BIOLOGICAL SIGNALS

PROCESSING
Introduction
Assoc. Prof. Vladimr Kraja, MSc., PhD.
Department of neurology Faculty Hospital Na Bulovce,
Prague, Czech Republic
phone +420-2-6608 2307
e-mail krajcav@fnb.cz

Source materials on web www.skolicka.fbmi.cvut.cz

password: signaly
Contents of web pages:
e-learning courses (2009, 10 lectures, in Czech)
selected publications - international journals and conferences
video - EEG, EMG, EP signals recording in EEG lab FN Bulovka and
FN Ostrava
requirements and terms of exams (enrolment in KOS)
e-learning course (in Czech - pictures, formulas)
Mohylov J., Kraja V. Zpracovn signl v lkastv, Ostrava 2007
animated examples and simulations (some in DOS),
programs for simulation of filtering, brain mapping, cluster analysis
homeworks

Methods of computer-assisted
electroencephalogram analysis realized
in EEG lab FN Na Bulovce
Overview
Examples of real world EEG biosignal processing.
Case studies from clinical practice and research.

Outline of lecture
1.

Introduction what it is electroencephalogram, properties of

the signal

2.

Problems of visual evaluation

3.

Selection of proper methods of analysis

4.

Practical assets of methods

5.

Publications overview, courses , source materials

1. What is electroencephalogram (EEG) ?

complex elektrical biosignal, measurement on the scull by

electrodes (V)

reflects the electrical activity of brain functions

apart from structural methods (CT - computer tomography), it

shows dynamic functional manifestation of living brain

basic diagnostic tool for the treatment and diagnosis of epilepsy

and sleep analysis

manifests behavioural states (psychology), consciousnes,

disturbances of brain functions, sleep stages, coma, lesions

1.a. Basic spectral activity - waves, graphoelements

Principal frequency content for diagnosis (background

activity)

0.5 - 4 Hz
4 - 8 Hz
8 - 13 Hz
13 - 22 Hz

- children, deep sleep, tumours

- normal
- awake, eyes closed, blocked by eyes opened
- normal, attention, pain, unrest

Graphoelements

Delta
Theta
Alpha
Beta

epileptic abnormalities - transients - spikes, spike and wave complexes

(SWC)
spike - transient clearly distinctive from the background activity,
pointed peak, 70 msec wide (sharp wave 200msec)

Artefacts

Defects in recordings technical (50/60 Hz noise, drop off of electrode)

and physiologic (sweating, movement) caused by external influence.
Must be displaceed from recording (detection, ICA, PCA)

1.b. Examples

Epileptic spikes

Amplitude artefact

2. Problems of visual evaluation - why use

computers

1.

Visual evaluation / interpretation

subjective

more art than science - evaluation depends on the teacher and his
experience

education of top specialists is difficult ( 5 years of maturation)

tedious, requires permanent attention

2.

3.

Length of recording

ambulatory recording - 20 min -> epileptic activity doesn't have to manifest

itself

long term monitoring is necessary (24 hours and more)

sleep analysis - 8 hours = 864 m of paper recording

Archivation - (paper machines obsolete); DVD is compact, databases provide
fast information retrieval

4.
5.

Data processing (montage changing, filtering, not possible on paper

traces )

Numeric EEG quantification and analysis (qEEG, digital signal processing)

2.a. Aims of computer-assisted analysis

Support of physician's decision

Extension of his capabilities by objective data
Graphic data presentation
Normal/abnormal activity distinction
Signal classification
Trends evaluation
Data reduction and archiving
Quantification - assesment of exact value of
dominant frequency
Hidden information extraction (not visible by a
naked eye)
Concentration on interesting parts of long-term
recordings an skipping the uninterested parts (by
artificial intelligence)

3. Long-term x detailed analysis

Long-term EEG

significant events
detection
significant
graphoelements (spikes)
searching
trends evaluation
sleep stages classifiation
epileptic seizures
detection

Detailed analysis

topographic mapping of
frequenct bands power
local and interhemispheric
coherence mapping
frequency shifts in spectrum
source derivation
dipole analysis
phase specrum- epileptic
focus localization

