Introduction to Medical Image Processing

Biomedical Image Processing
Introduction to Medical Image Processing
Nilesh Bhaskarrao Bahadure
Ph.D., M.E., B.E.
Sanjay Ghodawat University
Atigre, Kolhapur, Maharashtra
nbahadure@gmail.com
https://www.sites.google.com/site/nileshbbahadure/home
February 11, 2021
Nilesh Bhaskarrao Bahadure Ph.D., M.E., B.E. (Sanjay Ghodawat University)
Biomedical Image Processing February 11, 2021 1 / 44

Overview
1 Syllabus - Unit 6
2 Introduction to CT, MRI, PET and SPECT
Computerised Tomography (CT)
Magnetic Resonance Imaging (MRI)
Functional Magnetic Resonance Imaging (fMRI)
Positron Emission Tomography (PET)
Single Photon Emission Computed Tomography (SPECT)
3 Tumor types and their therapy
4 Treatment
Surgery
Radiotherapy
Chemotherapy
Immunotherapy
5 Magnetic Resonance Imaging
6 Questions
7 Thank You

Syllabus - Unit 6
Syllabus Highlights
1 Introduction to CT, MRI, PET and SPECT,
2 tumor types and their therapy,
3 magnetic resonance imaging.
4 Advancement in healthcare technologies.
5 Case studies of biomedical signal and image processing

Introduction to CT, MRI, PET and SPECT
Brain imaging has greatly advanced in the last 20 years, due to better
understanding of the electromagnetic spectrum and radiofrequency waves, in
relation to protons in individual molecules within the cells of the brain. New
technologies allow non-invasive spatial mapping, (morphology), and observations
of processes within the brain during set tasks. By sequencing scanned sections of
the brain, activity between neurons in different parts of the brain can be observed
and monitored. There are a range of scanning techniques such as CT, MRI, fMRI,
PET, SPECT, DTI, and DOT etc, their purpose and limitations are described
below:

Figure : from left to right: DTI MRI fMRI T1-MRI DTI

Introduction to CT, MRI, PET and SPECT Computerised Tomography (CT)
Computerised Tomography scans use X-rays to show the structure of the brain,
with details such as blood perfusion, the resultant images are two dimensional and
of comparatively low resolution, however, the quality has been much improved
since 1998. With improved technology, the single section has now become a
multisection and the speed has increased eight times, giving well-defined 3-D
pictures. A CT scan may reveal underdeveloped parts of the brain or sites of
injury from impact, tumours, lesions or infection.

Figure : detectors for a single-section scanner and a multisection scanner

Figure : Sample CT image for brain

1 The blue colour shows total blood perfusion throughout the brain.
2 The red colour shows blood perfusion to the left side of the brain only.
Before a CT scan, the patient may drink but is asked not to eat for four hours
beforehand, and not to take strenuous exercise. A CT brain scan will take about
30 minutes and the patient must lie still for the duration. An EEG may be
attached to monitor heart rate, and for some investigations, a tracer injection
(iodinated contrast fluid), may be required to highlight blood vessels, sometimes
leaving a ’taste’ at the back of the throat for a short time afterwards. The
radiologist needs to know if the patient is diabetic, pregnant or on medication.
The procedure is painless, but does involve exposure to radiation at a very low
level.

Introduction to CT, MRI, PET and SPECT Magnetic Resonance Imaging (MRI)
Figure : Digitally enhanced MRI images of the brain.
An MRI scanner uses a strong magnetic field and radio waves to create pictures of
the tissues and other structures inside the brain, on a computer.

The magnetic field aligns the protons (positively charged particles) in hydrogen
atoms, like tiny magnets. Short bursts of radio waves are then sent to knock the
protons out of position, and as they realign, (relaxation time), they emit radio
signals which are detected by a receiving device in the scanner. The signals
emitted from different tissues vary, and can, therefore, be distinguished in the
computer picture

An MRI scanner can create clear detailed pictures of the structure of the brain
and detect any abnormalities or tumours. Sometimes a dye, or tracer, such as
gadolinium may be introduced via a vein in the arm, to improve contrast in the
image. Images can be enhanced by differences in the strength of the nuclear
magnetic resonance signal recovered from different locations in the brain. The
relaxation times, T1, T2, and T2* are measured after the scanner’s pulse
sequence, and can be chosen to look at specific tissue within the brain.For
example, at a T2 setting, water and fluid containing tissue appears bright, whilst
fat containing tissue is dark, and this can be used to distinguish damaged tissue
from normal tissue. A T1 setting gives a clear image for the contrast between
white and grey matter in the brain. T2* imaging uses a marker, eg. gadolinium,
to measure cerebral blood volume and flow. It may be seen that by selecting
different relaxation times and manipulating radio frequencies, specific brain tissue
can be highlighted for examination by the physician

