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Spacial Brain Tumour
Spacial Brain Tumour
comprises of many different types of imaging methods likes CT scans, X-Ray and
MRI. These techniques allow us to identify even the smallest abnormalities in the
human body. The primary goal of medical imaging is to extract meaningful and
accurate information from these images with the least error possible. Out of the
various types of medical imaging processes available to us, MRI is the most
reliable and safe. Brain tumors are the most common malignant neurologic tumors
with the highest mortality and disability rate. Because of the delicate structure of
the brain, the clinical use of several commonly used biopsy diagnosis is limited for
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CHAPTER 1
INTRODUCTION
1.1 Brain
The brain is an organ that serves as the center of the nervous system in all
vertebrate and most invertebrate animals. The brain is located in the head, usually
close to the sensory organs for senses such as vision. The brain is the most
complex organ in a vertebrate's body. In a human, the cerebral cortex contains
approximately 10–20 billion neurons, and the estimated number of neurons in the
cerebellum is 55–70 billion. Each neuron is connected by synapses to several
thousand other neurons. These neurons communicate with one another by means of
long protoplasmic fibers called axons, which carry trains of signal pulses called
action potentials to distant parts of the brain or body targeting specific recipient
cells.
Physiologically, the function of the brain is to exert centralized control over the
other organs of the body. The brain acts on the rest of the body both by generating
patterns of muscle activity and by driving the secretion of chemicals called
hormones. This centralized control allows rapid and coordinated responses to
changes in the environment. Some basic types of responsiveness such as reflexes
can be mediated by the spinal cord or peripheral ganglia, but sophisticated
purposeful control of behavior based on complex sensory input requires the
information integrating capabilities of a centralized brain.
A brain tumor occurs when abnormal cells form within the brain. There are two
main types of tumors: malignant or cancerous tumors and benign tumors.
Cancerous tumors can be divided into primary tumors, which start within the brain,
and secondary tumors, which have spread from elsewhere, known as brain
metastasis tumors. All types of brain tumors may produce symptoms that vary
depending on the part of the brain involved. These symptoms may include
headaches, seizures, problems with vision, vomiting and mental changes. The
headache is classically worse in the morning and goes away with vomiting. Other
symptoms may include difficulty walking, speaking or with sensations. As the
disease progresses, unconsciousness may occur.
1.2 MRI
MRI was originally called NMRI (nuclear magnetic resonance imaging) and is
a form of NMR, though the use of 'nuclear' in the acronym was dropped to avoid
negative associations with the word. Certain atomic nuclei are able to absorb and
emit radio frequency energy when placed in an external magnetic field. In clinical
and research MRI, hydrogen atoms are most often used to generate a detectable
radio-frequency signal that is received by antennas in close proximity to the
anatomy being examined. Hydrogen atoms are naturally abundant in people and
other biological organisms, particularly in water and fat. For this reason, most MRI
scans essentially map the location of water and fat in the body. Pulses of radio
waves excite the nuclear spin energy transition, and magnetic field gradients
localize the signal in space. By varying the parameters of the pulse sequence,
different contrasts may be generated between tissues based on the relaxation
properties of the hydrogen atoms therein.
Although many efforts have been made to independently improve each step in
radiomics analyses, a complete framework that can systematically address the
challenges in radiomics is still lacking. In recent years, using sparse representation
as the driving force for addressing image processing, data analysis and pattern
recognition problems has received growing research attention. In these
applications, sparse representation has the following advantages. First, sparse
representation normally exploits adaptive learning dictionaries rather than the
traditional analytically designed dictionaries with fixed basis (e.g., discrete-cosine-
transform, wavelet) to represent images, and it therefore provides the ability to
extract or represent various small textures and details, especially for singular lines
and surfaces. Furthermore, these singular features in images usually play decisive
roles in image classification. Second, sparse representation considers the natural
signal as a linear combination of a few atoms from an over complete dictionary.
Therefore, based on effective sparse coding algorithms, sparse representation can
accurately and efficiently select the most essential features used to express data
and delete redundant information.
CHAPTER 2
LITERATURE REVIEW
In the past decade, the field of medical image analysis has grown
exponentially, with an increased number of pattern recognition tools and an
increase in data set sizes. These advances have facilitated the development of
processes for high-throughput extraction of quantitative features that result in the
conversion of images into mineable data and the subsequent analysis of these data
for decision support; this practice is termed radiomics. This is in contrast to the
traditional practice of treating medical images as pictures intended solely for visual
interpretation. Radiomic data contain first-, second-, and higher-order statistics.
These data are combined with other patient data and are mined with sophisticated
bioinformatics tools to develop models that may potentially improve diagnostic,
prognostic, and predictive accuracy. Because radiomics analyses are intended to be
conducted with standard of care images, it is conceivable that conversion of digital
images to mineable data will eventually become routine practice. This report
describes the process of radiomics, its challenges, and its potential power to
facilitate better clinical decision making, particularly in the care of patients with
cancer.
2.6 J. Yu, Z. Shi, Y. Lian, Z. Li, Y. Gao, Y. Wang, L. Chen, and Y. Mao,
“Noninvasive IDH1 mutation estimation based on a quantitative radiomics
approach for grade II glioma,” Eur Radiol, pp. 1-14, 2016.
