t-tests, ANOVAs &

Regression
and their application to the statistical
analysis of neuroimaging
 OVERVIEW
• Basics, populations and samples
• T-tests
• ANOVA
• Beware!
• Summary Part 1
• Part 2
 Basics
• Hypotheses • Descriptive vs
– H0 = Null-hypothesis inferential statistics
– H1 = experimental/ • (Gaussian)
research hypothesis distributions

• p-value & alpha-level

(probability and
significance)
Activation in the left occipitotemporal
regions , esp the visual word form
area, is greatest for written words.
 Populations and samples
Population
 z-tests and
distributions

Sample
(of a population)
t-tests and
distributions

NOTE: a sample can be 2 sets of scores, eg fMRI data from 2 conditions

Comparison between Samples

Are these groups

different?
Comparison between Conditions
(fMRI)
Reading aloud (script) vs “Reading” finger spelling (sign)

Reading aloud vs Picture naming

 t-tests
comp
infer

12

10

95% CI
8

Left hemisphere right hemisphere

Exp. 1lesion site Exp. 2

• Compare the mean between 2 samples/ conditions

• if 2 samples are taken from the same population,
then they should have fairly similar means
 if 2 means are statistically different, then the
samples are likely to be drawn from 2 different
populations, ie they really are different
 t-test in VWFA
• Exp. 1: activation patterns
are similar, not significantly
different  they are similar
comp
tasks and recruit the VWFA
infer
in a similar way
12

10 • Exp. 2: activation patterns

95% CI

are very (and significantly)

8
different reading aloud
recruits the VWFA a lot
6
more than naming
Left hemisphere right hemisphere
Exp. 1 lesion site
Exp. 2
 Formula
Difference between the means divided by the pooled standard
error of the mean

x1  x 2
t
s x1  x2
Reporting convention: t= 11.456, df= 9, p< 0.001
 Formula cont.

x1  x 2
t
s x1  x2

2 2
s1 s2
Cond. 1 Cond. 2
s x1  x2  
n1 n2
 Types of t-tests
Independent Related
Samples Samples
also called dependent means
test

Interval Independent Paired samples

measures/ samples t-test* t-test**
parametric
Ordinal/ non- Mann-Whitney Wilcoxon test
parametric U-Test

* 2 experimental conditions and different participants were assigned to each condition

** 2 experimental conditions and the same participants took part in both conditions of the experiments
 Types of t-tests cont.
• 2-tailed tests vs • 2 sample t-tests vs 1
one-tailed tests sample t-tests

2.5% 2.5%

Mean Mean

A known
value

Mean
5%
Comparison of more than 2
samples

Tell me the
difference
between these
groups…
Thank God I have
ANOVA
 ANOVA in VWFA (2x2)
comp
infer
• Is activation in VWFA for
12
different for a) naming and
reading and b) influenced by
10
age and if so (a + b) how so?
95% CI

8 • H1 & H0
• H2 & H0
6
• H3 & H0
• 
Left hemisphere right hemisphere

Naminglesion site Reading reading causes significantly

stronger activation in the VWFA
TASK
but only in the older group so
the VWFA is more strongly
Naming Reading activated during reading but this
Aloud seems to be affected by age
AGE Young
(related to reading skill?)

Old
 ANOVA
• ANalysis Of VAriance (ANOVA)
– Still compares the differences in means between groups but it
uses the variance of data to “decide” if means are different

• Terminology (factors and levels)

• F- statistic
– Magnitude of the difference between the different conditions
– p-value associated with F is probability that differences between
groups could occur by chance if null-hypothesis is correct
– need for post-hoc testing (ANOVA can tell you if there is an
effect but not where)
Reporting convention: F= 65.58, df= 4,45, p< .001
 Types of ANOVAs

Type 2-way ANOVA for independent repeated measures ANOVA mixed ANOVA
groups
Participants Condition Condition II Condition Condition II Condition Condition II
I I I

Task I Participan Participant Task I Participan Participant Task I Participa Participant

t group A group B t group A group A nt group group B
A
Task Participan Participant Task Participan Participant
II t group C group D II t group A group A Task Participa Participant
II nt group group B
A

Between- Within-subject both

subject design design

NOTE: You may have more than 2 levels in each condition/ task
BEWARE!
• Errors
– Type I: false positives
– Type II: false negatives

• Multiple comparison problem

 esp prominent in fMRI
 SUMMARY
• t-tests compare means between 2 samples and
identify if they are significantly/ statistically
different
• may compare two samples to each other OR
one sample to a predefined value
• ANOVAs compare more than two samples, over
various conditions (2x2, 2x3 or more)
• They investigate variances to establish if means
are significantly different
• Common statistical problems (errors, multiple
comparison problem)
PART 2

Correlation
- How much linear is the relationship of two
variables? (descriptive)

Regression
- How good is a linear model to explain my data?
(inferential)
 Correlation:
- How much depend the value of one variable on the value of
the other one?

