. The training set
consists of 60 samples and test sample is classified based on the trained data.
5.1 GLCM FEATURE’S MEAN AND STANDARD DEVIATION
Table 4.1 GLCM Features Mean and SD
Sl.No Feature Normal AD

(Mean ± (Mean ± SD)
SD)
1 Angular Second Moment (0.34±0.03) (0.36 ± 0.03)
2 Contrast (0.12±0.02) (0.12 ± 0.02)
3 Correlation (0.96±0.01) (0.95 ± 0.01)
4 Difference Entropy (0.35±0.04) (4.81 ± 0.82)
5 Difference Variance (0.10±0.01) (0.94 ± 0.01)
6 Entropy (2.23±0.17) (3.73 ± 0.27)

images
7 Information Measure of (-0.71±0.03) (19.37 ± 3.27)

Correlation I
8 Information Measure of (0.95±0.01) (1.42 ± 0.11)
Correlation II
9 Inverse Difference Moment (0.94±0.01) (2.18 ± 0.18)
10 Maximal Correlation Coefficient (0.17±0.03) (0.11 ± 0.02)
11 Sum Average (3.97±0.37) (0.37 ± 0.04)
12 Sum Entropy (1.46±0.10) (-0.68 ± 0.02)
13 Sum Variance (21.84±4.61) (0.94 ± 0.01)
14 Variance (5.43±1.15) (0.15 ± 0.02)
5.2 GLCM FEATURE’S OF NORMAL AND AD
The plots shown in fig 5.1 to fig 5.14 are the 14 Haralick texture features calculated using
GLC matrix extracted from MR images. The plots are the comparison of AD and NORMAL
features values.
Angular Second Moment

0.5
0.4
0.3
0.2
0.1
0
0 5 10 15 20 25 30 35
NORMAL AD
Fig 5.1 Angular Second Moment of AD vs NORMAL

images
Contrast
0.2
0.15
0.1
0.05
0
0 5 10 15 20 25 30 35
NORMAL AD
Fig 5.2 Contrast of AD vs NORMAL
Correlation
0.98
0.97
0.96
0.95
0.94
0.93
0 5 10 15 20 25 30 35
NORMAL AD
Fig 5.3 Correlation of AD vs NORMAL

images
Variance
10
8
6
4
2
0
0 5 10 15 20 25 30 35
NORMAL AD
Fig 5.4 Variance of AD vs NORMAL
Inverse Difference Moment

0.98
0.96
0.94
0.92
0 5 10 15 20 25 30 35
NORMAL AD
Fig 5.5 Inverse Difference of AD vs NORMAL

images
Sum Average
5
4
3
2
1
0
0 5 10 15 20 25 30 35
NORMAL AD
Fig 5.6 Sum Average of AD vs NORMAL
Sum Variance
40
30
20
10
0
0 5 10 15 20 25 30 35
NORMAL AD
Fig 5.7 Sum Variance of AD vs NORMAL

images
Sum Entropy
2
1.5
0.5
0
0 5 10 15 20 25 30 35
NORMAL AD
Fig 5.8 Sum Entropy of AD vs NORMAL
Entropy
3
2.5
1.5
0.5
0
0 5 10 15 20 25 30 35
NORMAL AD
Fig 5.9 Entropy of AD vs NORMAL

images
Difference Variance
0.15
0.1
0.05
0
0 5 10 15 20 25 30 35
NORMAL AD
Fig 5.10 Difference Variance of AD vs NORMAL
Difference Entropy
0.5
0.4
0.3
0.2
0.1
0
0 5 10 15 20 25 30 35
NORMAL AD
Fig 5.11 Difference Entropy of AD vs NORMAL

images
Information Measure of Correlation I

-0.6
0 5 10 15 20 25 30 35
-0.65
-0.7
-0.75
-0.8
NORMAL AD
Fig 5.12 Information Measure of Correlation I of AD vs NORMAL
Information Measure of Correlation II

0.98
0.96
0.94
0.92
0.9
0 5 10 15 20 25 30 35
NORMAL AD
Fig 5.13 Information Measure of Correlation II of AD vs NORMAL

images
Maximal Correlation Coefficient

0.3
0.25
0.2
0.15
0.1
0.05
0
0 5 10 15 20 25 30 35
NORMAL AD
Fig 5.14 Maximal Correlation Coefficient AD vs NORMAL
5.3 PERFORMANCE OF K-NN CLASSIFIER
TP=23; TN=20; FP-7; FN=10
Table 5.2 K-NN classification results

