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FIL

November 2011

ONLINE SOURCES

Web Guides

http://mathworld.wolfram.com/LinearAlgebra.html

http://www.maths.surrey.ac.uk/explore/emmaspages/option1.html

http://www.inf.ed.ac.uk/teaching/courses/fmcs1/

Online introduction:

- http://www.khanacademy.org/video/introduction-to-

matrices?playlist=Linear+Algebra

What Is MATLAB?

- And why learn about matrices?

Math and computation

Algorithm development

Modelling, simulation, and prototyping

Data analysis, exploration, and visualization

Scientific and engineering graphics

Application development, including Graphical User

Interface building

Everything in MATLAB is a matrix !

Zero-dimentional matrix

A Scalar - a single number is really a 1 x 1 matrix in Matlab! 4

1 dimentional matrix

A vector is a 1xn matrix with 1 row [1 2 3]

n

m 2 7 4

A matrix is an mxn matrix

3 8 9

Building matrices I MATLAB

with [ ]:

2 7 4

A = [2 7 4]

2

A = [2; 7; 4] 7

4

; separates the different rows

2 7 4

A = [2 7 4; 3 8 9] 3 8 9

: separates collums

Matrix formation in MATLAB

X = [1 2 3; 4 5 6; 7 8 9] = 1 2 3

4 5 6

7 8 9

Submatrices in MATLAB

Subscripting each element of a matrix can be addressed with a pair

of numbers; row first, column second

X(2,3) = 6

X(3,:) = ( 7 8 9 )

1 2 3

X( [2 3], 2) = 5

4 5 6

7 8 9 8

Matrix addition and subtraction

Addition

Subtraction

Matrix Multiplication I

Scalar multiplication

Matrix multiplication II

Sum product of respective rows and columns

n l

k

Matrix multiplication rule: m a11 a12 a13 b11 b12

Elementwise multiplication

Matrix multiplication rule:

a21 a22 a23 X b21 b22

Matrixes need the exact same m a31 a32 a33 b31 b32

Transposition reorganising matrices

In Matlab: AT = A

Identity matrices

Tool to solve equation

This identity matrix Is a matrix which plays a similar role as the

number 1 in number multiplication

1 0 0

0 1 0

0 1

0

Worked example 1 2 3 1 0 0 1+0+0 0+2+0 0+0+3

A In = A 4 5 6 X 0 1 0 = 4+0+0 0+5+0 0+0+6

for a 3x3 matrix: 7 8 9 0 0 1 7+0+0 0+8+0 0+0+9

Inverse matrices

Definition: Matrix A is invertible if there exists a matrix B such that:

2 -1 2+1 -1 + 1

1 1 X = = 1 0

3 3 3 3 3 3

1 1 -2+ 2 1+2

-1 2 0 1

3 3 3 3 3 3

Determinants

Determinant is a function:

if det(A) 0

In Matlab: det(A) = det(A)

With more than 1 equation and more

than 1 unknown

1

Can use solution x a b from the single

equation to solve

2 x1 3x2 5

For example x1 2 x2 1

2 3 x1 5

In matrix form 1 2 x2 1 AX = B

Need to find determinant of matrix A (because X =A-1B)

a b

From earlier det( A) ad bc

c d

2 3

(2 x -2) (3 x 1) = -4 3 = -7 1 2

So determinant is -7

To find A-1:

1 1 2 3 1 2 3 1

A

(7) 1 2 7 1 2

4

if B is

1 2 3 1 1 14 2

X

7 1 2 4 7 7 1 So

scalars, vectors and matrices in

SPM

Scalar: Variable described by a single

number e.g. intensity of each voxel in MRI scan

Here we talk about column of numbers e.g. voxel intensity at a different

times or different voxels at the same time

x1

v

v

n x 2

v

e

xn

.

