A Ph.D.

Synopsis on

Recognition, Analysis and Interpretation of
Certain Brain MRI Images



Submitted by: Prakash H. Unki
Assistant Professor
Department of Computer Science
B.L.D.E.As Dr. P.G.H College of Engg. and Tech.,Bijapur



Under the Guidance : Dr. Basavaraj S. Anami
Professor and Head
Department of Computer Science
Basaveshwar Engineering College, Bagalkot



Research Centre
Department of Computer Science
Basaveshwar Engineering College, Bagalkot

Visvesvaraya Technological University (VTU)
Belgaum, Karnataka
Recognition, Analysis and Interpretation of Certain Brain MRI
Images

Digital Image Processing (DIP) refers to processing of digitized images through

computers and finds varieties of applications in the most diverse areas of business,
science and technology. Any typical image processing application comprises of
extraction of important features of a given image, using which later description,
interpretation, or understanding of an image is provided. DIP techniques are used today
in solving varieties of problems related to medical, office and industrial automation,
remote sensing, science, criminology, image transmission and storage, astronomy,
space, meteorology, information technology, entertainment, consumer electronics,
printing, graphic arts and defense. Digital images are captured through imaging devices
and cover almost the entire frequency spectrum, ranging from gamma to radio waves.
The images generated by these devices include ultrasound, MRI, electron microscopy
etc. to which humans, many a times, are not accustomed to. Medical applications of
DIP include: ECG, EEG, EMG analysis; cytological, histological and stereological
applications; automated radiology and pathology; X-ray image analysis; mass
screening of medical images such as chromosome slides for detection of various
diseases, mammograms, cancer smears; CAT, MRI, PET, SPECT, USG, and other
tomographic images; routine screening of plant samples; 3-D reconstruction and
analysis, et cetera.

In the recent years, the most important diagnostic tool in medical applications is
medical imaging. This is a group of non-invasive techniques, pioneered by Wilhelm
Roentgen, for visual probing of the human body. The impressive range of sophisticated
and versatile medical imaging devices, with popular acronyms such as
CT/DXA/MRI/PET/SPECT/USG, accentuates the need for a shift from manually
assessed images towards efficient, accurate and reproducible computer-based methods.
These methods aim at assisting medical experts in their decisions by providing them
with quantitative measures inferred from the above-mentioned imaging modalities.
These are the most helpful modalities in the study of brain and its related diseases.

The brain is the most fascinating and least understood organ in the human body. For
centuries, scientists and philosophers have pondered the relationship between behavior,
emotion, memory, thought, consciousness, and the physical body. The study of the
human brain has entered a new era, offering new insights into neurology, psychiatry,
psychology and perhaps even contributing to the philosophical debate about the
relationship between mind and brain. There are various types of brain diseases like
Cerebrovascular Diseases- (stroke or brain attack) which includes Multiple embolic
infarction, Acute stroke, Subacute stroke, Chronic subdural hematoma, Cavernous
angioma, Arteriovenous malformation, Vascular dementia, Hypertensive
encephalopathy, Fatal stroke, Cerebral hemorrhage, Neoplastic Disease- (brain tumor)
which includes Glioma, Metastatic bronchogenic carcinoma, Meningioma, Sarcoma,
Degenerative Disease which includes Mild Alzheimer's disease, Alzheimer's disease,
Huntington's disease, Motor neuron disease, Cerebral calcinosis, Pick's disease,
Inflammatory or Infectious Disease which includes Multiple sclerosis. There are
several types of non-invasive brain imaging techniques such as electroencephalography
(EEG), magneto encephalography (MEG), anatomical magnetic resonance imaging
(MRI), functional MRI (fMRI), positron emission tomography (PET) and others.