Average Average Average
Accuracy Sensitivity Specificity
74.73 % 72.09 % 75.72 %
5.4 MATLAB OUTPUT

images
CHAPTER - 6
CONCLUSION
Alzheimer is a complex neuro-degenerative disorder which results in the atrophy of brain

structures. Ventricle enlargement is a useful structural biomarker for the diagnosis of AD.
MRI is a useful non-invasive way of brain imaging to monitor and diagnose AD.
Characterizing the variations of ventricles for the normal and AD is a challenging task due to
its complex shape and size. The images for this study are obtained from Open Access Series
of Imaging Studies public domain database. This database contains images of subjects
covering full adult life span, older subjects without dementia and individuals before middle
age. GLCM feature extraction is used to extract the texture features of the MR images and
those features are used in K-NN classifier to characterize the AD and NORMAL. The
Euclidean distance values are statistically identified and are used to train and test the k-NN
classifier. The proposed system is applied on the 60 images (30 Normal and 30 AD) of
OASIS database. The accuracy, Sensitivity and Specificity of the proposed system is
respectively 74.73%, 72.09 % and 75.72 %.

images
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TEXTURE FEATURE EXTRACTION AND CLASSIFICATION

OF NORMAL AND ALZHEIMER SUBJECTS USING MR

V. LAKSHMI SRUJANA A.RAJESH KUMAR

Under the Esteemed Guidance of

DEPARTMENT OF ELECTRONICS AND COMMUNICATION ENGINEERING

GMR Nagar, Rajam – 532 127,

CLASSIFICATION OF NORMAL AND ALZHEIMER SUBJECTS USING MR

IMAGES submitted by V. LAKSHMI SRUJANA, BALAJI MOHANTY, A. RAJESH

degree of Bachelor of Technology in Electronics and Communication Engineering of

Signature of Supervisor Signature of HOD

Dr. T. Prabhakar Dr. M. V. Nageswara Rao

We would like to take this opportunity to thank our beloved Principal

V. Lakshmi Srujana (14341A04H3)

Balaji Mohanty (15345A0425)

A. Rajesh Kumar (15345A0426)

Alzheimer's Disease (AD) is a common form of dementia and logically a lethal

TABLE NO TITLE PAGE NO

5.1 GLCM Features Mean and SD 40

5.2 K-NN classification results 48

FIGURE NO TITLE PAGE NO

1.2 Damaging of Neurons 6

1.3 MR imaging equipment 10

1.4 Flow chart 12

1.5 MRI image of AD 14

1.6 MRI image of NORMAL 14

5.1 Angular Second Moment of AD vs NORMAL 41

5.2 Contrast of AD vs NORMAL 42

5.3 Correlation of AD vs NORMAL 42

5.4 Variance of AD vs NORMAL 43

5.5 Inverse Difference of AD vs NORMAL 43

5.6 Sum Average of AD vs NORMAL 44

5.7 Sum Variance of AD vs NORMAL 44

5.8 Sum Entropy of AD vs NORMAL 45

5.9 Entropy of AD vs NORMAL 45

5.10 Difference Variance of AD vs NORMAL 46

5.11 Difference Entropy of AD vs NORMAL 46

5.12 Information Measure of Correlation I of AD vs NORMAL 47

5.13 Information Measure of Correlation II of AD vs NORMAL 47

5.14 Maximal Correlation Coefficient AD vs NORMAL 48

1.1 ALZHEIMER’S DISEASE

Department of ECE, GMRIT 1

Department of ECE, GMRIT 2

1.2 STATISTICS OF ALZHEIMER’S

Department of ECE, GMRIT 3

1.3 HOW ALZHEIMER’S AFFECTS THE BRAIN

Department of ECE, GMRIT 4

Department of ECE, GMRIT 5

Fig 1.2 Damaging of Neurons

1.4 STAGES OF THE DISEASE

Department of ECE, GMRIT 6

1.4.1 Early-stage Alzheimer’s

1.4.2 Middle-stage Alzheimer’s

1.4.3 Late-stage Alzheimer’s

1.5 DETECTION OF ALZHEIMER’S

Department of ECE, GMRIT 7

1.6 BRAIN IMAGING OR NEUROIMAGING

1.7 MAGNETIC RESONANCE IMAGING

Department of ECE, GMRIT 8

Department of ECE, GMRIT 9

1.7.1 Working of MRI

Fig 1.3 MR Imaging Equipment.

Department of ECE, GMRIT 10

1.8 WORK FLOW

File type: .GIF,