.

xn1xnn

Vectorial Space and Matrix Rank

Vectorial space: is a space that contains vectors and all the those that can be

obtained by multiplying vectors by a real number then adding them (linear

combination). In other words, because each column of the matrix can be

represented by a vector, the ensemble of n vector-column defines a vectorial

space for a matrix.

independents from each other. So, if there is a linear relationship between the

lines or columns of a matrix, then the matrix will be rank-deficient (and the

determinant will be zero). For example, y

relationship between X1 and X2,

and the determinent is zero.

4

x2

And the Vectorial space defined

will has only 1 dimension. 2 x1

x

1 2

Eigenvalues et eigenvectors

Eigenvalues are multipliers. They are numbers that represent how much linear transformation or

stretching has taken place. An eigenvalue of a square matrix is a scalar that is represented by the

Greek letter (lambda).

Eigenvectors of a square matrix are non-zero vectors, after being multiplied by the matrix, remain

parallel to the original vector. For each eigenvector, the corresponding eigenvalue is the factor by

which the eigenvector is scaled when multiplied by the matrix.

All eigenvalues and eigenvectors satisfy the equation Ax = x for a given square matrix A. i.e.

Matrix A acts by stretching

the vector x, not changing its direction, so x is an

eigenvector of A.

One can represent eigenvectors of A as a

set of orthogonal vectors representing different

dimensions of the original matrix A.

(Important in Principal Component Analysis, PCA)

Matrix Representations of Neural

Connections

Can create a mathematical model of the

connections in a neural system

Matrix Representations of Neural

Connections

#2 Excitatory = Makes it easier for the

post synaptic cell to fire

-1

Inhibitory = Makes it harder for the

#1 +1 #3 post synaptic cell to fire

Input vector = (1 1) relates to activity (#1 #2)

Weight vector = (1 -1) relates to connection weight (#1 #2)

Activity of Neuron 3 1

1 1. (11) (1 1) (1) (1) 0

Input x weight 1

Cancels out! But it is more

complicated than this!

How are matrices relevant to fMRI data?

Basics of MR Physics

Angular Momentum: Neutrons, protons and electrons spin about their axis.

The spinning of the nuclear particles produces angular momentum.

charge, and spins, it produces a small magnetic field. This small magnetic

field is referred to as the magnetic moment that is a vector quantity with

magnitude and direction and is oriented in the same direction as the angular

momentum.

orientation (so no overall magnetic field). However, when exposed to an

external magnetic field (B0), nuclei begin to align. To detect net

magnetisation signal a second magnetic field is introduced (B1) which is

applied perpendicular to B0, and it has to be at the resonant frequency.

How are matrices relevant to fMRI

data?

Y = X . +

Observed = Predictors * Parameters + Error

BOLD = Design Matrix * Betas + Error

Y

Each column represents a single

voxel sampled at successive time

points.

Time

Each voxel is considered as

independent observation

So, we analysis of individual voxels

over time, not groups over space

Intensity

Explanatory variables Solve equation for

These are assumed to be tells us how

Response variable

measured without error. much of the BOLD

A single voxel sampled

May be continuous, indicating signal is explained

at successive time points.

levels of an experimental by X

Each voxel is considered as

factor.

independent observation.

a

m

b3

N of scans

b4

= b5

+

b6

b7

b8

b9

Y = X b + e

Observed Predictors

Pseudoinverse

In SPM, design matrices are NOT

square matrices (more lines than

columns, especially for fMRI).

there is more than one solution

possible.

called the pseudoinverse, which is an

approximation, where the solution is

constrained to be the one where the

b values that are minimum.

How are matrices relevant to fMRI?

Image time-series

Spatial filter Design matrix Statistical Parametric Map

Statistical RFT

Normalisation Inference

Anatomical p <0.05

reference Parameter estimates

In Practice

Estimate MAGNITUDE of signal changes and

MR INTENSITY levels for each voxel at various

time points

Relationship between experiment and voxel

changes are established

Calculation require linear algebra and matrices

manipulations

SPM builds up data as a matrix.

Manipulation of matrices enables unknown

values to be calculated.

Thank you!

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