Experimental Design for Functional MRI
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Transcript of Experimental Design for Functional MRI
Experimental Designfor
Functional MRI
David GlahnUpdated by JLL
General Experimental Design
• What is the question you are trying to ask?
• What are the appropriate controls?
Experimental Design: Terminology
• Variables– Independent vs. Dependent – Categorical vs. Continuous
• Contrasts– Experimental vs. Control– Parametric vs. subtractive
• Comparisons of subjects– Between- vs. Within-subjects
• Confounding factors • Randomization,
counterbalancing
From Scott Huettel, Duke
Donder’s Method: Subtraction
• A random series of A’s and B’s presented and the subject must:– Task 1 - Respond whenever event A or B occurs (RT1)– Task 2 - Respond only to A not to B (RT2)– Task 3 - Respond X to A and Y to B (RT3)
RT = reaction time
• RT1 = RT(detect) + RT(response)• RT2 = RT(detect) + RT(discrimination) + RT(response)• RT3 = RT(detect) + RT(discrimination) + RT(choice) +
RT(response)• RT(discrimination) = RT2 - RT1
• RT(choice) = RT3 - RT2
Example: How long does it take to choose between alternatives? (Mental Chronometry)
Criticisms of Donder
• Assumes that adding components does not affect other components (i.e. assumption of pure insertion)
• One should pick tasks that differ along same dimension
• Although resting baseline is good to include, it may limit inference
(e.g. Sternberg, 1964)
What types of hypotheses are possible for fMRI data?
From Scott Huettel, Duke
Experimental Design for fMRI
Hemodynamic Response Function(HRF)
Savoy et al., 1995
Linear Systems Analysis Boynton et al. 1996
• The linear transform model of fMRI hypothesizes that responses are proportional to local average neural activity averaged over a period of time. – fMRI responses in human primary visual cortex (V1) depend on
both stimulus timing (8 Hz) and stimulus contrast (black/white). – Responses to long-duration stimuli can be predicted from HRC
derived from shorter duration stimuli. – The noise in the fMRI data is independent of stimulus contrast
and temporal period.
• Because the linear transform model is consistent with our data, we proceeded to estimate the temporal fMRI response function and the underlying (presumably neural) contrast response function using HRF…
• Assumption is that HRF is linear and shift-invariant!
Linearity of BOLD responseDale & Buckner, 1997
Sync each differential response to start of trial
Not quite linear but good enough for first order approximations
Reversing Checkerboard (8 Hz)
One-trial = 1 stimulus
Two-trial – 2 stimuli
Three-trial = 3 stimuli
Stim duration (SD) = 1 s
Inter-stim interval (ISI) = 2 s
fMRI Design Types
1) Blocked Designs2) Event-Related Designs
a) Periodic Single Trial b) Jittered Single Trial
3) Mixed Designs- Combination blocked/event-
related
Blocked Designs
What are Blocked Designs?
• Blocked designs segregate different cognitive tasks into distinct time periods
Task A Task B Task A Task B Task A Task B Task A Task B
Task A Task BREST REST Task A Task BREST REST
“Loose” vs. “Tight” Block Designs
• Loose: 1 Task, 1 contrast (with Baseline)
• Tight: more than 1 Task, multiple contrasts (including baseline)
Choosing Length of Blocks
• Longer block lengths allow for stability of extended responses– Hemodynamic response saturates following extended stimulation
• After about 10s, activation reaches plateau– Many tasks require extended intervals
• Brain processing may differ throughout the task period
• Shorter block lengths move your signal to higher frequencies– Away from low-frequency noise: scanner drift, etc.– Not possible in O-15 PET rCBF studies
• Periodic blocks may result in aliasing of other variance in the data– Example: if the person breathes at a regular rate of 12
breaths/min and the blocks are 10s long (6 blocks/min)
From Scott Huettel, Duke
Types of Blocked Design
• Task A vs. Task B (… vs. Task C…)– Example: Squeezing Right Hand vs. Left Hand– Allows you to distinguish differential activation
between conditions– Does not allow identification of activity common to
both tasks• Can control for uninteresting activity
• Task A vs. No-task (… vs. Task C…)– Example: Squeezing Right Hand vs. Rest– Shows you activity associated with task– May introduce unwanted results if not matched
properly(e.g. Rest with eyes closed but task had eyes open)
Adapted from Gusnard & Raichle (2001)
Adapted from Gusnard & Raichle (2001)
Oxygen Extractio
n Fraction
Cerebral Metabolic Rate of
O2
Cerebral Blood Flow
A True Baseline?
Depends on what is measured!
Non-Task Processing
• In experiments activation can be greater in baseline conditions than in task conditions!– Requires interpretations of significant activation
• Suggests the idea of baseline/resting mental processes– Gathering/evaluation about the world around you– Awareness (of self)– Online monitoring of sensory information– Daydreaming
• This collection of processes is often called the “Default Mode Network”
Default Mode!
Damoiseaux 2006 analyzed separate 10-subject resting-state data sets, using
Independent Components analysis (ICA).
Vision.
Memory.
Power in Blocked Designs
1. Summation of responses results in large signals then plateaus (at 8-16 s duration)
1. Duration does not plateau
Stimulus duration
and interval
short compared with HRF
What are the temporal limits?What is the shortest stimulus duration that fMRI can detect?
Blamire et al. (1992) – 2 secBandettini (1993): 0.5 secSavoy et al (1995): 34 msec
• With enough averaging, anything seems possible.
• Assume that the shape of the HRF is predictable.
• Event-related potentials (ERPs) are based on averaging small responses over many trials.
• Can we do the same thing with fMRI?
Assumption of steady-state dynamics.
