Functional Magnetic Resonance Imaging
or fMRI
How does a brain get red
and yellow spots ?
Created by Armin Fuchs
 Center for Complex Systems and Brain Sciences, 2000
fMRI – What is does
fMRI is a modern noninvasive imaging
technology which can be used to identify
regions in the brain that get activated
when participants perform certain tasks.
In contrast to conventional MRI scans
showing brain structure, fMRI provides
information about brain function.
fMRI – How it works
In a nutshell: The oxygen carrier in blood is
the hemoglobin molecule. When this molecule
releases oxygen to a cell its magnetic
properties change from a so-called
diamagnetic to a paramagnetic state. This
difference can be found in image series taken
by the scanner. With the assumption that in
activated regions more oxygen is released
compared to inactive regions, blood serves as
a natural contrast agent for detecting brain
activity.
So we detect the deoxygenated
hemoglobin ?
Well, not exactly. Because the blood flow in the
brain overcompensates the actual need of
oxygen, there is more oxygenated hemoglobin
inside the active regions than can be used. So
what we detect is the unused blood or the
oxygenated hemoglobin. This is known as the
Blood Oxygen Level Dependent or BOLD
contrast.
How do we do that ?
MRI scanners can collect a variety of different images
depending on the scan sequence like the ones below:
T1 weighted
images
T2 weighted
images
Proton
density
images
Inversion
recovery
images
Echo planar
images
 T1 weighted images are used to obtain brain structure for
reconstructions of the cortical surface or as overlay images
for for functional activity. They show fluid in dark and the
brain ‘right’, i.e. white matter bright and gray matter gray.
 T2 weighted images are used in most medical scans. Fluid
appears bright and gray matter is brighter than white
matter.
 Inversion recovery scans allow for suppressing tissue with
certain properties and for optimal control of the contrast.
 Echo planar images certainly don’t have the same
resolution as the other scans. In fact, they look pretty bad,
but they can be taken extremely fast and make functional
imaging possible.
Typical Scanning Times
The time a scan takes depends on many things like resolution,
intended signal to noise ratio and more. The following
times are for standard sequences we typically use.
T1 weighted full head scan (120 slices, 256x256 pixel per
slice with a voxel size of 1x1x2mm3) takes about 10min.
T2 weighted and inversion recovery scans are comparable.
The echo planar sequence we typically use takes 20 slices
with 64x64 pixels and a voxel size of 3.5x3.5x7.5mm3
IN 3 (THREE) SECONDS !!!
O.K., but what do we see on them ?
By just looking at them not much. Below are two sets of echo
planar images taken while the subject was moving a
finger (top) and during rest (bottom).
So how does it work then?
Well, every three seconds we collect a volume of 20 or so
slices and we tell our participant in the scanner to keep her
eyes closed and just rest. We then scan for 30sec which
gives us ten volumes of the brain as a base line.
Now we tell our subject to perform a task, say move your
right index finger back and forth, and we keep her doing
that for another 30sec or ten volumes.
Then we tell her to rest again. This pair of rest and task
30sec each we call a block. The participant will perform
four blocks of task and rest lasting four minutes during
which we scan the volume 80 times or collect 1600 slices.
Now we have a 4-dimensional dataset which three
spatial dimensions (the volumes) and one
dimension in time. Each volume consists of 20
slices consisting of 64x64 pixels (for ‘picture
elements’) or 20x64x64=81920 little volumes of
3.5x3.5x7.5mm3 each called voxels (for ‘volume
elements’). We have taken 80 of these volumes
and now we look at how the activity in individual
voxels changes as a function of time, i.e. whether
they are related to the periods of rest and task the
subject performed during the scan. A typical
example of time series of voxels from a single
slice looks like this :
What did I see in this picture ?
On the left you see the time series corresponding to the
the voxels inside the green box on the slice in the middle
right. Obviously, certain voxels follow the task function,
i.e. off-on-off-on … plotted in red above the time series
in the middle. This function is delayed by about 6sec to
account for the time it takes the hemo-dynamic system to
respond. The bottom right blow-up of one voxel shows
that this curve and the intensity recorded from the voxel
match quite well. Now the correlation between the task
function and the time series from all 81920 voxels are
calculated. If the correlation is less than 0.5 it is ignored.
