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Page 1: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Basic fMRI Design and Analysis

Preprocessing

Page 2: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

fMRI Preprocessing

• Slice timing correction

• Geometric distortion correction

• Head motion correction

• Temporal filtering

• Intensity normalization

• Spatial filtering

Page 3: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

fMRI Preprocessing

• Slice timing correction

• Geometric distortion correction

• Head motion correction

• Temporal filtering

• Intensity normalization

• Spatial filtering

Page 4: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Slice timing

correction Smoothing

Normalization

General linear model

Image

time series

Parameter estimates

Design matrix

Template

Kernel

Field map

Realignment

FIL Methods Group

Outlier

Detection

Page 5: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

EPI Data Are Acquired Serially

Page 6: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

descending

EPI Data Are Acquired Serially

Page 7: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

interleaved

descending

EPI Data Are Acquired Serially

Page 8: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

interleaved

descending

EPI Data Are Acquired Serially

Page 9: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Two Approaches to Slice Timing

Correction

• Addition of temporal

basis functions to the

first-level statistical

model

• Correction using

temporal interpolation

?

Page 10: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Slice Timing Correction

Time

Slic

e

TR

Page 11: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Slice Timing Correction

Time

Slic

e

reference

slice

interpolation

Page 12: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Sladky et al., Neuroimage (2011)

Slice Time Correction Improves Sensitivity Using

a Visuomotor Task

Page 13: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

What is the best time to do

slice timing correction?

Slice timing correction can be done either before or after realignment, depending on the amount of head motion.

Field map

Realignment

Realignment

Page 14: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Slice Timing

•Siemens system

•For interleaved acquisition

• If odd number of slices:

– 1,3,5,7,…..2,4,6,8….

If even number of slices:

2,4,6,….24,1,3,5,7…23 E.g. [2:2:24 1:2:23]

Acquisition is from inferior -> superior

Page 15: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

fMRI Preprocessing

• Slice timing correction

• Geometric distortion correction

• Head motion correction

• Temporal filtering

• Intensity normalization

• Spatial normalization

• Spatial filtering

Page 16: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Slice timing

correction Smoothing

Normalization

General linear model

Image

time series

Parameter estimates

Design matrix

Template

Kernel

Field map

Realignment

FIL Methods Group

Outlier

Detection

Page 17: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Signal Dropout and Geometric Distortion

Page 18: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Jezzard and Balaban, MRM (1995)

Page 19: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Original EPI

Corrected EPI

Page 20: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

fMRI Preprocessing

• Slice timing correction

• Geometric distortion correction

• Head motion correction

• Temporal filtering

• Intensity normalization

• Spatial normalization

• Spatial filtering

Page 21: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Head Motion in fMRI

• The goal is to compare brain locations across

time

• Subjects move relative to the recording system

• Individual voxel time series are affected by this

motion

• Motion effects on signal amplitude are non-

linear and complex

• Motion therefore inflates the residual variance

and reduces detection sensitivity

• Task correlated motion is particularly

problematic

Page 22: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Head Motion Can Cause Partial

Volume and Spin History Effects

50%

Page 23: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

100%

Head Motion Can Cause Partial

Volume and Spin History Effects

Page 24: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

50%

Head Motion Can Cause Partial

Volume and Spin History Effects

Page 25: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

0%

Head Motion Can Cause Partial

Volume and Spin History Effects

Page 26: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

50%

Head Motion Can Cause Partial

Volume and Spin History Effects

Page 27: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Whitfield-Gabrieli

Head Motion Can Cause Partial

Volume and Spin History Effects

Page 28: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Head Motion Detection

•compute time series center-of-intensity

•compute variance map of time series

• single-slice animation

Page 29: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Head Motion Detection

•compute time series center-of-intensity

Page 30: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Head Motion Detection

•compute time series center-of-intensity

•compute variance map of time series

• single-slice animation

Page 31: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel
Page 32: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Mitigation of Head Motion Effects

• Prevention

• Prospective correction

• Realignment

• Covariate correction with head motion estimates

• Movement by distortion effect correction with fieldmaps

• Covariate correction with outlier identification

Page 33: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Mitigation of Head Motion Effects

• Prevention

• Prospective correction

• Realignment

• Covariate correction with head motion estimates

• Movement by distortion effect correction with fieldmaps

• Covariate correction with outlier identification

Page 34: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel
Page 35: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Mitigation of Head Motion Effects

• Prevention

• Prospective correction

• Realignment

• Covariate correction with head motion estimates

• Movement by distortion effect correction with fieldmaps

• Covariate correction with outlier identification

Page 36: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Prospective Motion Correction

time

?

Prospective motion correction makes predictions that

may be dependent on outdated information.

