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Basics of fMRI Time-Series Analysis

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Title: Understanding Differential Responses in fMRI Through Linear Simulation Author: marc burock Last modified by: greve Created Date: 4/13/1998 11:11:17 PM – PowerPoint PPT presentation

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Title: Basics of fMRI Time-Series Analysis


1
Basics of fMRI Time-Series Analysis
  • Douglas N. Greve

2
fMRI Analysis Overview
3
Overview
  • Neuroanatomy 101
  • fMRI Contrast Mechanism
  • Hemodynamic Response
  • Univariate GLM Analysis
  • Hypothesis Testing

4
Neuroantomy
  • Gray matter
  • White matter
  • Cerebrospinal Fluid

5
Functional Anatomy/Brain Mapping
6
Visual Activation Paradigm
Flickering Checkerboard
Visual, Auditory, Motor, Tactile, Pain,
Perceptual, Recognition, Memory, Emotion,
Reward/Punishment, Olfactory, Taste, Gastral,
Gambling, Economic, Acupuncture, Meditation, The
Pepsi Challenge,
  • Scientific
  • Clinical
  • Pharmaceutical

7
MRI Scanner
8
Magnetic Resonance Imaging
BOLD-weighted Contrast
T1-weighted Contrast
9
Blood Oxygen Level Dependence (BOLD)
Neurons
Deoxygenated Hemoglobin (ParaMagnetic)
Oxygenated Hemoglobin (DiaMagnetic)
Lungs
Contrast Agent
Oxygen
CO2
10
Functional MRI (fMRI)
Sample BOLD response in 4D Space (3D) voxels
(64x64x35, 3x3x5mm3, 50,000) Time (1D) time
points (100, 2 sec) Movie
Time 3
Time 1
Time 2
11
4D Volume
85x1
64x64x35
12
Visual/Auditory/Motor Activation Paradigm
  • 15 sec ON, 15 sec OFF
  • Flickering Checkerboard
  • Auditory Tone
  • Finger Tapping

13
Block Design 15s Off, 15s On
Voxel 1
Voxel 2
14
Contrasts and Inference
Voxel 1
Voxel 2
p 10-11, sig-log10(p) 11
p .10, sig-log10(p) 1
15
Statistical Parametric Map (SPM)
Significance t-Map (p,z,F) (Thresholded plt.01)
Contrast Amplitude bON-bOFF
Contrast Amplitude Variance (Error Bars)
Massive Univariate Analysis -- Analyze
each voxel separately
16
Statistical Parametric Map (SPM)
Signficance Map sig-log10(p) Signed by
contrast Massive Univariate Analysis --
Analyze each voxel separately
17
Hemodynamics
  • Delay
  • Dispersion
  • Grouping by simple time point inaccurate

18
Hemodynamic Response Function (HRF)
TR (2sec)
Equilibrium (16-32sec)
Delay (1-2sec)
19
Convolution with HRF
  • Shifts, rolls off more accurate
  • Loose ability to simply group time points
  • More complicated analysis
  • General Linear Model (GLM)

20
GLM
Data fom one voxel
Baseline Offset (Nuisance)
Task

bTask
bbase

bbaseboff
  • bTaskbon-boff
  • Implicit Contrast
  • HRF Amplitude

21
Matrix Model
y X b
bTask bbase

Observations
Vector of Regression Coefficients (Betas)
Design Matrix
Design Matrix Regressors
Data from one voxel
22
Two Task Conditions
y X b
bOdd bEven bbase

Observations
Design Matrix
Design Matrix Regressors
Data from one voxel
23
Working Memory Task (fBIRN)
0. Scrambled low-level baseline, no
response 1. Encode series of passively viewed
stick figures Distractor respond if there is a
face 2. Emotional 3. Neutral Probe
series of two stick figures (forced choice) 4.
Following Emotional Distractor 5. Following
Neutral Distractor
fBIRN Functional Biomedical Research Network
(www.nbirn.net)
24
Five Task Conditions
y X b
bEncode bEmotDist bNeutDist bEmotProbe bNeutProbe

25
GLM Solution
y X b
  • Set of simultaneous equations
  • Each row of X is an equation
  • Each column of X is an unknown
  • bs are unknown
  • 142 Time Points (Equations)
  • 5 unknowns


26
Estimation of bs
27
Estimates of the HRF Amplitude

28
Hypotheses and Contrasts
Which voxels respond more/less/differently to the
Emotional Distractor than to the Neutral
Distractor?
Contrast Assign Weights to each Beta
29
Hypotheses
  • Which voxels respond more to the Emotional
    Distractor than to the Neutral Distractor?
  • Which voxels respond to Encode (relative to
    baseline)?
  • Which voxels respond to the Emotional
    Distractor?
  • Which voxels respond to either Distractor?
  • Which voxels respond more to the Probe following
    the Emotional Distractor than to the Probe
    following the Neutral Distractor?

30
Which voxels respond more to the Emotional
Distractor than to the Neutral Distractor?
  • Only interested in Emotional and Neutral
    Distractors
  • No statement about other conditions

Condition 1 2 3 4 5 Weight 0 1 -1 0 0
Contrast Matrix C 0 1 -1 0 0
31
Which voxels respond to Encode (relative to
baseline)?
  • Only interested in Encode
  • No statement about other conditions

Condition 1 2 3 4 5 Weight 1 0 0 0 0
Contrast Matrix C 1 0 0 0 0
32
Which voxels respond to the Emotional Distractor
(wrt baseline)?
  • Only interested in Emotional Distractor
  • No statement about other conditions

Condition 1 2 3 4 5 Weight 0 1 0 0 0
Contrast Matrix C 0 1 0 0 0
33
Which voxels respond to either Distractor (wrt
baseline)?
  • Only interested in Distractors
  • Average of two Distractors
  • No statement about other conditions

Condition 1 2 3 4 5 Weight 0 ½ ½ 0 0
Contrast Matrix C 0 0.5 0.5 0 0
  • Dont have so sum to 1, but usual
  • Could have used an F-test instead of average

34
Which voxels respond more to the Probe following
the Emotional Distractor than to the Probe
following the Neutral Distractor?
  • Only interested in Probes
  • No statement about other conditions

Condition 1 2 3 4 5 Weight 0 0 0 1 -1
Contrast Matrix C 0 0 0 1 -1
35
Contrasts and the Full Model
36
fMRI Analysis Overview
37
Time Series Analysis Summary
  • Correlational
  • Design Matrix (HRF shape)
  • Estimate HRF amplitude (Parameters)
  • Contrasts to test hypotheses
  • Results at each voxel
  • Contrast Value
  • Contrast Value Variance
  • p-value (Volume of Activation)
  • Pass Contrast Value and Variance up to higher
    level analyses

38
(No Transcript)
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