Issues in Experimental Design fMRI Graduate Course October 26, 2005.
Experimental design of fMRI studies
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Transcript of Experimental design of fMRI studies
Experimental design of fMRI studies
Methods & models for fMRI data analysisNovember 2012
Sandra Iglesias
Translational Neuromodeling Unit (TNU)Institute for Biomedical Engineering, University of Zurich & ETH Zurich
With many thanks for slides & images to:
Klaas Enno Stephan,FIL Methods group, particularly Christian Ruff
Overview of SPM
Realignment Smoothing
Normalisation
General linear model
Statistical parametric map (SPM)Image time-series
Parameter estimates
Design matrix
Template
Kernel
Gaussian field theory
p <0.05
Statisticalinference
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Overview of SPM
General linear model
Statistical parametric map (SPM)
Parameter estimates
Design matrix
Gaussian field theory
p <0.05
Statisticalinference
Research question:Which neuronal structures support face recognition?
Hypothesis:The fusiform gyrus is
implicated in face recognition
Experimental design
• Categorical designsSubtraction - Pure insertion, evoked / differential
responsesConjunction - Testing multiple hypotheses
• Parametric designsLinear - Adaptation, cognitive dimensionsNonlinear - Polynomial expansions, neurometric
functions • Factorial designs
Categorical - Interactions and pure insertionParametric - Linear and nonlinear interactions
- Psychophysiological Interactions
Overview
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• Aim: – Neuronal structures underlying a single process P?
• Procedure: – Contrast: [Task with P] – [control task without P ] = P the critical assumption of „pure insertion“
• Example:
Cognitive subtraction
[Task with P] – [task without P ] = P
– =
– =
- P implicit in control condition?
„Queen!“ „Aunt Jenny?“
• „Related“ stimuli
- Several components differ!
• „Distant“ stimuli
Name Person! Name Gender!
- Interaction of task and stimuli (i.e. do task differences depend on stimuli chosen)?
• Same stimuli, different task
Cognitive subtraction: Baseline problems
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A categorical analysis
Experimental design
Face viewing FObject viewing O
F - O = Face recognitionO - F = Object recognition
…under assumption of pure insertion
Kanwisher N et al. J. Neurosci. 1997;
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Categorical design
• Categorical designsSubtraction - Pure insertion, evoked / differential
responsesConjunction - Testing multiple hypotheses
• Parametric designsLinear - Adaptation, cognitive dimensionsNonlinear - Polynomial expansions, neurometric
functions • Factorial designs
Categorical - Interactions and pure insertionParametric - Linear and nonlinear interactions
- Psychophysiological Interactions
Overview
• One way to minimise the baseline/pure insertion problem is to isolate the same process by two or more separate comparisons, and inspect the resulting simple effects for commonalities
• A test for such activation common to several independent contrasts is called “conjunction”
• Conjunctions can be conducted across a whole variety of different contexts:• tasks• stimuli• senses (vision, audition)• etc.
• Note: the contrasts entering a conjunction must be orthogonal !
Conjunctions
ConjunctionsExample: Which neural structures support object recognition,
independent of task (naming vs. viewing)?
Task (1/2)
Viewing Naming
Stim
uli (
A/B
)O
bjec
ts
Col
ours
Visual Processing V Object Recognition RPhonological Retrieval P
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A1 A2
B1 B2
Conjunctions
(Object - Colour viewing) [B1 - A1] &
(Object - Colour naming) [B2 – A2]
[ V,R - V ] & [ P,V,R - P,V ] = R & R = R
Price et al. 1997 Common object recognition response (R)
A1 B1 A2 B212
A1Visual Processing V
B1Visual Processing V Object Recognition R
B2Visual Processing V Phonological Retrieval PObject Recognition R
A2Visual Processing V Phonological Retrieval P
Stim
uli (
A/B
)O
bjec
ts
C
olou
rs
Task (1/2) Viewing Naming
Which neural structures support object recognition?
Conjunctions
• Test of global null hypothesis: Significant set of consistent effects
“Which voxels show effects of similar direction (but not necessarily individual significance) across contrasts?”