The process of having a scan is painless and safe, there is no exposure to
radiation, but occasionally, a patient may have a reaction to the tracer dye.
Pregnant mothers are not recommended to undertake the procedure unless there
is no alternative, since it is not known whether the effects of a strong magnetic
field may affect the developing baby

Figure : Dataset for sample MR images

Introduction to CT, MRI, PET and SPECT Functional Magnetic Resonance Imaging (fMRI)
Functional magnetic resonance imaging can show which part of the brain is active,
or functioning, in response to the patient performing a given task, by recording
the movement of blood flow. All atoms and molecules have magnetic resonance,
emitting tiny radio wave signals with movement, because they contain protons.
Different molecules have different magnetic resonance and two components of
blood are tracked to observe brain activity.

Haemoglobin in the blood carries oxygen; oxyhaemoglobin, around the brain and
when it is used up, it becomes desoxyhaemoglobin. Where the oxygen is being
’used up’ shows the site of activity in the brain. The picture is made by
monitoring the ratio of the tiny wave frequencies between these two states whilst
the patient carries out a task, eg. tapping a finger, which highlights the area of
the brain functioning to carry out this task

Figure : An fMRI scan showing regions of activation, including the primary visual cortex

An fMRI scan is painless and harmless and can, therefore, be carried out at
regular intervals to monitor the progress of a patient under treatment.

Introduction to CT, MRI, PET and SPECT Positron Emission Tomography (PET)
Positron emission tomography scanning produces a three-dimensional image of
functional processes in the brain, (not just the structure). PET is a nuclear
medicine imaging technique which requires the patient to receive a small injection
of radio-active material (a sugar tracer; fluorodeoxyglucose), into the bloodstream.
The radio-active material causes the production of gamma-rays, these are a form
of electromagnetic radiation like X-rays, but of higher energy. The radio-active
material is transported around the body and into the brain. A ring of detectors
outside the head is used to detect pairs of gamma rays emitted indirectly by the
positron-emitting radionuclide (tracer), in each part of the brain under
examination.

The areas of the brain that command the greater volumes of blood produce the
most gamma-rays, and it is these areas that are computed and displayed by the
PET scan. As the tracer decays, there is a point when gamma photons are
emitted almost opposite to each other, (’annihilation’ in the Figure 7), the timing
of this event is detected and will ultimately improve the detail of the image. This
system not only identifies the activated area of the brain, but also measures the
degree of activity.

Figure : Schematic view of the PET process.

A patient may only have one PET scan, due to radiation dosage regulations. PET
has proved to be particularly useful in monitoring visual problems, tumours and
metabolic processes.

Introduction to CT, MRI, PET and SPECT Single Photon Emission Computed Tomography (SPECT)
Figure : SPECT scan showing blood perfusion

The single photon emission computed tomography records the signals from
gamma rays,using two or more synchronised gamma cameras, and the multiple
2-D images are computed, tomographically reconstructed, to 3-D. A section may
be examined from several angles, but is slightly less clear than a PET image. A
SPECT scanner is less expensive than a PET scanner and uses longer-lived, more
easily obtained radioisotopes. Tracing blood flow within the brain identifies where
metabolic activity is occurring, enabling assessment of brain functions.

The patient will not have to fast before the procedure, but will have to remain
absolutely still for 15 to 20 minutes in a scanner, similar to the MRI. A
radiopharmaceutical (tracer) will be injected via a catheter in the arm. The
amount of radiation the patient will be exposed to is very small, about 1 to 3
times normal human annual exposure to background radiation. The procedure is
painless and the patient may resume normal activities immediately afterwards.

Tumor types and their therapy
Tumor is basically an uncontrolled growth of cancerous cells in the body, whereas
brain tumor is classified as uncontrolled or abnormal growth of cancerous cells in
the brain. Brain tumor can be a benign or a malignant. Any tumor that arises
from the glial cells of the brain or from the supportive tissue of the brain is called
“Glioma”. One class of the Glioma tumor is the astrocytoma1
. According to
World Health Organization and American Brain Tumor Association, the tumor
may also be classified according to the grading mechanism, from grade I to grade
IV. The tumor class belongs to grade I and II also referred as low-grade brain
tumors, whereas grade III and IV are referred as high-grade brain tumors.
1is a star-shaped brain cells in the cerebrum called astrocytes

The low-grade brain tumor observed slow growth of cancerous cells, whereas
high-grade brain tumor observed rapid growth of cancerous cells. On the scale of
grading mechanism grade I glioma is surely be considered as benign type of
tumor, and complete surgical excursion in this case is considered to be curative.
Grade II glioma is observed as a low-grade brain tumor and often considered to be
the class of benign tumor, but the patient infected with grade II Gliomas require
serial monitoring by MRI, CT or other modern imaging modalities scan in every 6
to 12 months. If the low-grade brain tumor is left untreated then it is likely to
develop into high-grade brain tumors and hence early detection and diagnosis of
the brain tumor is primary concern by the radiology department. The summary of
benign and malignant tumors are shown in Table 1.