4. Methods overview
LORETA
LORETA
NEONATAL
NEONATAL
SLEEP
SLEEP
ANALYSIS
ANALYSIS

WAVE
FINDER

Photic
driving

SPIKE
DETECTION

CORDANCE
POWER
SPECTRUM

3D
3D PROJECTION
PROJECTION

ARTEFACT
ELIMINATION

PRINCIPAL
COMPONENT
ANALYSIS

SPECTRUM
ANALYSIS

LONG- TERM
PROCESSING

NEURAL
NETWORKS

PRE -PROCESSING
DIGITAL FILTERING
TRENDS REMOVING

EEG SIGNAL

PHASE
MAPPING

LOCAL
COHERENCE

BRAIN
MAPPING

CSA

PCA
SEGMENT
ATION

DETAILED
ANALYSIS

INDEPENDENT
COMPONENT
ANALYSIS

4.1. Cooperation
Cooperation
with VUT

Cooperation
with SZ
SZ

and PMD

LORETA
LORETA

NEONATAL
NEONATAL
SLEEP
SLEEP
ANALYSIS
ANALYSIS

WAVE
FINDER

Photic
driving

SPIKE
DETECTION

Cooperation with
Technical
University Ostrava

Cooperation with Psychiatric

Center
CORDANCE
POWER
SPECTRUM
3D
3D PROJECTION
PROJECTION

ARTEFACT
ELIMINATION

PRINCIPAL
COMPONENT
ANALYSIS

PROCESSING

NEURAL
NETWORKS

PRE -PROCESSING
DIGITAL FILTERING
TRENDS REMOVING

EEG SIGNAL

INDEPENDENT
COMPONENT
ANALYSIS

Cooperation with
Academy of
Science

SPECTRUM
ANALYSIS

LONG- TERM

PHASE
MAPPING

LOCAL
COHERENCE

BRAIN
MAPPING

CSA

PCA
SEGMENT
ATION

DETAILED
ANALYSIS

Signal Processing - visualisation

Amplitude topographic mapping

V

13.5

Conversion of num bers

into color scale
13.5

-100

-98.3

-98.3

85.0
85.0

5.6

5.6

+100

a)
1. iteration

Average from four

neigbours

b)
2. iteration

The new points are

included into com puting

c)

Topographic m ap

. . . till the whole area is

covered

Mapping of amplitude
mV

1. In multichannel signal choose a time

instant Fig. a)
Numbers are replaced by colors

13.5

-100
13.5 -98.3

98.3
85.0

5.6

2. iteration

1. iteration

average of 4 neighbours

100

b)

a)

new computed values

enter next iteration

c)

Example in DOS

3. In several iterations do interpolation

from neigbouring points Fig. c)

85.0

5.6

Topographic map

. . . final map

2. Numerical values are replaced by

colors with from a color scale Fig. b)

4. Repeat (refine) interpolation by

including the new values to cover all
plane
5. The values of EEG amplitude are
color coded into topographic map.

amplitude brain mapping - between cursors

4.3.1. Signal processing - unprocessed signal

4.3.1. FIR filtering

4.3.3. Spectral components

Signal + noise 50 Hz

Filtering 0.5-25 Hz

5. Spectrum anlysis
Assesment of frequency components in a single / all
channels
Four main EEG frequency bands / single spectral
line (power spectrum density)

Spectrum analysis EEG 1 channel

Spectrum analysis - numbers

Spectrum analysis - frequency curves

Spectrum analysis - detailed maps for

every frequency line

Spectrum analysis - frequency bands

Spectrum analysis, 3D model - spherical splines

6. Case report : Local and interhemispheric coherence

Local coherence indicator of cross correlation (cooperation) of

neighbouring areas of the brain cortex (prof. Rappelsberger)

Interhemispheric coherence analysis of interhemispheric synchrony

Quantitative evaluation of focal lesion, not visible in native EEG

Used also for topographic spectrum and

coherence mapping

Local coherence - normalized cross spectrum

auto-spectrum

G x ( f ) = E [ X ( f ) X ( f )]
Cross-spectrum

G x y ( f ) = E [ X ( f ) Y ( f )]
magnitude squared coherence

COH xy =

G 2xy
G xG y

amplitude coherence

COH xy =

G xy
Gx Gy

Examples (expert evaluation - without conclusive focal changes):

