Signal Processing for Medical Applications Frequency ...1.Basics of Brain – i) Brain signals - EEG/ MEG; ii) Muscle signals - EMG; iii) Magnetic resonance imaging – MRI iv) Tremor

Muthuraman Muthuraman Christian-Albrechts-Universität zu Kiel Department of Neurology / Faculty of Engineering Digital Signal Processing and System Theory

Signal Processing for Medical Applications –

Frequency Domain Analyses

Digital Signal Processing and System Theory| Signal Processing for Medical Applications | Introduction Slide I-2

1.Basics of Brain –

i) Brain signals - EEG/ MEG;

ii) Muscle signals - EMG;

iii) Magnetic resonance imaging – MRI

iv) Tremor disorders

2. Quantities measured from time series in frequency domain

i) Power spectrum

ii) Modelling time series using AR2 processes

ii) Coherence spectrum

- Different windows used for the estimation

iii) Phase spectrum

iv) Delay between signals

3. Source analysis in the frequency domain

- Forward problem

- Inverse problem

- Different Solutions

Lecture 1 & 2

Lecture 3

Lecture 4

Lecture 5

Lecture 6-10

Contents


• Basics of MRI

> Magnets

> Hydrogen atoms

• Creating a image

• Visualization

Lecture 2 – Magnetic resonance imaging (MRI)


• Magnets The biggest and the most important part component in a

MRI system is the magnet, unit-tesla. There is horizontal tube running

through the magnet from front to back, this tube is the bore of the magnet.

• Superconducting Magnet Principle(Superconductivity) Metals and

ceramic materials cooled to temp. near absolute zero no electrical

resistance electrons can travel through them freely carry large amounts

of current long periods of time without losing energy as heat.

• Gradient Magnet There are 3 gradient magnets inside the MRI

machines. These magnets are very, very low strength compared to the

main magnetic field, range-18 to 27 millitesla.

• The main magnet immerses the patient in a stable and very intense

magnetic field, and the gradient magnets create a variable field.

Basics Of MRI(Magnetic Resonance Imaging)



Magnets



• Hydrogen atoms- It is an ideal atom for MRI because its nucleus

has a single proton and a large magnetic moment

• When placed in a magnetic field, the hydrogen atom has a strong

tendency to line up with the direction of the magnetic field

Hydrogen atoms



Creating a Image

• Inside the bore of the scanner, the magnetic field runs straight down the center of

the tube in which we place the patient. The hydrogen protons in the body will

lineup in the direction of either the feet or the head.

• The vast majority of protons will cancel each other only a couple remains which is

used to create images.

• The MRI machine applies an RF pulse that is specific only to hydrogen, the

system directs the pulse towards the area of the body we want to examine. The

RF pulse causes the protons in that area to absorb the energy required to make

them spin at a particular frequency in a particular direction. The specific frequency

of resonance is the larmour frequency and is calculated based on the

particular tissue being imaged and the strength of the magnetic

field.



• The three gradient magnets are arranged in such a manner inside the main

magnet that when they are turned on and off very rapidly in a specific manner,

they alter the main magnetic field on a very local level, which means we can

pick exactly which area we want a picture of the brain.

• The RF pulse is turned off, the hydrogen protons begin to slowly return to their

natural alignment within the magnetic field and release there excess stored

energy. They give off a signal that the coil picks up and sends it to the

computer system. With the Fourier transform the mathematical data is

converted into a picture to put on film.

Creating a Image



Visualization

• MRI works by altering the local magnetic field in the tissue being

examined.

• Normal and abnormal tissue will respond slightly altered, giving us

different signals.

• These varied signals are transfered to the images, allowing us to

visualize many different types of tissue abnormalities.



Review: Image Formation

•Data gathered in k-space (Fourier domain of image)

•Gradients change position in k-space during data acquisition (location in k-space is integral of gradients)

•Image is Fourier transform of acquired data

k-space image space

Fourier transform

ky

kx

Visualization



Sagittal Coronal Axial

Magentic Resonance Imaging (MRI)





Sagittal

Axial / Horizontal

Coronal / Frontal




Sagittal Axial / Horizontal Coronal / Frontal




Susceptibility and Susceptibility Artifacts

Adding a nonuniform object (like a person) to B0 will make the total magnetic field B nonuniform

This is due to susceptibility: generation of extra magnetic fields in materials that are immersed in an external field

For large scale (10+ cm) inhomogeneities, scanner-supplied nonuniform magnetic fields can be adjusted to “even out” the ripples in B — this is called shimming