If the value is greater than 0.5 the voxel gets a color
corresponding to the intensity between its min and max.
Why didn’t we see this earlier?
There was no difference !
Actually, there was. It’s just that the difference between the task and
the rest is very small compared to the baseline (only a few %) so we
couldn’t see it. After subtracting this baseline the differences are quite
striking. Certain locations in the brain (the active voxels) follow the
task-rest cycles, others are completely unaffected. Calculating the
correlation between the task function and the voxel time series is one
way to have a computer find active regions (another method is to
compare the distributions during the task and rest periods by a t-test to
find the voxels where the difference is significant).
Now what about these color spots?
Of course, the images don’t come out of the
scanner with these colors. They are marks of
regions where the computer found high
correlations and represent the difference
between the average intensity in the task
condition compared to rest.
In a last step the low-resolution echo planar
image is replaced by a T1 weighted image
(while keeping the color spots) which is a
much better representation on the underlaying
anatomy. Here we see a finger movement task
which involves motor cortex (on the left) and a
region called supplementary motor area (or
SMA) in the middle.
And that’s it ???
Essentially, yes. Now we just have to study
the activity related to different tasks and
find the active regions inside the brain. We
show a few simple examples of what can be
done with this technology.
Right, left and bimanual
The next slide is an example for finger sequencing. In the
top row the task is performed with the right hand, in the
middle row with the left hand and in the bottom row
bimanually. Top, the activity over sensory-motor areas is
strongest on the right-hand side of the image (which is
actually the left side of the brain, the way radiologists like
to have their images because when they look at their
patients they see the left side on the right and vice versa).
In the middle row the activity is strongest on the left (the
right hemisphere of the brain), and on the bottom the
activation is approximately the same in both hemispheres.
right
left
both
Motor versus Sensory
The brain regions where movement is controlled for a
certain limb are very close to those which get the sensory
inputs from that limb (and there are probably good
reasons for that). They are, however, on different sides on
the central sulcus. The next slide shows in the right
column the activity from a finger movement, in the
middle a sensory stimulation of the same finger (simply
by rubbing), and on the right moving this finger against
an obstacle. It is evident that in the first case the activity
is more anterior (towards the nose), in the second case it
is more posterior (further back), and the third row shows
simply both, i.e. motor and sensory activity.
movement
sensory
both
Syncopate and Synchronize
Brain activity not only depends on the task itself but also on the
context in which this task is executed. The task in next slide was
press a small air pillows held between the thumb and index fingers
of both hands at a rate of 1.33Hz paced by an auditory
metronome. In the top row the instruction was to press the pillow
on the beat, i.e. to synchronize with the metronome. For the
middle row the task was to execute the movement in the middle
between two consecutive beats, i.e. to syncopate. The metronome
was the noise made by the scanner where we recorded four slices
every three second leading to pings at 1.33Hz. The bottom row
shows the relation between the metronome beats (red bars) and the
average movements (black lines), measured as pressure changes in
the pillows for both hands and task conditions.
Syncopate
Synchronize
Syncopate and Synchronize
The slices are taken in the coronal plane because we were mainly
interested in activation in the cerebellum, a structure known to be
involved in timing tasks. It is know that syncopation is a more
difficult task then synchronization. In fact, if subjects are asked to
syncopate at higher movement rate (like 2.5Hz) they are unable to
to that whereas synchronization at this frequency is no problem.
We see the difference in task difficulty in the cerebelar activity
which is much higher during syncopation than synchronization.
Finally a little movie
Right Hand Figure Sequencing Task
•Subject continually touched thumb to
the finger of the right hand in the
sequence 4235 during the “on” period.
•This movie shows the comparison of on
and off period of the functional scans
rendered with a whole head volume of
the same subject.
•Note the bilateral activation of the precentral region (area M1) which is
strongest in the contralateral
hemisphere.
•Also note the strong activation in SMA
and the ipsilateral cerebellum.
That’s it, thanks
for watching.
Armin Fuchs
Center for Complex
Systems & Brain Sciences