Ischmie l.dx vpravo (EEG zvr: bez prkaznch loiskovch zmn)

Classic spectrum
mapping - symmetrical

Local coherence mapping - focus

temporally right in agreement with
CT

Ictus (CMP) - right side hemiparesis

7. Long-term analysis CSA - compressed

spectral arrays

CSA compressed spectral arrays

Spectral curves from 2 sec segments in pseudo

3D projection, like in theater

Intensive Care Units - spectral shifting, brain

nmonitoring

7. CSA- epileptic seizure

CSA - change of view

Case study: Photic driving in workers exposed to mercury

Vapers - cooperation with prof. Urbanem, SZ
Photic driving reaction of EEG to photostimulation for
difference freq of stroboscope (respons of harmonics in EEG
corresponding to stimulation).
Aim asses CSA for indication of changes in PD for early
neurotoxical contamination of workers exposed to Mercury
vapors.
Significant changes in PD in comparison with the control group
early before clinical manifestations

CSAs in a person with well expressed photic driving

Background
activity

Driving on the
fundamental
frequency

Driving on the
1st harmonic
frequency

Driving on the
2nd harmonic
frequency

CSAs in a person with absent photic driving

Background
activity

Automatically generated protocol

Quantitative
params

8. Long-term signal analysis - significant

graphoelements identification by WF

WaveFinder: Hierarchic system of automated

EEG processing
1.
2.
3.
4.

adaptive segmentation
features extraction
automatic classification
visualization and quantification

System properties

Long-term (24 hours) signal processing

Warning of the physician about some event - physician can

make his own conclusion bazsed on the original EEG

Mimetic technique - physicians work immitation during EEG

evaluation

Precision is not a goal - suspected events 10 % , 5%

artefacts/false warnings - time saving for 24 hours of EEG

User (physician) friendly, no parameter setting necessary

Graphic presentation of results

Transparent - switching to and from real original EEG signal.

Adaptive segmentation based on two connected windows

1 dv
spojen
okna
Two
connected
windows

Segment
boundary
hranice
segmentu

EEG nonstationary signal, but

quasistationary (piece-wise
stationary). Fixed segments
does not respect signal
properties. Better way - divide it
into variable length segments
depending on the occurence of
EEG graphoelements
Adaptive segmentation
(Bodenstein and Praetorius,
Michel and Houchin, Kraja,
Varri) :

Difference
2 mra
rozdlu oken
measure
Threshold for small
fluctuations
mez

Local
3 lokln
maximum
maximum

1. Two connected windows are

sliding along the signal
2. The deviation of stationarity
is estimated from the
difference of parameters of
the two indows
3. The segment boundary is
located at the local maxima
of the difference measure

Adaptive segmentation of a single channel

EEG signal and

segments boundary
Amplitude difference
measure

Frequency difference
measure

Total difference
measure
and the threshold

Multichannel adaptive segmentation

Color identification of graphoelements by cluster analysis

Features extraction

Classification should be relevant to the visual

evaluation of the physician

Set of 10 features describing the time and frequency properties

of the signal graphoelements:

variance of amplitude of the segment

difference of maximal positive and minimal negative amplitude

power spectrum in delta, theta, alpha, beta1 a beta2 frequency bands

maximal value of the first derivative of the signal (proportional to the slope)

maximal value of the second derivative of the signal (proportional to the sharpness)

average value of the frequency of the signal

now - research of the relevant features (selection, evaluation)

Automated classification: supervised and unsupervised,

classical and fuzzy

Motivation - to detect the hidden data structure, EEG graphoelements

identification

Methods of classification:
CLUSTER ANALYSIS

searching the natural data structure (if exists)

learning without a teacher (unsupervised) - NO apriori information
about the data
data in a cluster is more similar (close) than data in different classes
feature oriented classification method (statistical pattern recognition)
on-line classification not possible (all segments enter the computing)

LEARNING CLASSIFIER

the new incomer is compared to etalon, prototype (identified by a

teacher during the learning phase

problems with object unknown in the etalons selection during learning

phase

cluster analysis can be used in learning phase for etalons

identification

Classical methods and Neural Networks

Classic and Fuzzy sets theory

k-means algorithm (MacQueen)