Susceptibility Artifact

-occurs near junctions between air and tissue

• sinuses, ear canals

sinuses

ear

canals


How Susceptibility Affects Signal

Susceptibility nonuniform precession frequencies

RF signals from different regions that are at different frequencies will

get out of phase and thus tend to cancel out

Sum of 500 Cosines with

Random Frequencies Starts off large when all phases are about equal

Decays away as different

components get different phases




FMRI (Functional Magnetic Resonance Imaging)

• FMRI measures brain activity indirectly through changes in blood

vasculature that accompany neural activity

An intial increase in oxygen consumption owing to increased

metabolic demand

After a delay of 2 secs, a large increase in local blood flow, which

overcompensates for the amount of oxygen being extracted

Local increase in cereberal blood volume

• The increase in blood oxyhaemoglobin is what we measure in FMRI.

This is so called the BOLD (Blood oxygen level dependent) response.





The Bold effect

BOLD: Blood Oxygenation Level Dependent

Deoxyhemoglobin (dHb) has different resonance frequency than water

dHb acts as endogenous contrast agent

dHb in blood vessel creates frequency offset in surrounding tissue (approx as dipole pattern)




Frequency spread causes signal loss over time

BOLD contrast: Amount of signal loss reflects [dHb]

Contrast increases with delay (TE = echo time)




Vascular

Response

to Activation O2 metabolism

dHb

dHb

HbO2

HbO2

dHb HbO2

HbO2

dHb dHb

HbO2

blood flow [dHb]

dHb = deoxyhemoglobin HbO2 = oxyhemoglobin

capillary

blood volume

neuron

HbO2

HbO2

HbO2

HbO2

dHb

dHb

dHb

dHb dHb

dHb

HbO2

HbO2

dHb HbO2

HbO2

dHb dHb

HbO2




Very indirect measure of activity (via hemodynamic response to neural activity)!

Complicated dynamics lead to reduction in [dHb] during activation (active research area)

Neuronal activity Metabolism

Blood flow

Blood volume

[dHb] BOLD signal




Hemodynamic Response Function

% signal change

= (point – baseline)/baseline

usually 0.5-3%

initial dip

-more focal

-somewhat elusive so far

time to rise

signal begins to rise soon after stimulus begins

time to peak

signal peaks 4-6 sec after stimulus begins

post stimulus undershoot

signal suppressed after stimulation ends




The Canonical FMRI Experiment

Subject is given sensory stimulation or task, interleaved with control or rest condition

Acquire timeseries of BOLD-sensitive images during stimulation

Analyse image timeseries to determine where signal changed in response to stimulation

Predicted BOLD signal

time

Stimulus pattern

on

off

on

off

on

off

on

off off




What is required of the scanner?

Must resolve temporal dynamics of stimulus (typically, stimulus lasts 1-30 s)

Requires rapid imaging: one image every few seconds (typically, 2–4 s)

Anatomical images take minutes to acquire!

Acquire images in single shot (or a small number of shots)

1 2 3 … image


High-resolution FMRI at 7T High-res 7T: 0.58 x 0.58 x 0.58 mm3 = 0.2 mm3

High-res 3T: 1 x 1 x 1 mm3 = 1 mm3

Conventional 3T: 3 x 3 x 3 mm3 = 27 mm3






Diffusion

Tensor

Imaging (DTI)

Water diffusion restricted along white matter

Sensitize signal to diffusion in different directions

Measure along all directions, infer tracts

Diffusion direction




Complementary information to FMRI

FMRI: gray matter, information processing

DTI: white matter, information pathways

Tractography: tracing white matter pathways between gray matter regions

Tract-based connectivity

Color-coded directions x

y

z


Tremor Disorders

Tremor:

Tremor is defined as rhythmic non-voluntary oscillatory activity of body parts. The

body parts affected by this disorder are the hands, arms, head, face, vocal cords,

trunk and legs.

Parkinsonian tremor:

The classical form of Parkinsonian tremor is the rest tremor which is present when

the limb is at rest. But pure rest tremor is not so common; it is usually in combination of

both rest and postural or kinetic tremors.

- 1% of the population above 50 years

Essential tremor:

This tremor occurs while doing voluntary actions and remains constant till the action is

performed, it usually disappears at rest.

- 4% of the population above 65 years

Lecture 2 – Tremor Disorders


PD ET

PD and ET Tremor Patients




PD and ET Tremor Patients

STIM OFF STIM ON


Deep Brain Stimulation


Documents

Signal Processing for Medical Applications Frequency ...1.Basics of Brain – i) Brain signals - EEG/ MEG; ii) Muscle signals - EMG; iii) Magnetic resonance imaging – MRI iv) Tremor