1. Hi, kids! My name
is Vickie Voxel. I’m
going to tell you
● ●
about fMRI, HRF &
BOLD.
Intro to fMRI
Part I: HRF & BOLD
Dr. Russell James, Texas Tech University

2. An fMRI picture of the
brain is made up of
thousands of boxes, called
voxels, just like me!
● ●

3. We voxels
are small –
usually
about the
size of one ● ●
peppercorn

4. Inside each
of us
voxels are
thousands
of neurons
● ●

5. When a lot of
these neurons
start to fire,
the body
rushes in
● ● oxygen to help

6. This rush of
oxygen comes
through the
blood and
makes me
● ● start to
change color

7. As my blood
oxygen
increases, I
get redder
● ●

8. And redder
● ●

9. If this keeps
going, I will be
totally red
from all of the
oxygen in my
● ● blood

10. But then, if
the neurons
don’t keep
firing, the
body will stop
● ● rushing oxygen
to me

11. And my color
will start to
return to
normal
● ●

12. I can get a bit
blue at the end
if my oxygen
drops too low,
right before it
● ● returns to
normal

13. In 20 seconds
after the
neurons fired,
I will be back
to my normal
● ● color again

14. This whole
color change
process is
called my
hemodynamic
● ● response

15. “Hemo” means
blood. “Dynamic”
means change.
● ●
So, hemodynamic
response is my
“blood-change”
Blood Oxygen Level
● ● ● ●
response.
● ● ● ●
● ● ● ● ● ● ● ● ● ●
● ●
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
SECONDS after neurons fire

16. When we model
this change with
math, we call it a
● ●
hemodynamic
response function
Blood Oxygen Level
● ● ● ●
● ● ● ●
● ● ● ● ● ● ● ● ● ●
● ●
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
SECONDS after neurons fire

17. But, saying
“hemodynamic
response
● ●
function” takes
too long, so we
will just call it
Blood Oxygen Level
● ● ● ●
the HRF
● ● ● ●
● ● ● ● ● ● ● ● ● ●
● ●
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
SECONDS after neurons fire

18. ● ● The HRF
Blood Oxygen Level
● ● ● ●
● ● ● ●
● ● ● ● ● ● ● ● ● ●
● ●
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
SECONDS after neurons fire

19. The fMRI machine can see my color
change because blood with a lot of
oxygen (red) is less attracted to
magnets than blood without much
oxygen (pink or blue).
● ●
● ●

20. But, instead of showing pictures
in red, pinks, and blues, the fMRI
creates black and white pictures.
Differences in
magnetism are
shown as shades of
light and dark.
● ● ● ●
● ●
● ●

21. The fMRI machine is measuring a BOLD
signal because the color is
Blood
Oxygen
Level
Dependent
● ● ● ● High blood oxygen
Low blood oxygen
● ●
● ●

22. So, instead of an
HRF looking like
this…
● ●
Blood Oxygen Level
● ● ● ●
● ● ● ●
● ● ● ● ● ● ● ● ● ●
● ●
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
SECONDS after neurons fire

23. The fMRI shows
an HRF that looks
like this…
● ●
Blood Oxygen Level
● ● ● ●
● ● ● ●
● ● ● ● ● ● ● ● ● ●
● ●
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
SECONDS after neurons fire

24. Because the color
tells us the blood
oxygen level, we
● ●
really don’t need
a vertical axis…
Blood Oxygen Level
● ● ● ●
● ● ● ●
● ● ● ● ● ● ● ● ● ●
● ●
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
SECONDS after neurons fire

25. We can just use
one line
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
SECONDS after neurons fire

26. And, if we always
take a picture
every 2 seconds,
then we don’t even
need the seconds
on the bottom
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
SECONDS after neurons fire

27. So, all of our HRF
information is
shown on the
Neuron timeline below
firing
starts
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●

28. But, instead of a
Neuron
firing
series of colors,
starts the fMRI
machine gives us
numbers
180 200 250 305 249 201 182 172 180
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●

29. The fMRI records a
Neuron number for the
firing magnetism of each voxel
starts at each time
180 200 250 305 249 201 182 172 180
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●

30. If we take a picture every 3
seconds for 7 minutes, we get 140
numbers for each voxel

31. And we might have 100,000 or so
voxels in the whole brain

32. 20 images per minute X 7 minutes
X 100,000 voxels X 20 people =
280 million data points
We can’t track it by hand!

33. So we have to ask
the computer to
analyze the data

34. But the computer
needs to know
WHAT to look for
and WHEN to look
for it

35. So WHAT are we
looking for?

36. We are looking for changes in the
signal that look like this
● ●
Blood Oxygen Level
● ● ● ●
● ● ● ●
● ● ● ● ● ● ● ● ● ●
● ●
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
SECONDS

37. We are looking for changes in the
signal that look like this
● ●
Blood Oxygen Level
● ● ● ●
● ● ● ●
● ● ● ● ● ● ● ● ● ●
● ●
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
SECONDS

38. We are looking for changes in the
signal that look like this…
because this looks like an HRF,
meaning it was caused by a large
group of neurons firing
180 200 250 305 249 201 182 172 180
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●

39. We are looking for changes in the
signal that look like this…
because this looks like an HRF,
meaning it was caused by a large
group of neurons firing
180 200 250 305 249 201 182 172 180
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●

40. WHEN are we
looking for this
HRF-like signal?

41. We are interested in the HRF-like
signals that happen right after the
subject experiences something
+ + + + +

42. Then we can estimate the
likelihood that a voxel, or group of
voxels, is responding to the
stimulus

43. This simple concept can be
difficult in practice because:
1. The signal change is small
2. The brain is noisy

44. This simple concept can be
difficult in practice because:
1. The signal change is small
2. The brain is noisy
Overcoming these barriers
requires:
Good study design
+
Good data analysis

45. Bye for now!
Next time we will
look at how to
create a good study
● ●
design.
Intro to fMRI
Part I: HRF & BOLD
Dr. Russell James, Texas Tech University