1. Cluster centers, prototypes are selected
randomly (can be the data)
2. The (Euclidean) distances forom the
centers to all the data are computed
3. The object is classified to the cluster
with minimal distance to the center

4. The new centers ( of gravity) are recomputed

5. If the optimum is not reached (class

membership does not change), go to the
step 2

Learning k-NN classifier

LEARNING PHASE
Etalons, prototypes are determined with the help of the teacher
- which etalons belongs to the specific class

CLASS1

CLASS 2

CLASS3

CLASSIFICATION PHASE
1. The newcomer is compared with all prototypes

2. It is put into the closest class (most similar)

3. Next objects are evaluated

Hard and fuzzy sets (Lofti Zadeh, 1970)

Classic sets

no class sharing in different classes

object belongs/does not belong to the set (class)
black and white view

Fuzzy sets

multiple class membership with a different grade

X={ x1, x2,....xN }, set of objects.
Classic set
|
Fuzzy set
_____________________________________|____________________________
characteristic function uA: X - > {0,1}
uAi(xk) = {

1 , xk

0 , xk

Ai
Ai

|
|
|
|
|

generalization

uA: X -> <0,1>

uAi(xk)=uik fuzzy membership

Fuzzy sets and classification

FUZZY TDN

KLASICK (HARD) TDN

70 % JABLKA

OVOCN
MOTY

70 % JABLKA

30 % VIN

JABLKA

VIN

VESTKY

Tda 1

Tda 2

0.70

0.30

1.0

0.20

0.25

0.55

1.0

0
0.80
smen objekt me patit
do rznch td s rznm
stupnm lenstv

JABLKA

Tda 3

0.20

30 % VIN

Tda 1

VIN
Tda 2

VESTKY
Tda 3

0 ... pat do tdy

promnn stupe
lenstv v intervalu 0 -

!!!

1
0
smen objekt mus
bt zaazen do jedn z td

1 ... nepat

Automated classification of EEG graphoelements

Motivation - disclose the hidden structure of data, EEG

graphoelements identification.

Method Cluster analysis

Example of classic clustering

Classic class number 5.

Class 6 with mixed objects of class 5

Fuzzy elimination of hybrid segments (grey color)

alpha cut 0.5

Summary sheets
Typical, representative segments
(closest to the center of gravity),
percentual occurence - multichannel
summary information
Temporal profile shows dynamic
class membership in the course of
time
Classes are ranged according to the
decreasing amplitude
Color - indicates the segment class
membership in original EEG recording

Color graphic EEG segments identification

Significant graphoelements are identified by a color in the original EEG record

Temporal profiles - dynamic changes in EEG, significant events detection

Lka m k dispozici efektivn nstroj,

umoujc pomoc kursoru vybrat pslunou
st originlnho zznamu a pokraovat v
prohlen buto v asov oblasti EEG, nebo ve
schematickm diagramu. K tomu me vyvolat
sumrn multikanlovou informaci o typu EEG
aktivity

EEG with a seizure

asov profil dlouhodobch EEG. Pklad zobrazen 20 minut. Monost zobrazit a 3 hodiny
zznamu na jedn strnce. Dva epileptick zchvaty o trvn 2 minuty.

Z a te k e p ile p tic k h o z c h v a tu v 1 1 m in u t ,v y b ra n k u r so r e m z

Sleep EEG analysis (1.5 hour/page, 1 channel)

Comparison with another methods - CSA - spectral information only,

shape of graphoelements is lost

Case study: Detection and quantification of sleep stages in

newborns (Dr. Paul, PMD Podol)

Temporal profiles processing - sleep stages detection in neonatal EEG (120

min of recordings)

VISUAL EVALUATION
AWAKE

QUIET SLEEP

ACTIVE SLEEP

QUIET SLEEP

ACTIVE SLEEP QSLEEP AWAKE

Selected publications with impact factor - www.skolicka.fbmi.cvut.cz

Book chapter

Book chapter

Courses

Cooperation with Psychiatric Center

Prague (Dr. Brunovsky, PhD)