Magnetic resonance imaging (MRI) is a very versatile imaging modality which is used
to acquire several different types of images. Some examples include anatomical
images, images showing local brain activation and images depicting different types of
pathologies. It is based on the phenomenon of nuclear magnetic resonance (NMR). It
produces images of the human body with excellent soft tissue contrast, allowing
neurologists to distinguish between grey and white matter, study brain function and
various brain defects such as tumors, stroke etc. Since MRI involves no ionizing
radiation, the subjects are at minimized risks. Radio waves are used in MRI and
produce pictures in any plane. This technique places a patient in a powerful magnetic
medium, and passes radio waves through the body in short pulses. Each pulse causes a
responding pulse of radio waves to be emitted by the patients tissues. The location
from which these signal originate and their strengths are determined by a computer,
which generates a two-dimensional picture of a section of the patients body.

The literature survey carried out related to technology impact in the study of brain
related diseases revealed that a fair amount of research has gone into this area. Analysis
and diagnosis of various brain related diseases like brain stroke using neural
network[1], atherosclerotic disease in human carotid arteries[2], basal ganglia for
accurate detection of human spongiform encephalopathy[3], brain tumors[4],
Alzheimers disease(AD)[5], brain infarct, infection, hamartoma, and tumor[6],
neurosarcoidosis(NS)[7], cystic or necrotic brain tumors[8], different pathologic
situations[9], nodular enhancement of the oculomotor nerve [10],
Hemangioblastoma(Tumors) of the conus medullaris[11], MS lesions[12][13],
Parkinsons disease[14], pathological/normal brain[15], HIV/AIDS[16] are being cited
in literature on processing of Brain MRI images.

Brain MRI segmentation (for different applications) by applying different techniques
such as nonparametric density estimation[17], Topology-preserving, anatomy-driven
segmentation (TOADS)[18], atlas-based whole brain segmentation method with an
intensity renormalization procedure[19], a knowledge-driven algorithm[20],
tractography techniques[21], fuzzy logic[22][23][24], self-organizing map(SOM)
neural network[25], k-means objective function combined genetic algorithm[26],
Hidden Markov Model (HMM) [27], analysis of brain MRI data using registration-
based on deformation tensor morphometry [28], learning-based method[29], active
markers[30] are being cited in the literature.

We have come across works like detection of brain activation using conditional
random field (CRF)[31], age-related changes brain white matter(WM)[32], analyzing
regions of neuronal activation[33], brain development and fetal brain pathology[34],
effect of caffeine on verbal working memory task[35], neural correlates of retrieval
success for music memory[36] and early functional brain development with data
collected from children during natural sleep[37].

Extraction of texture properties of the brains white matter (WM)[38], spherical
wavelet transformation to extract shape features of cortical surfaces[39],single cell
detection[40], Bayesian decision theory applied to brain tissue classification[41],
computation and visualization of volumetric white matter connectivity in diffusion
tensor(DT) MRI[42], topological visualization of human brain diffusion MRI[43],
labeling of structures in 3D brain MRI data sets using expert anatomical knowledge
that is coded in fuzzy sets and fuzzy rules[44] are found in literature.

This being the state-of-the-art in the area of brain Magnetic Resonance Imaging used to
identify diseases, effect of external stimulus on brain functions, segmentation of
specific section in brain to study brain activities and registration of brain images, we
are motivated to investigate the MRI imaging in interpretation, analysis of brain
diseases commonly found in North Karnataka and South Maharasthra regions. In these
regions, commonly found brain diseases are tuberculoma, neurocysticercosis,
infarction, hematoma, tumor and multiple sclerosis. Statistics shows that everyday one
or two patients are diagnosed with these diseases. Not much work is cited in the
literature, to the best of our knowledge, connected to these diseases. Scope exists for
identification, interpretation and analysis of these important brain diseases. Even
though some work is done for identification of tumors, but classification and
quantification of tumors based on size, location, orientation etc. is considered to be a
difficult and challenging task.

