Random Field Theory

Mkael Symmonds, Bahador Bahrami

Random Field Theory

Mkael Symmonds, Bahador Bahrami

Overview

Spatial smoothing

Statistical inference

The multiple comparison problem

and what to do about it

Overview

Spatial smoothing

Statistical inference

The multiple comparison problem

and what to do about it

Statistical inference

Aim
to decide if the data represents convincing
evidence of the effect we are interested in.

How
perform a statistical test across the whole
brain volume to tell us how likely our data
are to have come about by chance (the
null distribution).

Inference at a single
voxel
NULL hypothesis, H0: activation is zero

t-distribution

t-value = 2.42
p-value: probability of getting
a value of t at least as extreme
as 2.42 from the t distribution (= 0.01).
= p(t>t-value|H0)
t-value = 2.02

t-value = 2.42

alpha = 0.025

As p < , we reject the null hypothesis

Sensitivity and
Specificity
ACTION
Dont
Reject

Reject

Chance

H0 True

TN

FP type I error

Not by chance

H0 False

FN

TP

Specificity = TN/(# H True) = TN/(TN+FP) = 1 -

Sensitivity = TP/(# H False) = TP/(TP+FN) = power

Many statistical tests

In functional imaging, there are many voxels, therefore

many statistical tests

If we do not know where in the brain our effect will

occur, the hypothesis relates to the whole volume of
statistics in the brain

We would reject H0 if the entire family of statistical

values is unlikely to have arisen from a null distribution
a family-wise hypothesis

The risk of error we are prepared to accept is called the

Family-Wise Error (FWE) rate what is the likelihood that
the family of voxel values could have arisen by chance

How to test a familywise hypothesis?

Height thresholding

This can localise significant test results

How to set the

threshold?

Should we use the same alpha as

when we perform inference at a
single voxel?

Overview

Spatial smoothing

Statistical inference

The multiple comparison problem

and what to do about it

How to set the

threshold?
Signal + Noise

Use of uncorrected alpha, =0.1

11.3% 11.3% 12.5% 10.8% 11.5% 10.0% 10.7% 11.2% 10.2%
Percentage of Null Pixels that are False Positives
LOTS OF SIGNIFICANT ACTIVATIONS OUTSIDE OF OUR SIGNAL
BLOB!

9.5%

How to set the

threshold?

So, if we see 1 t-value above our

uncorrected threshold in the family of tests,
this is not good evidence against the
family-wise null hypothesis

If we are prepared to accept a false positive

rate of 5%, we need a threshold such that,
for the entire family of statistical tests,
there is a 5% chance of there being one or
more t values above that threshold.

Bonferroni Correction

For one voxel (all values from a null distribution)

Probability of a result less than the threshold = 1-

Probability of a result greater than the threshold =

For n voxels (all values from a null distribution)

Probability of all n results being less than the threshold
=

(1-)n

Probability of one (or more) tests being greater than the

threshold:

= 1-(1-)n

~= n. (as alpha is small)

FAMILY WISE
ERROR RATE

Bonferroni Correction

So,

Set the PFWE < n.

n.
Gives a threshold = PFWE / n

Should we use the Bonferroni

correction for imaging data?

100 x 100 voxels normally

distributed independent
random numbers

10,000 tests 5% FWE rate

Apply Bonferroni correction to give
threshold of 0.05/10000 =
0.000005
This corresponds to a z-score of
4.42

NULL HYPOTHESIS TRUE

100 x 100 voxels
averaged

We expect only 5 out of 100 such

images to have one or more zscores > 4.42
Now only 10 x 10 independent
numbers in our image
The appropriate Bonferroni
correction is 0.05/100= 0.0005
This corresponds to z-score = 3.29
Only 5/100 such images will have
one or more z-scores > 3.29 by
chance

Spatial correlation
Physiological Correlation
Spatial pre-processing
Smoothing
Assumes Independent Voxels
Independent Voxels

Spatially Correlated Voxels

Bonferroni is too conservative for brain images, but how to tell how many
independent observations there are?

Overview

Spatial smoothing

Statistical inference

The multiple comparison problem

and what to do about it

Spatial smoothing
Why do you want to do it?

Increases signal-to-noise ratio

Enables averaging across

subjects

Allows use of Gaussian Random

Field Theory for thresholding

Spatial Smoothing
What does it do?

Reduces effect of high frequency variation in

functional imaging data, blurring sharp
edges

Spatial Smoothing
How is it done?

Typically in functional
imaging, a Gaussian
smoothing kernel is used
Shape similar to normal
distribution bell curve
Width usually described using
full width at half maximum
(FWHM) measure
e.g., for kernel at 10mm FWHM:
-5

Spatial Smoothing
How is it done?

Gaussian kernel defines shape of function

used successively to calculate weighted
average of each data point with respect to
its neighbouring data points

Raw data

Gaussian function

Smoothed data

Spatial Smoothing
How is it done?

