fmri study design
DESCRIPTION
A simple introduction to fMRI study design for social science and other researchers outside the field who might want to design a study using fMRI brain scanning technologyTRANSCRIPT
fMRI Study Design
The basic framework
Russell James, J.D., Ph.D.Texas Tech University
Goals of fMRI Study Design
1. Create a desired
cognitive state
(standard experimental design issues)
2. Detect brain signals
associated with that state
(fMRI-specific experimental design issues)
We want to estimate the likelihood that a voxel, or group of voxels, is
responding to the stimulus
But, fMRI data is not like this
Activation
fMRI data is like this
Activation
The signal change is small.The signal is noisy.
Activation
The signal
change is small
½% to 3% change in intensity with a 1.5 T scanner
The signal is noisy
1. The brain is noisy
2. The scanner is noisy
The brain is constantly active, constantly firing, constantly receiving input, constantly sending instructions
The brain is noisy
Even conscious thought is scattered. Did you think about something other than fMRI in the last 3 minutes?
The brain is noisy
1. Contrasts 2. Repetition
How do we
design for noisy brains?
Think in contrasts
Task A Task BTask A-Task B
A single image contains much
unrelated brain activations
A contrast can subtract out
the noise
Think of study design in terms of contrasts
Image of task
A
Image of task
B
Image of task A-
Image of task B
The comparison task can be “rest”
Image of task
A
Image of task
B
Image of task A-
Image of task B
We can use a “cognitive subtraction”
comparison to isolate an activity
- =
Cognitive subtraction: the comparison task is
identical, except for one variation of interest
Cognitive subtraction: View famous faces v. non-famous faces
How might you improve cognitive subtraction in this picture selection?
Match gender? Color pallet? Expressions? Clothing choice?
Levels of cognitive subtraction
• Basic cognitive subtraction: Rational argument of validity
• Cognitive conjunction: Two cognitive subtraction designs show same activation difference
• Parametric design: Increasing levels of a factor correspond with increasing levels of activation
Stron
ger Resu
lts
Cognitive conjunction
Memorizingnumbers
Memorizingletters
Reading numbers
v.
v.
Parametric design
Memorize 9 numbers
Memorize 6 numbers
Memorize 3 numbers
Memorize 1 number Incr
easi
ng
acti
vati
on
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● ●
● ●
Design for BIG contrasts
fMRI is too noisy to be good at subtle cognitive differences
Contrast extreme differences first
1. Contrasts 2. Repetition
How do we
design for noisy brains?
Design for repeated activations
In fMRI we get 25 people to do a task 40 times
for 1,000 activations
In social sciences we may get 1,000 people to make one
decision on a survey
Block Design
Two common design types
Event Related Design
Block Design
Time
Within a certain range, repeating a stimulus will cause the HRF to stack linearly.
This causes large total signal change in block designs.
Stacking the HRFs
Event Related Design
• Easiest way to detect differences among two comparison states
• Largest HRF activation
• More robust to unexpected HRF shapes
Block design advantages
BOLD response in block v. event related (slow)
• Modeling incorrect responses (can’t know in advance)
• Habituation may prevent activations
Can precisely observe the actual HRF
Permits self-paced trials
Event related design advantages
Block designs may not work
Barriers to repeating the activation
Barriers to repeating the activation
• Repetitions can get boring or predictable, reducing activation
• Emotional states may not be induced or changed quickly
• Some decisions are difficult to repeat
• Some biases can be added once, but not removed
Repetitions can get boring or predictable, reducing activation
+ + +
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Emotional states may not be induced or changed quickly
Think of the happiest moment of your life for 12 seconds
Think of the most painful moment for 12 seconds
Think of the 2nd happiest moment for 12 seconds
Think of the 2nd most painful moment for 12 seconds
Some decisions are difficult to repeat
“If you died today what percentage of your estate would you want to leave to your children?”
Are you sure?
Any second thoughts?