Table : Differences between benign and malignant tumors
Benign tumors
Malignant tumors
Non-cancerous
Cancerous
Abnormal cells incapable of spreading
Abnormal cells capable of spreading
Cells multiply slowly
Cells multiply rapidly
Grades I and II
Grades III and IV
Easier to remove and does not recur after
excision
Difficult to remove and recurs after ex-
cision
Mass is mobile
Mass is fixed
Homogeneous in structure
Heterogeneous in structure
Surgical excursion is considered to be cu-
rative
Surgery, radiotherapy, chemotherapy or
combination thereof is needed

Figure : Tumor types (a) Benign tumor (b) Malignant tumor

Treatment
Treatment
To obtain an accurate diagnosis, the patients are process through various stages of
treatment, because to offer a better treatment and to increase the chances of the
survival of the patient, early detection of the tumor stage, its size and location is
very important and plays a critical role in the diagnosis. If the patients are
detected with the benign tumor then only surgery is enough to cure the patient,
but if the malignant tumor is detected then continuous monitoring in every 6 to 12
month is needed with surgery, radiotherapy, chemotherapy or combination thereof.

Treatment Surgery
Surgery
The extreme case of tumor stage is Glioblastoma and the first step in the
treatment of Glioblastoma is surgery. Now a days with the advancement of
modern techniques, surgery is safe for most patients. The purpose of surgery are
to obtain tumor tissues for diagnosis and further treatment planning. To obtain
the exact location of the tumor in the brain, a biopsy may be done in place of
surgery. The astrocytoma and Glioblastoma kind of malignant tumors have
tentacle-like cells and grows into the surrounding tissue, and because of
heterogeneous in structure and rapid growth, these tumors cannot be removed
completely. So, for partial removal of the tumor and obtained the confirmation of
the tumor type, surgery is employed, and then radiation, chemotherapy and or
immunotherapy or combination thereof are used to treat the remaining tumor.

Treatment Radiotherapy
Radiotherapy
If the malignant type of tumors such as Glioblastoma and astrocytoma is
detected, then radiation therapy usually follows a biopsy or surgery. There are
different types of radiation is employed at different intervals and schedules.
Conventional fractionated external beam radiation is a standard form of radiation
given to the patient in five days a week for five to six week. This form of radiation
is simple form of radiation and similar to the radiation effect cause by X-ray. To
operate on the tumor’s area directly, intensity modulated radiation therapy is
applied, this is also referred as conformal photon radiation. Image-guided
radiation therapy (IGRT) is the technique of using imaging technology at the time
of each treatment to verify that patients are in the right position within a
millimeter. To protect healthy tissue and reduces overall toxicity, proton bean
therapy is employed as an alternative to the standard radiation.

Treatment Chemotherapy
Chemotherapy
Chemotherapy is applied for newly diagnosed Glioblastoma type of tumor and it is
a six-week course of Temozolomide2
given concurrently with radiotherapy.
Temozolomide is an alkylating agent with reasonable blood-brain barrier
penetration. The main purpose of taking Temozolomide is to maximize the effect
of radio-sensitization and it is generally taken one hour prior to radiation therapy.
Similar type of treatment has also been routinely applied to the patient detected
with astrocytoma type of tumor. It is also observed that, during chemotherapy
drug normal cells of the patient is also affected and will result in the side effect
such as low white blood cell count, fatigue, and hair loss.
2is an oral chemotherapy drug

Treatment Immunotherapy
Immunotherapy
Immunotherapy is a new kind of treatment used to improve the immune system of
the patients with an aim to fight with the tumor cells and to stop or slow down
the tumor growth. These kind of therapy suggested some natural treatment by
means of healthy foods, cancer vaccines, antigens etc. To check and differentiate
between the healthy and bad tissues, checkpoint proteins, such as PD-L1
(Programmed death ligand 1) is also inserted in the body. The body needs PD-L1
to keep the immune system stronger and to protect healthy cells from the attack
by cancerous cells. The therapy system based on Immunotherapy is less hazardous
and may represent the next frontiers of the promising therapies in the coming
decade.

Magnetic Resonance Imaging
Now a days radiology department has many option for diagnosis of the tumor
stages from modern imaging modalities, but image contrast is the goal in all
imaging procedures. There are number of different imaging modalities are
available, notably, some of them are, MRI, CT, PET, SPECT. Table 2 outlines
some of the strength and weaknesses of the different imaging modalities. The
imaging modality used in our research is based on MRI, as it provides excellent
spatial resolution, no bone artifact, better contrast with high sensitivity, and low
risk because of no or low radiation in comparison to CT scan and other modern
imaging modalities. For diagnosis of the patient and to check time to time
evaluation and measure continuous monitoring is needed, magnetic resonance
imaging can be used several times on the patients because the absorbed radiation
is lowest in MRI. The magnetic resonance imaging is also called NMR is highly
versatile, because it can be used to study both structural and functional features
of brain with different configurations.