Gaussian kernel defines shape of function

used successively to calculate weighted
average of each data point with respect to
its neighbouring data points

Raw data

Gaussian function

Smoothed data

Spatial correlation
Physiological Correlation
Spatial pre-processing
Smoothing
Assumes Independent Voxels
Independent Voxels

Spatially Correlated Voxels

Bonferroni is too conservative for brain images, but how to tell how many
independent observations there are?

Overview

Spatial smoothing

Statistical inference

The multiple comparison problem

and what to do about it

Random Field Theory

(ii)
Methods for Dummies 2008
Mkael Symmonds
Bahador Bahrami

What is a random
field?

A random field is a list of random

numbers whose values are
mapped onto a space (of n
dimensions). Values in a random
field are usually spatially
correlated in one way or another,
in its most basic form this might
mean that adjacent values do not
differ as much as values that are
further apart.

Why random field?

To characterise the properties our

studys statistical parametric map under
the NULL hypothesis
NULL hypothesis =
if all predictions were wrong
all activations were merely driven by chance
each voxel value was a random number

What would the probability of getting a

certain z-score for a voxel in this situation
be?

Random Field

Thresholded
@ one

Thresholded
@ Zero

Measurement 1

Thresholded
@ three

Number of
blobs = 4

Measurement 2

Number of
blobs = 0

Measurement 3

Number of
blobs = 1

Number of
blobs = 2

Measurement
1000000000

Average number of blobs = (4 + 0 + 1 + + 2)/1000000000

The probability of getting a z-score>3 by chance

Therefore, for every z-score,

the expected value of number of blobs
=
probability of rejecting the null
hypothesis erroneously ()

The million-dollar
question is:

thresholding the random field at which

Z-score produces average number of
blobs < 0.05?
Or, Which Z-score has a probability =
0.05 of rejecting the null hypothesis
erroneously?
Any z-scores above that will be significant!

So, it all comes down to

estimating the average
number of blobs (that you
expect by
chance)
in
your
SPM
Random field theory does that for you!

Expected number of
blobs in a random field
depends on

Chosen threshold z-score

Volume of search region

Roughness (i.e.,1/smoothness) of the search region:
Spatial extent of correlation among values in the
field; it is described by FWHM

Volume and Roughness are combined into RESELs

Where does SPM get R from: it is calculated

from the residuals (RPV.img)
Given the R and Z, RFT calculates the
expected number of blobs for you:

E(EC) = R (4 ln 2) (2) -3/2 z exp(-z2/2)

Probability of Family
Wise Error
PFWE = average number of blobs under null hypothesis

= PFWE = R (4 ln 2) (2) -3/2 z exp(-z2/2)

Thank you

References:
Brett, Penny & Keibel. An introduction to Random
Field Theory. Chapter from Human Brain Mapping
Will Pennys slides
(http://www.fil.ion.ucl.ac.uk/spm/course/slides05/
ppt/infer.ppt#324,1,Random Field Theory )
Jean-Etienne Poirriers slides
(http://www.poirrier.be/~jeanetienne/presentations/rft/spm-rft-slidespoirrier06.pdf)
Tom Nichols lecture in SPM Short Course (2006)

False Discovery Rate

ACTION
Dont
Reject
TRUTH

At u1
Reject

H True (o)

TN=7

FP=3

H False (x)

FN=0

TP=10

FDR = FP/(# Reject)

= FP/(# H True)

FDR=3/13=23%
=3/10=30%

Eg. t-scores
from regions
that truly do and
do not activate

oooooooxxxooxxxoxxxx
u1

False Discovery Rate

ACTION
Dont
Reject
TRUTH

At u2

Reject

FDR=1/8=13%
=1/10=10%

H True (o)

TN=9

FP=1

H False (x)

FN=3

TP=7

FDR = FP/(# Reject)

= FP/(# H True)

Eg. t-scores
from regions
that truly do and
do not activate

oooooooxxxooxxxoxxxx
u2

False Discovery Rate

Noise

Signal

Signal+Noise

Control of Familywise Error Rate at 10%

Occurrence of Familywise Error

FWE

Control of False Discovery Rate at 10%

6.7% 10.4% 14.9% 9.3% 16.2% 13.8% 14.0% 10.5% 12.2% 8.7%
Percentage of Activated Pixels that are False Positives

Cluster Level Inference

We can increase sensitivity by trading off anatomical specificity

Given a voxel level threshold u, we can compute

the likelihood (under the null hypothesis) of getting a cluster
containing at least n voxels

CLUSTER-LEVEL INFERENCE

Similarly, we can compute the likelihood of getting c

clusters each having at least n voxels

SET-LEVEL INFERENCE

Levels of inference

voxel-level
P(c 1 | n > 0, t 4.37) = 0.048 (corrected)
At least one
cluster with
unspecified
number of
voxels above
threshold

n=1
2
n=82

set-level
P(c 3 | n 12, u 3.09) =
At least 3 0.019
clusters above
threshold

n=32
cluster-level
P(c 1 | n 82, t 3.09) = 0.029 (corrected)
At least one cluster with at least 82 voxels above threshold