The aim of this study was to investigate the potential of texture analysis,
applied to dynamic contrast-enhanced MRI (DCE-MRI), to predict the clinical and
pathological response to neoadjuvant chemotherapy (NAC) in patients with locally
advanced breast cancer (LABC) before NAC is started. Fifty-eight patients with
LABC were classified on the basis of their clinical response according to the
Response Evaluation Criteria in Solid Tumors (RECIST) guidelines after four
cycles of NAC, and according to their pathological response after surgery. T1 -
weighted DCE-MRI with a temporal resolution of 1 min was acquired on a 3-T
Siemens Trio scanner using a dedicated four-channel breast coil before the onset of
treatment. Each lesion was segmented semi-automatically using the 2-min post-
contrast subtracted image. Sixteen texture features were obtained at each non-
subtracted post-contrast time point using a gray level co-occurrence matrix.
Appropriate statistical analyses were performed and false discovery rate-based q
values were reported to correct for multiple comparisons. Statistically significant
results were found at 1-3 min post-contrast for various texture features for the
prediction of both the clinical and pathological response. Our results suggest that
texture analysis could provide clinicians with additional information to increase the
accuracy of prediction of an individual response before NAC is started.
SYSTEM ANALYSIS
In the testing stage, the training feature extraction dictionary, the selected
feature index, the training weights and the selected features of the training samples
itself are used to identify testing images. More technical details on the analysis
components are given in the following sections. Segmentation is a critical step in
radiomics because the segmented volumes are directly converted into quantitative
high-throughput features. Various previously reported deep learning-based
segmentation methods have achieved state-of-the-art segmentation performance. In
this paper, a convolutional neural network (SVM)-based method that we proposed
in our previous work is utilized to segment MRI images. As tumor segmentation is
not a major concern in this work, we present the network structure and
implementation process of our SVM-based classification.
Feature Feature
Input Image Preprocessing
Extraction Selection
Output SVM
Image Classification
This Flow chart consists of input data which explores the data
and the preprocessing step is done. Feature extraction and feature
selection process is done.
Fig 3.2 Flow Chart
3.4 Pre-Processing
A global hyper plane is sought by the SVM in order to separate both the
classes of examples in training set and avoid over fitting. This phenomenon of
SVM is more superior in comparison to other machine learning techniques
which are based on artificial intelligence. The mapping of the input-output
functions from a set of labeled training data set is generated by the supervised
learning method called SVM.
In a high dimensional feature space, SVM uses a hypothesis space of linear
functions which are trained with a learning technique from optimization theory that
employs a learning bias derived from statistical learning theory. In Support Vector
machines, the classifier is created using a hyper-linear separating plane. It provides
the ideal solution for problems which are not linearly separated in the input space.
The original input space is non-linearly transformed into a high dimensional
feature space, where an optimal separating hyper plane is found and the problem is
solved. A maximal margin classifier with respect to the training data is obtained
when the separating planes are optimal.
3.5.1 Applications
SOFTWARE DESCRIPTION
The name MATLAB stands for Matrix Laboratory. MATLAB was written
originally to provide easy access to matrix software developed by the c projects.
MATLAB is a high-performance language for technical computing. It integrates
computation, visualization, and programming in an easy-to-use environment where
problems and solutions are expressed in familiar mathematical notation.
Starting MATLAB
When start MATLAB, a special window called the MATLAB desktop appears.The
desktop is a window that contains other windows. The major tools within or
accessible from the desktop are:
Command window
Command history
The workspace
The current directory
The help browser
The start button
Command Window
Use the command window to enter variables and run functions and M-files.
Command History
Lines you enter in the Command Window are logged in the Command
History Window. In the Command history, you can view previously used
functions, and copy and execute selected lines. To save the input and output from a
MATLAB session to a file, use the function.
Help Browser
Use the Help browser to search and view documentation for all your Math
Works products. The Help browser is a Web browser integrated into the MATLAB
desktop that displays HTML documents.
Current Directory
MATLAB file operations use the current directory and the search path as
reference points. Any file you want to run must either be in the current directory or
on the search path.
Workspace
QUITTING MATLAB
1) To end your MATLAB session, type quit in the Command Window, or
select File →Exit MATLAB in the desktop main menu All the commands were
executed in the Command Window.The problem is that the commands entered in
the Command Window cannot be saved and executed again for several times.
Therefore, a different way of executing repeatedly commands with MATLAB is:
If needed, corrections or changes can be made to the commands in the file. The
files that are used for this purpose are called script files or scripts for short.This
section covers the following topics:
M-File Scripts
M-File Functions
M-file Scripts
M-file Functions
1. Indexed images
2. Intensity image
3. Binary images
4. RGB images
5. 8-bit images
All optional parameters, for other file formats can be found in the Matlab
documentation. A very useful function exists in Image Processing Toolbox.
Imshow is responsible for displaying an image. It works with black and white,
grayscale and color pictures. Simply, matrix that includes a graphic file or just a
filename can be treated as a parameter for this procedure. Alternatively, the image
can be displayed with its colormap. Map should be given after the comma in the
brackets, along the filename. The shown picture has to be in the current directory
or specified by the path to the file.
Other Functions
• Color Type – indicates type of the image, either ‘TrueColor’ for RGB image,
‘grayscale’ for grayscale image or ‘indexed’ for an indexed image.
Image Processing Toolbox function Impixel may become helpful when pixel color
values (red, green and blue) are required. For the most up-to-date information
about system requirements, see the system requirements page, available in the
products area at the Math Works Web site (www.mathworks.com).
CHAPTER 5
7.1 Conclusion