Want to think about it some more?
Some biases are not easily removed
1. How much of a $100 extra payment will you give to the United Way?
2. The United Way CEO made $1,037,140 last year.
3. How much of a $100 extra payment will you give to the United Way?
1st comparison works great, but can you repeat this?
The signal is noisy
1. The brain is noisy
2. The scanner is noisy
Designing for a noisy scanner
Physical issues
Timing issues
Physical issues of a noisy scanner
Machine Metal Movement
Machine
Optimizing machine, setting
parameters, region of
interest, speed v. resolution, etc.
Metal: Limit any ferrous content to avoid disturbances in magnetic field
Movement
• Motivated subjects
• Foam packing
Statistical adjustments (but, may not help task-related movement)
Keep the subject still during runs
Designing for a noisy scanner
Physical issues
Timing issues
Timing issues of a noisy
scanner signal
Scanner Drift
Over longer periods of time (2-10 minutes), the magnetic field of the scanner can slowly rise and fall.
Scanner Drift
Comparison across long (>2min) periods should be avoided.
Condition A Condition A
Condition B Condition B
A–B shows magnetic differences but not from HRF
What is wrong with this?
30 sec block of task A (version 1)30 sec block of task A (version 2)30 sec block of task A (version 3)30 sec block of task A (version 4)30 sec block of task B (version 1)30 sec block of task B (version 2)30 sec block of task B (version 3)30 sec block of task B (version 4)30 sec block of task C (version 1)30 sec block of task C (version 2)30 sec block of task C (version 3)30 sec block of task C (version 4)
What is wrong with this?
30 sec block of task A (version 1)30 sec block of task A (version 2)30 sec block of task A (version 3)30 sec block of task A (version 4)30 sec block of task B (version 1)30 sec block of task B (version 2)30 sec block of task B (version 3)30 sec block of task B (version 4)30 sec block of task C (version 1)30 sec block of task C (version 2)30 sec block of task C (version 3)30 sec block of task C (version 4)
Comparing A to C spans well over 120 seconds so we can’t distinguish from scanner drift
Block Design Timing Issues
Ideal timing 15-20 seconds on then 15-20 seconds off (or A then B)
• Long enough for HRF to relax in between presentations
• Short enough for many comparison blocks within short time
Slow Event-Related Timing Issues
Waiting 12+ seconds in between each event to allow HRF to calm down
Boring and inefficient
Rapid Event-Related DesignTiming Issues
Jitter spacing to record different parts of the HRF and to avoid correlation with other functions like heartbeat and breathing
Rapid Event-Related DesignTiming Issues
Gap spacing >4 seconds, else• HRF blurring: Not enough time
for noticeable HRF changes • Non-linearity: HRFs don’t stack
linearly foreverOptimum jittering estimation programs (e.g., OptSeq - Doug Greves; Genetic Algorithm - Tor Wager)
Session Timing
Typically, studies include groups of tasks of 4-10 min. with intervening 2 min. breaks.
Also need high resolution (T1) scan ~5 min.; Locater scans (~30 sec.); T2 axial scan for radiologist (~2 min.)
10 min. subject in and out
Locator – 20 seconds
Short Break
T2 axial: 2 min
Break
T1 high resolution: 5 min
Break - wake up
Block 1: 8 minutes
Break/Instructions: 2 min
Block 2: 8 minutes
Break/Instructions: 2 min
In a 48 minute session, you may get about 24-28 minutes of actual stimulus presentation
Block 3: 8 minutes
$650/hour scanner time ~$1300/hour stimulus time~$20+ per minute~$1+ every 3 seconds
Add 12 sec. to 25 subjects = $100+
With so many, many design issues to think about, what is
the best way to design your first study?
Stand on some shoulders!
Find a good prior study, copy the technical elements, but change your item of interest
fMRI Study Design
The basic framework
Russell James, J.D., Ph.D.Texas Tech University