For block designs we assume that the BOLD effect remains constant across the epoch of interest.
For PET this assumption is valid given the half-life of the tracers used to image the brain.
But the BOLD response is much more transient and more importantly may vary according to brain regions and stimulus durations and maybe even stimulus types.
Savoy et al., 1995
Limitations of Blocked Designs
• Sensitive to signal drift or MR instability
• Poor choice of conditions/baseline may preclude meaningful conclusions
• Many tasks cannot be conducted repeatedly
Event-Related Designs
What are Event-Related Designs?
• Event-related designs associate brain processes with discrete events, which may occur at any point in the scanning session.
• Can detect transient BOLD responses• Supports adapting task to response
Buckner et al., 1998
Event RelatedEvent Related
Why use event-related designs?
• Some experimental tasks are naturally event-related (future stimuli based on response)
• Allows studying of within-trial effects• Improves relation to behavioral factors
(behavior changes within blocks missed)• Simple analyses
– Selective averaging– General linear models (GLM)
Single Event
Averaging
Sorting Into Common Groups
- Behavior
- Physiological Measure
- Outlier Rejection
- Transient vs. Task level Responses
Periodic Single Trial Designs
• Stimulus events presented infrequently with long inter-stimulus intervals (ISIs)
500 ms 500 ms 500 ms 500 ms
18 s 18 s 18 s
Trial Spacing Effects: Periodic Designs
8sec 4sec
20sec 12sec
A20
A4
A8
A12
Need the signal amplitude to vary to distinguish responding areas of brain from those with no response.
Bandettini & Cox, 2000 • The optimal inter-stimulus interval (ISI) for a stimulus duration (SD), was determined.
• Empirical Observation: For SD=2sec, ISI=12 to 14 sec.• Theory Predicts: For SD<=2 sec, the optimal repetition interval (RI=ISI+SD)• Theory Predicts: For SD>2sec, RI = 8+(2*SD).
• The statistical power of ER-fMRI relative to blocked-design was determined
• Empirical: For SD=2, ER-fMRI was ~35% lower than that of blocked-design • Simulations that assumed a linear system demonstrated estimate ~65% reduction in power• Difference suggest that the ER-fMRI amplitude is greater than
that predicted by a linear shift-invariant system.
Jittered Single Trial Designs
• Varying the timing of trials within a run• Varying the timing of events within a trial
Effects of Jittering on Response
Stimulus
Response
Jittering allows us to sample BOLD response in more states
Effects of ISI on Detectability
Birn et al, 2002
Jittered ISI
Constant ISI
Detectability
Estimated
Accuracy of
HRF
Max when ½ stims are task state and ½
stims are control state
Dale and Buckner (1997)
Detecting Using Selective Averaging
Low Response
Fewer Samples
Good Response
More Samples
Best Response
Most samples
Visual stim duration = 1 s; acquisition 240 sec
Trials subtracted then correlation analysis with predicted response
Variability of HRF: EvidenceAguirre, Zarahn & D’Esposito, 1998• HRF shows considerable variability between subjects
• Within subjects, responses are more consistent, although there is still some variability between sessions
different subjects
same subject, same session same subject, different session
Variability of HRF: ImplicationsAguirre, Zarahn & D’Esposito, 1998• Generic HRF models (gamma functions) account for 70% of variance• Subject-specific models account for 92% of the variance (22% more!)• Poor modeling reduces statistical power• Less of a problem for block designs than event-related (why?)• Biggest problem with delay tasks where an inappropriate estimate of the initial and final components contaminates the delay component
• Possible solution: model the HRF individually for each subject
• Possible caveat: HRF may also vary between areas, not just subjects• Buckner et al., 1996:
• noted a delay of 0.5-1 sec between visual and prefrontal regions• vasculature difference?• processing latency?
• Bug or feature? • Menon & Kim – mental chronometry
Post-Hoc Sorting of Trials
From Kim and Cabeza, 2007
Using information about fMRI activation at memory encoding to predict behavioral performance at
memory retrieval.
Limitations of Event-Related Designs
• Low power (maybe)– Collecting lots of data, many runs
• The key issues are:– Can my subjects perform the task as
designed?– Are the processes of interest independent
from each other (in time, amplitude, etc.)?
Blocked (solid)
Event-Related (dashed)
Event-related model reaches peak sooner…
… and returns to baseline more
slowly.
In this study, some language-related
regions were better modeled by event-
related.
From Mechelli, et al., 2003
You can model a block with events…
Mixed Designs
Mixed: Combination Blocked/Event
• Both blocked and event-related design aspects are used (for different purposes)– Blocked design: state-dependent effects – Event-related design: item-related effects
• Analyses can model these as separate phenomena, if cognitive processes are independent.– “Memory load effects” vs. “Item retrieval effects”
• Or, interactions can be modeled.– Effects of memory load on item retrieval activation.
Mixed Design
Summary of Experiment Design
• Main Issues to Consider– What design constraints are induced by my task?– What am I trying to measure?– What sorts of non-task-related variability do I want to
avoid?
• Rules of thumb– Blocked Designs:
• Powerful for detecting activation• Useful for examining state changes
– Event-Related Designs: • Powerful for estimating time course of activity• Allows determination of baseline activity• Best for post hoc trial sorting
– Mixed Designs• Best combination of detection and estimation• Much more complicated analyses
What is fMRI Experimental Design?
• Controlling the timing and quality of cognitive operations to influence brain activation
• What can we control?– Stimulus properties (what is presented?)– Stimulus timing (when is it presented?)– Subject instructions (what do subjects do with it?)
• What are the goals of experimental design?– To test specific hypotheses (i.e., hypothesis-driven)– To generate new hypotheses (i.e., data-driven)