Table : Strengths and weaknesses of imaging modalities
Modalities Strength Weaknesses
MRI
no or low radiation cost is very high
excellent spatial resolution used mainly for soft tissues
better contrast
low risk
no bone artifact
detect flowing blood and cryptic vascular
malformations
CT
widely available because of low cost low contrast so poor visibility
excellent spatial resolution problem of bone artifact
higher radiation
PET
fair spatial resolution high cost
brain activation can be measured higher radiation
not widely available
SPECT
low cost poor spatial resolution
widely available higher radiation
regional brain perfusion can be measure not widely available

The magnetic resonance imaging uses protons, especially hydrogen protons in the
body as a source of signal. This hydrogen protons induce a small magnetic field
due to the movement of atom’s. The acquisition of the MRI is based on the
following relaxation properties:
1 T1 relaxation (T1-weighted MRI)
2 T2 relaxation (T2-weighted MRI)
3 Proton density (PD-weighted MRI)
4 Fluid attenuated inverse recovery (FLAIR-weighted MRI)

In MRI scanning, when a patient is placed in the magnetic field, then the
hydrogen atoms in water of their body tissues will line up along the magnetic field
and then the Radio Frequency (RF) pulse is sent in, this causes spinning the
protons into another plane and allows them to be aligned in relax mode and stays
relax when the pulse is turned off. This process of applying RF pulse, allows
protons in relax alignment and then turned off RF pulse, known as relaxation.
This relaxation time varies from one type of tissues to another type and is used in
MRI to differentiate between normal tissues and infected tissues. Each tissue is
measure and characterized in MRI by two relaxations times, T1 (longitudinal
relaxation time) and T2 (transverse relaxation time). An external magnetic field
at the constant rate is employed to align the randomly oriented protons.

This alignment or magnetization of the proton element is next disrupted by
introduction of an external RF energy. By emphasizing through the various
relaxation processes, the protons are return to their resting alignment and doing
so it will emits RF energy. The emitted signals are measured after a certain period
following the initial sequence of RF. By changing and validating the sequence of
RF pulses applied and collected, different types of images are created, this images
are referred to as T1-weighted MR images, T2-weighted MR images, Proton
density weighted MR images and FLAIR-weighted MR images.The timing
constraint i.e. TR and TE are described below:

1 Repetition time (TR):
It is the time between the successive RF pulses applied during the
magnetization. A long repetition time allows the protons in all the tissues
such as WM, GM, CSF and other tumor infected tissues to relax back into
relax alignment, whereas short repetition time allows the protons in all the
tissues into not having fully relaxed alignment.
2 Echo time (TE):
It is the time at which the electrical signal induced by the spinning protons is
measured. A long echo time results in reduced signal in tissues, whereas a
short echo time reduces the amount of dephasing occurs in tissues like white
matter and gray matter.
The relationship between repetition time and echo time for the acquisition of the
different MRI sequences are shown in Figure 9

Figure : Relationship between TR and TE times

Table : MRI sequences with their approximate TR and TE values
MRI sequences Acquisition time Approximate time
TR (msec) TE (msec) TR (msec) TE (msec)
T1-weighted MRI (short TR and
short TE)
≤ 800 ≤ 30 500 14
T2-weighted MRI (long TR and
long TE)
≥ 2000 ≥ 80 4000 90
FLAIR-weighted MRI (very long
TR and very long TE)
≥ 3000 ≥ 80 9000 114
PD-weighted MRI (long TR and
short TE)
≥ 1000 ≤ 30 3000 14

Questions
Questions
1 Differentiate between benign and malignant tumors
2 Explain the treatments involved in brain tumor detection.
3 Explain PET and SPECT
4 Explain Magnetic Resonance Imaging and also give Strengths and weaknesses
of imaging modalities (CT, MRI, PET and SPECT)
5 Write short notes on
1 CT
2 MRI
3 PET
4 SPECT
6 Outlines the differences between different imaging modalities
7 Explain the TR and TE in MRI in details
8 Explain radiation effects in CT, MRI, PET and SPECT
9 Show the MRI sequences with their approximate TR and TE values
10 Explain what to avoid during CT, MRI and PET examination

Thank You
Thank you
Please send your feedback at nilesh.bahadure@sanjayghodawatuniversity.ac.in
This is Nilesh B. Bahadure from SGU Kolhapur
Thanks for joining
Goodbye, Have a nice day.
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Introduction to Medical Image Processing

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