Null hypothesis: No contrast is significant: k = 0 does not correspond to a logical AND !
• Test of conjunction null hypothesis: Set of consistently significant effects
“Which voxels show, for each specified contrast, significant effects?”
Null hypothesis: Not all contrasts are significant: k < n
corresponds to a logical AND
A1-A2
B
1-B
2 p(A1-A2) <
+p(B1-B2) <
+
Friston et al. (2005). Neuroimage, 25:661-667.
Nichols et al. (2005). Neuroimage, 25:653-660.
Two types of conjunctions
SPM offers both types of conjunctions
Friston et al. 2005, Neuroimage, 25:661-667.
specificity
sensitivity
Global null:k = 0
(or k<1)
Conjunction null:k < n
F-test vs. conjunction based on global null
Friston et al. 2005, Neuroimage, 25:661-667.
grey area:bivariate t-distriutionunder global null hypothesis
• Categorical designsSubtraction - Pure insertion, evoked / differential
responsesConjunction - Testing multiple hypotheses
• Parametric designsLinear - Adaptation, cognitive dimensionsNonlinear - Polynomial expansions, neurometric
functions • Factorial designs
Categorical - Interactions and pure insertionParametric - Linear and nonlinear interactions
- Psychophysiological Interactions
Overview
Parametric designs
• Parametric designs approach the baseline problem by:
– Varying the stimulus-parameter of interest on a continuum, in multiple (n>2) steps...
– ... and relating measured BOLD signal to this parameter
• Possible tests for such relations are manifold:• Linear• Nonlinear: Quadratic/cubic/etc. (polynomial expansion)• Model-based (e.g. predictions from learning models)
Parametric modulation of regressors by time
Büchel et al. 1998, NeuroImage 8:140-148
“User-specified” parametric modulation of regressors
Polynomial expansion&orthogonalisation
Büchel et al. 1998, NeuroImage 8:140-148
Investigating neurometric functions (= relation between a stimulus property and the neuronal
response)
Stimulusawareness
Stimulusintensity
PainintensityPain threshold: 410 mJ
P1 P2 P3 P4P0-P4: Variation of intensity of a laser stimulus applied to the right hand (0, 300, 400, 500, and 600 mJ)
Büchel et al. 2002, J. Neurosci. 22:970-976
Neurometric functions
Stimulus presence
Pain intensity
Stimulus intensity
Büchel et al. 2002, J. Neurosci. 22:970-976
Model-based regressors
• general idea:generate predictions from a computational model, e.g. of learning or decision-making
• Commonly used models:– Rescorla-Wagner learning model– temporal difference (TD) learning model– Bayesian learners
• use these predictions to define regressors
• include these regressors in a GLM and test for significant correlations with voxel-wise BOLD responses
Model-based fMRI analysis
Gläscher & O‘Doherty 2010, WIREs Cogn. Sci.
Model-based fMRI analysis
Gläscher & O‘Doherty 2010, WIREs Cogn. Sci.
Learning of dynamic audio-visual associations
CS Response
Time (ms)
0 200 400 600 800 2000 ± 650
or
Target StimulusConditioning Stimulus
or
TS
0 200 400 600 800 10000
0.2
0.4
0.6
0.8
1
p(fa
ce)
trial
CS1
CS2
den Ouden et al. 2010, J. Neurosci .
Bayesian learning model
observed events
probabilistic association
volatility
k
vt-1 vt
rt rt+1
ut ut+1
)exp(,~,|1 ttttt vrDirvrrp
)exp(,~,|1 kvNkvvp ttt
1kp
1: 1 1 1 1 1 1 1: 1 1 1
1: 11:
1: 1
prediction: , , , , , ,
, ,update: , ,
, ,
t t t t t t t t t t t t t
t t t t tt t t
t t t t t t t
p r v K u p r r v p v v K p r v K u dr dv
p r v K u p u rp r v K u
p r v K u p u r dr dv dK
Behrens et al. 2007, Nat. Neurosci.
