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SPM12 Manual

SPM12 Manual

The FIL Methods Group

(and honorary members)

John Ashburner

Gareth Barnes

Chun-Chuan Chen

Jean Daunizeau

Guillaume Flandin

Karl Friston

Darren Gitelman

Volkmar Glauche

Rik Henson

Chloe Hutton

Amirhossein Jafarian

Stefan Kiebel

James Kilner

Vladimir Litvak

Jérémie Mattout

Rosalyn Moran

Will Penny

Christophe Phillips

Adeel Razi

Klaas Stephan

Sungho Tak

Ashley Tyrer

Peter Zeidman

Functional Imaging Laboratory

Wellcome Centre for Human Neuroimaging

UCL Queen Square Institute of Neurology

12 Queen Square, London WC1N 3BG, UK

October 15, 2021

https://www.fil.ion.ucl.ac.uk/spm/ 2

Contents

I Temporal processing

19

1 Slice Timing21

1.1 Data

22

1.1.1 Session

22

1.2 Number of Slices

22

1.3 TR

22

1.4 TA

22

1.5 Slice order

22

1.6 Reference Slice

23

1.7 Filename Prefix

23

II Spatial processing

25

2 Realign27

2.1 Realign: Estimate

27

2.1.1 Data

27

2.1.2 Estimation Options

2 8

2.2 Realign: Reslice

29

2.2.1 Images

2 9

2.2.2 Reslice Options

29

2.3 Realign: Estimate & Reslice

30

2.3.1 Data

30

2.3.2 Estimation Options

3 0

2.3.3 Reslice Options

31

3 Realign & Unwarp

33

3.1 Data

36

3.1.1 Session

36

3.2 Estimation Options

36

3.2.1 Quality

36

3.2.2 Separation

36

3.2.3 Smoothing (FWHM)

36

3.2.4 Num Passes

37

3.2.5 Interpolation

37

3.2.6 Wrapping

37

3.2.7 Weighting

37

3.3 Unwarp Estimation Options

37

3.3.1 Basis Functions

37

3.3.2 Regularisation

37

3.3.3 Reg. Factor

37

3.3.4 Jacobian deformations

38

3.3.5 First-order effects

38

3.3.6 Second-order effects

38

3.3.7 Smoothing for unwarp (FWHM)

38
3

4CONTENTS

3.3.8 Re-estimate movement params

38

3.3.9 Number of Iterations

38

3.3.10 Taylor expansion point

38

3.4 Unwarp Reslicing Options

3 9

3.4.1 Resliced images (unwarp)?

39

3.4.2 Interpolation

39

3.4.3 Wrapping

39

3.4.4 Masking

39

3.4.5 Filename Prefix

39

4 Coregister41

4.1 Coregister: Estimate

41

4.1.1 Fixed Image

42

4.1.2 Moved Image

42

4.1.3 Other Images

42

4.1.4 Estimation Options

4 2

4.2 Coregister: Reslice

4 2

4.2.1 Image Defining Space

42

4.2.2 Images to Reslice

4 2

4.2.3 Reslice Options

43

4.3 Coregister: Estimate & Reslice

4 3

4.3.1 Fixed Image

43

4.3.2 Moved Image

44

4.3.3 Other Images

44

4.3.4 Estimation Options

4 4

4.3.5 Reslice Options

44

5 Segment47

5.1 Data

48

5.1.1 Channel

48

5.2 Tissues

49

5.2.1 Tissue

49

5.3 Warping & MRF

5 0

5.3.1 MRF Parameter

50

5.3.2 Clean Up

51

5.3.3 Warping Regularisation

51

5.3.4 Affine Regularisation

51

5.3.5 Smoothness

52

5.3.6 Sampling distance

52

5.3.7 Deformation Fields

52

5.3.8 Voxel sizes

52

5.3.9 Bounding box

5 2

6 Normalise53

6.1 Normalise: Estimate

5 3

6.1.1 Data

54

6.1.2 Estimation Options

5 4

6.2 Normalise: Write

5 5

6.2.1 Data

55

6.2.2 Writing Options

5 6

6.3 Normalise: Estimate & Write

5 6

6.3.1 Data

56

6.3.2 Estimation Options

5 7

6.3.3 Writing Options

5 8

CONTENTS5

7 Smooth59

7.1 Images to smooth

59

7.2 FWHM

59

7.3 Data Type

59

7.4 Implicit masking

59

7.5 Filename prefix