Y Y

X X X

high positive correlation poor negative correlation no correlation

How to describe correlation (1):

Covariance

- The covariance is a statistic representing the degree to which 2

variables vary together

 ( x  x)( y
i i  y)
cov( x, y )  i 1
n

(note that Sx2 = cov(x,x) )

cov(x,y) = mean of products of each point desviation from mean
values

Geometrical interpretation: mean of ‘signed’ areas from

rectangles defined by points and the mean value lines

 ( x  x)( y
i i  y)
cov( x, y )  i 1
n
sign of covariance =
sign of correlation

Y
Y Y

X X X

Positive correlation: cov > 0 Negative correlation: cov < No correlation. cov ≈ 0
0
How to describe correlation (2):

Pearson correlation coefficient (r)

cov( x, y)
rxy  (S = st dev of sample)
sx s y

- r is a kind of ‘normalised’ (dimensionless) covariance

- r takes values fom -1 (perfect negative correlation) to 1 (perfect

positive correlation). r=0 means no correlation
Pearson correlation coefficient (r)

Problems:

- It is sensitive to outlayers

- r is an estimate from the sample, but does it represent the population

parameter?
Linear regression:
- Regression: Prediction of one variable from knowledge of one or more
other variables
- How good is a linear model (y=ax+b) to explain the relationship of two
variables?
- If there is such a relationship, we can ‘predict’ the value y for a given
x. But, which error could we be doing?

(25, 7.498)
Preliminars:
Lineal dependence between 2 variables
Two variables are linearly dependent when the increase of one
variable is proportional to the increase of the other one

y
x

Samples: - Energy needed to boil water

- Money needed to buy coffeepots
The equation y= mx+n that connects both variables has
two parameters:
-‘m’ is the unitary increase/decerease of y (how much
increases or decreases y when x increases one unity)
- ‘n’ the value of y when x is zero (usually zero)

y2  y1
m
x2  x1

y (1)  n
m m
1 0
n

0 1
Samples: ‘m’= Energy needed to boil one liter of water , ‘n’=0
‘m’ = prize of one coffeepot, ‘n’= fixed tax/comission to add
Fiting data to a straight line (o viceversa):
Here, ŷ = ax + b
– ŷ : predicted value of y
– a: slope of regression line
– b: intercept
ŷ = ax + b

εi

= ŷi, predicted
= yi , observed
εi = residual

Residual error (εi): Difference between obtained and predicted values of y (i.e. yi- ŷi)

Best fit line (values of b and a) is the one that minimises the sum of squared errors
(SSerror) (yi- ŷi)2
 Adjusting the straight line to data:
• Minimise (yi- ŷi)2 , which is (yi-axi+b)2

• Minimum SSerror is at the bottom of the curve where the gradient is zero
– and this can found with calculus

• Take partial derivatives of (yi-axi-b)2 respect parametres a and b and

solve for 0 as simultaneous equations, giving:

rs y
a b  y  ax
sx
• This calculus can allways be done, whatever is the data!!
How good is the model?
• We can calculate the regression line for any data, but how well does it fit the
data?

• Total variance = predicted variance + error variance: Sy2 = Sŷ2 + Ser2

• Also, it can be shown that r2 is the proportion of the variance in y that is

explained by our regression model
r2 = Sŷ2 / Sy2
• Insert r2Sy2 into Sy2 = Sŷ2 + Ser2 and rearrange to get:
Ser2 = Sy2 (1 – r2)

• From this we can see that the greater the correlation the smaller the error
variance, so the better our prediction
Is the model significant?

• i.e. do we get a significantly better prediction of y from our regression

equation than by just predicting the mean?
complicated
rearranging

• F-statistic:
sŷ2 r2 (n - 2)2
F(df ,df ) = =......=
ŷ er
ser 2 1 – r2

r (n - 2)
• And it follows that:
t(n-2) =
√1 – r2

So all we need to know are r and n

!!!
Generalization to multiple variables

• Multiple regression is used to determine the effect of a number of

independent variables, x1, x2, x3 etc., on a single dependent variable, y

• The different x variables are combined in a linear way and each has its
own regression coefficient:
y = b0 + b1x1+ b2x2 +…..+ bnxn + ε

• The a parameters reflect the independent contribution of each

independent variable, x , to the value of the dependent variable, y

• i.e. the amount of variance in y that is accounted for by each x variable

after all the other x variables have been accounted for
Geometric view, 2 variables:
‘Plane’ of regression: Plane nearest all the sample points distributed over a 3D space:

y = b 0 + b 1 x 1 + b 2 x2 + ε

x2

x1 ŷ = b0 + b1x1+ b2x2
Multiple regression in SPM:

y : voxel value

x1, x2,… : parameters that are supposed to justify y variation (regressors)

GLM: given a set of values yi, (voxel value at a determinated position for a
sample of images) and a set of explanatories variables xi (group, factors, age,
TIV, … for VBM or condition, movement parameters,…. for fMRI) find the
(hiper)plane nearest all the points. The coeficients defining the plane are
named b1, b2,…, bn

equation: y = b0 + b1x1+ b2x2 +…..+ bnxn + ε

Matrix representation and results:
Last remarks:

- Correlated doesn’t mean related.

e.g, any two variables increasing or decreasing over time would show a
nice correlation: C02 air concentration in Antartica and lodging rental cost
in London. Beware in longitudinal studies!!!

- Relationship between two variables doesn’t mean causality

(e.g leaves on the forest floor and hours of sun)

- Cov(x,y)=0 doesn’t mean x,y being independents

(yes for linear relationship but it could be quadratic,…)
 Questions ?
Please don’t! 
 REFERENCES
• Field, A. (2005). Discovering Statistics
Using SPSS (3rd ed). London: Sage
Publications Ltd.
• Field, A. (2009). Discovering Statistics
Using SPSS (2nd ed). London: Sage
Publications Ltd.
• Various stats websites (google yourself
happy)
• Old MfD slides, esp 2008