Page 37: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

“We drive into the future using only our

rearview mirror.” - Marshall McLuhan

Page 38: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Mitigation of Head Motion Effects

• Prevention

• Prospective correction

• Realignment

• Covariate correction with head motion estimates

• Movement by distortion effect correction with fieldmaps

• Covariate correction with outlier identification

Page 39: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Slice timing

correction Smoothing

Normalization

General linear model

Image

time series

Parameter estimates

Design matrix

Template

Kernel

Field map

Realignment

FIL Methods Group

Outlier

Detection

Page 40: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Spatial Realignment

•Realignment (of same-modality images from

same subject) involves two stages:

– Registration - determining the 6 parameters that

describe the rigid body transformation between

each image and a reference image

– Reslicing - re-sampling each image according

to the determined transformation parameters

Henson

Page 41: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Spatial Realignment

Henson

Yaw

Roll

Translation

Rotation

X

Y

Z

Pitch

Page 42: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Spatial Realignment: Registration

• Determine the rigid body transformation that minimises the sum of

squared difference between images

• Rigid body transformation is defined by:

– 3 translations - in X, Y & Z directions

– 3 rotations - about X, Y & Z axes

• Operations can be represented as affine

transformation matrices:

x1 = m1,1x0 + m1,2y0 + m1,3z0 + m1,4

y1 = m2,1x0 + m2,2y0 + m2,3z0 + m2,4

z1 = m3,1x0 + m3,2y0 + m3,3z0 + m3,4

Squared Error

Henson

Page 43: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

•Iterative procedure

(Gauss-Newton

ascent)

•Additional scaling

parameter

•Nx6 matrix of

realignment

parameters written to

file (N is number of

scans)

•Orientation matrices

in header of image

file (data not changed

until reslicing)

Spatial Realignment: Registration

Henson

Page 44: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

•Application of registration parameters involves re-sampling the image to create new voxels by interpolation from existing voxels

•Interpolation can be nearest neighbour (0-order), tri-linear (1st-order), (windowed) fourier/sinc, or nth-order “b-splines”

d1 d2

d3

d4

v1

v4

v2

v3

Nearest Neighbour

Linear

Full sinc (no alias)

Windowed

sinc

Henson

Spatial Realignment: Reslicing

Page 45: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

before

correction

after

correction

Page 46: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Effects of Realignment on

Statistical Maps

before

after

Page 47: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Residual Error After Realignment

Even after realignment a considerable amount of the

variance can be accounted for by movement

Causes:

1. Movement between and within slice

acquisition

2. Interpolation artifacts due to resampling

3. Non-linear distortions and drop-out due to

inhomogeneity of the magnetic field

Page 48: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Mitigation of Head Motion Effects

• Prevention

• Prospective correction

• Realignment

• Covariate correction with head motion estimates

• Movement by distortion effect correction with fieldmaps

• Covariate correction with outlier identification

Page 49: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel
Page 50: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Realignment with Movement

Covariates

Friston et al., Movement-related effects in fMRI

time series. Magn. Reson. Med. 35:346-355

(1996)

- estimate motion parameters

- use estimates as confounds in the

statistical model

Page 51: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Slice timing

correction Smoothing

Normalization

General linear model

Image

time series

Parameter estimates

Design matrix

Template

Kernel

Field map

Realignment

FIL Methods Group

Outlier

Detection

Page 52: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

tmax=13.38

No correction

tmax=5.06

Covariate

correction

tmax=9.57

Unwarp

correction

Movement Correction

FIL Methods Group

Page 53: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Mitigation of Head Motion Effects

• Prevention

• Prospective correction

• Realignment

• Covariate correction with head motion estimates

• Movement by distortion effect correction with fieldmaps

• Covariate correction with outlier identification

Page 54: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Original EPI

Corrected EPI

Page 55: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Movement-by-Distortion Interactions

Time dependent fMRI signal changes are

dependent upon:

•position of the object in the scanner

geometric distortion

B0 field effects

slice select gradient edge effects

•history of the position of the object

spin history effects

Page 56: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Movement-by-Distortion Interactions

FIL Methods Group

Page 57: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

tmax=13.38

No correction

tmax=5.06

Covariate

correction

tmax=9.57

Unwarp

correction

Movement Correction

FIL Methods Group

Page 58: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Mitigation of Head Motion Effects

• Prevention

• Prospective correction

• Realignment

• Covariate correction with head motion estimates

• Movement by distortion effect correction with fieldmaps

• Covariate correction with outlier identification

Page 59: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Outlier Identification

Translation

Rotation

Global

mean

Global

Std. Dev.