The study of these brain disorders requires accurate tissue segmentation from MRI
images of the brain. Manual delineation of the three brain tissues, white matter(WM),
gray matter (GM), and cerebrospinal fluid(CSF), in MRI images by a human expert is
too time-consuming for studies involving larger databases. Here, the doctors can avail
the technology support. In addition, the lack of clearly defined edges induces large
intra and inter observer variability, which deteriorates the significance of the analysis
of the resulting segmentation, thus calling for efficient automatic segmentation
methods. Manual interpretation of these diseases is also less accurate, varies from
doctor to doctor and their expertise. Looking at all these facts, it is evident that there is
a dire need for investigation for technological support in this area and hence following
are the broad objectives of the proposed work.

The methodology being devised would certainly assist medical experts in their
decisions in terms of quantitative measures resulting in automated analysis and
interpretation of brain MRI images. Interpretation pertains not only partitioning of an
image into object and background, but also to provide descriptions of functional
properties and relations inferred from MRI images. Providing such high-level
descriptions, also called image understanding, would help the doctors in their
diagnosis. Constructing a complete system that infers functional indices from brain
MRI images without manual interaction and preferably within a reasonable timeframe
is also an objective of this work. Quantitative analysis of the developed methods
would be taken up. Surprisingly, this seems not always to be the case in the medical
image analysis literature. Existing methods present qualitative results in a few subjects
and completely lack quantitative validation, which are of very little use to the clinical
practitioners. This would remain the ultimate goal of the proposed work.

Furthermore, the work involves collection of brain MRI images from different
hospitals, radiology centers, both normal and abnormal. A web database for researchers
will be created from the images so collected, as such databases are a few in numbers at
present. The tissue segmentation process is carried out to separate WM, GM, and CSF
using different techniques. The different shape features(location, area, orientation etc.),
texture features (GLRM(Grey level Run Length Matrix), GLCM(Grey level
Cooccurrence Matrix), texture anisotropy, laminarity etc.) and histogram features will
be extracted and a database is going to be created. These features will be used to
interpret, analyze, classify and recognize the above mentioned brain diseases. It will
help the radiologists, physicians and surgeons in their decision process by providing
accurate data within reasonable timeframe. The work can be extended to analyze the
other brain diseases.

The work on medical image analysis is typically highly interdisciplinary. It will draw
on results from multivariate statistics, numerical analysis, linear algebra, wavelet
theory, medicine, MR physics, computational geometry, computer science, computer
graphics, etc. In this work, the technologies like Artificial Neural Network(ANN),
Fuzzy Logic, Genetic Algorithm, Hidden Markov Model(HMM), Support Vector
Machine(SVM), Wavelets, Level sets will be explored to interpret, analyze, and
recognize the various brain diseases.






To summarize, the proposed work aims at recognition, interpretation, and analysis of
MRI brain images concerned with diseases such as tuberculoma, neurocysticercosis,
infarction, hematoma, tumor and multiple sclerosis. It aims to provide fast, automatic
methods and to introduce more robustness and regularity for interpretation of these
diseases.

Acknowledgement
The authors wish to thank Dr. Prashant B. Katakol, Neurosurgeon, Sanjivini
Diagnostics, Bijapur, Dr. Ramesh V. Manakare, Radiologist, Dr. Bhagavati,
Neurophysician, BLDEAs B.M. Patil medical college and research centre, Bijapur,
Dr. M.S. Kotennavar, Al-ameen medical college, Bijapur, Dr. Ashutosh Pavale,
Radiologist, Keludi hospital and research centre, Bagalkot and Dr. Avinash Vernekar,
Radiologist, Sushruth CT and MRI Centre, Solapur for their help and valuable
suggestions in formulating the problem.


Signature of the Candidate Signature of the Guide



Prakash H. Unki, Dr. Basavaraj S. Anami,
Asst. Prof., Dept. of CSE, Prof. & Head, Dept. of CSE,
BLDEAs Dr. P.G.H College of Engg.and Tech., Basaveshwar Engineering
College
Bijapur-586103 BAGALKOT 587 102




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