60

III fMRI Statistics

61

8 fMRI model specification

63

8.1 Timing parameters

63

8.1.1 Units for design

6 4

8.1.2 Interscan interval

64

8.1.3 Microtime resolution

64

8.1.4 Microtime onset

64

8.2 Data & Design

6 5

8.2.1 Subject/Session

66

8.3 Factorial design

67

8.3.1 Factor

68

8.4 Basis Functions

6 8

8.4.1 Canonical HRF

68

8.4.2 Other basis sets

6 8

8.5 Model Interactions (Volterra)

69

8.6 Directory

69

8.7 Global normalisation

69

8.8 Explicit mask

69

8.9 Serial correlations

70

8.10 Reviewing your design

70

9 fMRI model estimation

73

9.1 Select SPM.mat

73

9.2 Method

73

9.2.1 Classical

73

9.2.2 Bayesian 1st-level

74

9.2.3 Bayesian 2nd-level

77

9.3 Output files

78

9.3.1 Classical 1st-level

78

9.3.2 Bayesian 1st-level

78

9.4 Model comparison

78

10 Factorial design specification

81

10.1 Directory

82

10.2 Design

82

10.2.1 One-sample t-test

82

10.2.2 Two-sample t-test

82

10.2.3 Paired t-test

83

10.2.4 Multiple regression

83

10.2.5 One-way ANOVA

84

10.2.6 One-way ANOVA - within subject

85

10.2.7 Full factorial

86

10.2.8 Flexible factorial

88

10.3 Covariates

90

10.3.1 Covariate

90

10.4 Multiple covariates

90

10.4.1 Covariates

91

10.5 Masking

91

6CONTENTS

10.5.1 Threshold masking

91

10.5.2 Implicit Mask

92

10.5.3 Explicit Mask

92

10.6 Global calculation

92

10.6.1 Omit

92

10.6.2 User

92

10.6.3 Mean

93

10.7 Global normalisation

9 3

10.7.1 Overall grand mean scaling

93

10.7.2 Normalisation

93

IV EEG/MEG

95

11 SPM for MEG/EEG overview

97

11.1 Welcome to SPM for M/EEG

97

11.2 Changes from SPM8 to SPM12

98

12 EEG/MEG preprocessing - Reference

99

12.1 Conversion of data

99

12.2 Converting arbitrary data

101

12.3 The M/EEG SPM format

101

12.4 Preparing the data after conversion and specifying batch inputs

102

12.4.1 Prepare (batch)

106

12.5 Integration of SPM and Fieldtrip

106

12.6 Loading data into workspace

106

12.7 Themeegobject. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

12.7.1 Constructormeeg. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .107

12.7.2 Array-like interface

107

12.7.3 display

107

12.7.4 Number methods

107

12.7.5 Reading and manipulation of information

107

12.7.6 Reading of information

110

12.7.7 Manipulations of the data on disk

111

12.7.8 Struct-like interface

112

12.8 SPM functions

112

12.8.1 Epoching the data:spm_eeg_epochs. . . . . . . . . . . . . . . . . . . . . .112

12.8.2 Filtering the data:spm_eeg_filter. . . . . . . . . . . . . . . . . . . . . .113

12.8.3 Baseline correction:spm_eeg_bc. . . . . . . . . . . . . . . . . . . . . . . .113

12.8.4 Artefact detection and rejection:spm_eeg_artefact. . . . . . . . . . . . .113

12.8.5 Downsampling:spm_eeg_downsample. . . . . . . . . . . . . . . . . . . . .114

12.8.6 Rereferencing:spm_eeg_montage. . . . . . . . . . . . . . . . . . . . . . . .114

12.8.7 Grand mean:spm_eeg_grandmean. . . . . . . . . . . . . . . . . . . . . . .114

12.8.8 Merge:spm_eeg_merge. . . . . . . . . . . . . . . . . . . . . . . . . . . . .114

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