Page 60: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Outliers

Thresholds

MOTION

OUTLIERS

INTENSITY

OUTLIERS

COMBINED

OUTLIERS

Translation

Rotation

Global

mean

Std. Dev.

Page 61: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Slice timing

correction Smoothing

Normalization

General linear model

Image

time series

Parameter estimates

Design matrix

Template

Kernel

Field map

Realignment

FIL Methods Group

Outlier

Detection

Page 62: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

fMRI Preprocessing

• Slice timing correction

• Geometric distortion correction

• Head motion correction

• Temporal filtering

• Intensity normalization

• Spatial normalization

• Spatial filtering

Page 63: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Temporal Filtering

Time

Page 64: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Lund et al., Neuroimage (2006)

Respiration Modulates BOLD Contrast

Page 65: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Lund et al., Neuroimage (2006)

Cardiac Motion Modulates BOLD Contrast

Page 66: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Birn et al., Neuroimage (2006)

Respiration

Modulates BOLD

Contrast Time

Series

Page 67: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Birn et al., Neuroimage (2006)

Respiration Modulates BOLD Contrast

Page 68: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Birn et al., Neuroimage (2006)

Respiration Modulates BOLD Contrast at Rest

Page 69: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Birn et al., Neuroimage (2006)

Respiration Modulates BOLD Contrast at Rest

Page 70: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Cardiovascular and Respiratory Artifacts

Poncelet et al., Brain parenchyma motion: measurement with

cine echo-planar MR imaging. Radiology 185:645-651

(1992).

Biswal et al., Reduction of physiological fluctuations in fMRI

using digital filters. Magn. Reson. Med. 35:107-113 (1996).

Hu et al., Retrospective estimation and correction of

physiological fluctuation in functional MRI. Magn. Reson.

Med. 34:201-212 (1995).

Page 71: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Slice timing

correction Smoothing

Normalization

General linear model

Image

time series

Parameter estimates

Design matrix

Template

Kernel

Field map

Realignment

FIL Methods Group

Outlier

Detection

Page 72: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Regressors (m)

High-Pass Filter

Time

(n)

Regressors (m)

Task Effect

Page 73: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

fMRI Preprocessing

• Slice timing correction

• Geometric distortion correction

• Head motion correction

• Temporal filtering

• Intensity normalization

• Spatial filtering

Page 74: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel
Page 75: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Global Intensity Variation

•machine instability

•global blood flow changes

– arousal

– respiratory effects

– drug effects

Page 76: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Global Intensity Correction

•Proportional global intensity

normalization

•ANCOVA global intensity

normalization

Page 77: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

No Global

Intensity Correction

Proportional Global

Intensity Correction

ANCOVA Global

Intensity Correction

Page 78: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Global Intensity Correction

• Global intensity normalization per

time point

– PET

•Global intensity normalization per

session

– fMRI

Page 79: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Time

Global Intensity Normalization

420 440 470 380 420 400 390

Intensity normalization per time point

Page 80: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Time

Global Intensity Normalization

500 500 500 500 500 500 500

Intensity normalization per time point

Page 81: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Time

Global Intensity Normalization

Intensity normalization per session

480

Page 82: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Slice timing

correction Smoothing

Normalization

General linear model

Image

time series

Parameter estimates

Design matrix

Template

Kernel

Field map

Realignment

FIL Methods Group

Outlier

Detection

Page 83: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

fMRI Preprocessing

• Slice timing correction

• Geometric distortion correction

• Head motion correction

• Temporal filtering

• Intensity normalization

• Spatial filtering

Page 84: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Spatial filtering

Page 85: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Slice timing

correction Smoothing

Normalization

General linear model

Image

time series

Parameter estimates

Design matrix

Template

Kernel

Field map

Realignment

FIL Methods Group

Outlier

Detection

Page 86: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Spatial Filtering

Time

Page 87: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Gaussian Kernel

amplitude

1

0

space

FWHM

Page 88: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Spatial Filtering

Slice from

nonsmoothed noise

volume

voxel size 1mm3

Same slice after 8mm

isotropic smoothing

Page 89: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

How much smoothing?

• Noise reduction

• Spatial normalization compensation

• Matched filter theorem

Page 90: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

fMRI Preprocessing

• Slice timing correction

• Geometric distortion correction

• Head motion correction

• Temporal filtering

• Intensity normalization

• Spatial filtering

Page 91: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

Realignment Smoothing

Normalization

General linear model

Statistical parametric map (SPM) Image

time series

Parameter estimates

Design matrix

Template

Kernel

Gaussian

field theory

p <0.05

Statistical

inference

FIL Methods Group

Page 92: Basic fMRI Design and Analysis Preprocessing...Slice timing correction Smoothing General linear model Normalization Image time series Parameter estimates Design matrix Template Kernel

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