Putamen Premotor cortex
Stimulus-independent prediction error
p < 0.05 (SVC)
p < 0.05 (cluster-level whole- brain corrected)
p(F) p(H)-2
-1.5
-1
-0.5
0
BO
LD re
sp. (
a.u.
)
p(F) p(H)-2
-1.5
-1
-0.5
0
BO
LD re
sp. (
a.u.
)
den Ouden et al. 2010, J. Neurosci.
• Categorical designsSubtraction - Pure insertion, evoked / differential
responsesConjunction - Testing multiple hypotheses
• Parametric designsLinear - Adaptation, cognitive dimensionsNonlinear - Polynomial expansions, neurometric
functions • Factorial designs
Categorical - Interactions and pure insertionParametric - Linear and nonlinear interactions
- Psychophysiological Interactions
Overview
Main effects and interactions
A1 A2
B2B1
Task (1/2)Viewing Naming
Stim
uli (
A/B
)
Obj
ects
C
olou
rs• Main effect of task: (A1 + B1) – (A2 +
B2)
• Main effect of stimuli: (A1 + A2) – (B1 + B2)
• Interaction of task and stimuli: Can show a failure of pure insertion
(A1 – B1) – (A2 – B2)
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Factorial design
A1 A2
B2B1
Task (1/2)Viewing Naming
Stim
uli (
A/B
)
Obj
ects
C
olou
rs
A1 B1 A2 B2
Main effect of task: (A1 + B1) – (A2 + B2)
32
Factorial design
A1 A2
B2B1
Task (1/2)Viewing Naming
Stim
uli (
A/B
)
Obj
ects
C
olou
rs
A1 B1 A2 B2
Main effect of stimuli: (A1 + A2) – (B1 + B2)
33
Factorial design
A1 A2
B2B1
Task (1/2)Viewing Naming
Stim
uli (
A/B
)
Obj
ects
C
olou
rs
A1 B1 A2 B2
Interaction of task and stimuli: (A1 – B1) – (A2 – B2)
Main effects and interactions
A1 A2
B2B1
Task (1/2)Viewing Naming
Stim
uli (
A/B
)
Obj
ects
C
olou
rs
Colours Objects
interaction effect (Stimuli x Task)
Viewing Naming
• Main effect of task: (A1 + B1) – (A2 + B2)
• Main effect of stimuli: (A1 + A2) – (B1 + B2)
• Interaction of task and stimuli: Can show a failure of pure insertion
(A1 – B1) – (A2 – B2)
Colours Objects
is the inferotemporal region implicated inphonological retrieval during object naming?
Example: evidence for inequality-aversion
Tricomi et al. 2010, Nature
Psycho-physiological interactions (PPI)
We can replace one main effect in the GLM by the time series of an area that shows this main effect.E.g. let's replace the main effect of stimulus type by the time series of area V1:
Task factorTask A Task B
Stim
1St
im 2
Stim
ulus
fact
or
TA/S1 TB/S1
TA/S2 TB/S2
eβVTT
βVTT y
BA
BA
3
2
1
1 )(1
)(
eβSSTT
βSSTT y
BA
BA
321
221
1
)( )()(
)(
GLM of a 2x2 factorial design:
main effectof taskmain effectof stim. type
interaction
main effectof taskV1 time series main effectof stim. typepsycho-physiologicalinteraction
PPI example: attentional modulation of V1→V5
attention
no attention
V1 activity
V5 a
ctiv
ity
SPM{Z}
time
V5 a
ctiv
ityFriston et al. 1997, NeuroImage 6:218-229Büchel & Friston 1997, Cereb. Cortex 7:768-778
V1
V1 x Att.
=V5
V5
Attention
PPI: interpretation
Two possible interpretations of the PPI
term:
V1
Modulation of V1V5 by attention
Modulation of the impact of attention on V5 by V1.
V1 V5 V1
V5
attention
V1
attention
eβVTT
βVTT y
BA
BA
3
2
1
1 )(1
)(
Thank you