1. Data Processing of Resting-State fMRI (Part 2)
YAN Chao-Gan
严超赣
Ph. D.
State Key Laboratory of Cognitive Neuroscience and Learning,
Beijing Normal University, China 1

2. Outline Statistical Analysis Results Viewing Multiple Comparisons
REST Image Calculator
Other Functions 2

3. Statistical Analysis One sample T test Two Sample T test Paired T test
ANOVA analysis 3

4. One sample T test ALFF: mALFF-1 Preparation fALFF: mfALFF-1
ReHo: smReHo-1
FC: zFC 4

5. One sample T test 5

6. One sample T test
smReHo
mALFF
g1-1 6

7. One sample T test 7

8. One sample T test m*-1 images zFC images Brain Mask Directory for
saving SPM.mat 8

9. One sample T test
The generated
spm.mat 9

10. One sample T test
The generated spm.mat 1 10

11. One sample T test spmT_0001.img
HeightthresholdT = {p<0.05(FDR)}
Extentthresholdk = 10 voxels 11

12. Two sample T test ALFF：mALFF Preparation fALFF: mfALFF ReHo: smReHo
FC: zFC
Mask 12

13. Two sample T test Mask Brain Mask
Mask=(Patient_1T.img>Thrd)+(CON_1T.img>Thrd)>0
Patient_1T.img
CON_1T.img
Mask_2T.img
(i1>1.96+i2>1.96)>0 13

14. Two sample T test Brain Mask or Mask_2T.img m* or zFC* images
for the two groups
Directory for
saving SPM.mat 14

15. Two sample T test
The generated
spm.mat 15

16. Two sample T test
The generated
spm.mat
1 -1 16

17. Two sample T test spmT_0001.img
HeightthresholdT = Inf {p<0.05(FDR)}
Extentthresholdk = 0 voxels 17

18. Paired T test 18

19. Paired T test
m* or zFC* images
for each pair
Brain Mask 19

20. Paired T test 20

21. ANOVA Analysis 21

22. ANOVA Analysis 3
Corresponding level
Images for this group 22

23. ANOVA Analysis 23

24. Statistical Analysis in REST24

25. One-Sample T-Test Brain Mask 0 for m*-1 images 1 for m* images
T Statistic Image 25

26. Two-Sample T-Test
T Statistic Image: positive corresponds to the mean of Group 1 is greater than the mean of Group 2 26

27. Two-Sample T-Test
Two-Sample T-Test with covariates: e.g. gray matter proportion images (Oakes et al., 2007, Neuroimage)
Please make sure the correspondence between the group images and the covariate images: order and voxel size
Other covariate can be also specified as text files. (E.g. age, brain size, IQ etc.) 27

28. Paired T-Test Situation 1 – Situation 2 Please make sure the
correspondence
T Statistic Image 28

29. ANOVA or ANCOVA
ANCOVA: e.g. gray matter proportion images (Oakes et al., 2007, Neuroimage)
F Statistic Image
Please make sure the correspondence between the group images and the covariate images: order and voxel size
Other covariate can be also specified as text files. (E.g. age, brain size, IQ etc.) 29

30. Correlation Analysis The imaging measure: ALFF maps Traits: e.g.
MMSE.txt 19 15 23 14 … 30

31. Outline Statistical Analysis Results Viewing Multiple Comparisons
REST Image Calculator
Other Functions 31

32. Results Viewing
SPM5
xjview
MRIcroN
REST Slice Viewer 32

33. Results Viewing - SPM5 33

34. Results Viewing - SPM5 34

35. Results Viewing - xjview35

36. 结果呈现—xjview 36

37. Results Viewing - MRIcroN37

38. REST
Slice
Viewer 38

39. 39

40. 40

41. For Voxel size = 3*3*3 Voxels are connected if their faces touch rmm=4
Voxels are connected if their faces or edges touch
rmm=5; SPM_Criterion
Voxels are connected if their faces, edges, or corners touch
rmm=6 41

42. 42

43. 43

44. 44

45. 45

46. 46

47. This report is based on CUI Xu's xjview. (http://www. alivelearn
Revised by YAN Chao-Gan and ZHU Wei-Xuan : suitable for different Cluster Connectivity Criterion: surface connected, edge connected, corner connected.
Number of clusters found: 7
Cluster 1
Number of voxels: 59
Peak MNI coordinate:
Peak MNI coordinate region: // Right Cerebrum // Temporal Lobe // Superior Temporal Gyrus // White Matter // undefined // Temporal_Inf_R (aal)
Peak intensity:
# voxels structure
59 --TOTAL # VOXELS--
40 Right Cerebrum
33 Temporal Lobe
20 White Matter
19 Temporal_Inf_R (aal)
16 Gray Matter
14 Superior Temporal Gyrus
13 Fusiform_R (aal)
11 brodmann area 38
8 Inferior Temporal Gyrus
7 Middle Temporal Gyrus
7 Limbic Lobe
6 Uncus
6 Temporal_Pole_Mid_R (aal)
5 brodmann area 20
3 Sub-Gyral
Cluster 2
Number of voxels: 98
Peak MNI coordinate: 47

48. 48

49. 49

50. Create Brodmann Mask Template\brodmann.nii Or
Template\Brodmann_61x73x61.nii 50

51. Create Brodmann Mask 51

52. Data Resample 0 – Nearest Neighbor 1 – Trilinear
2- 2nd degree b-spline 52

53. Outline Statistical Analysis Results Viewing Multiple Comparisons
REST Image Calculator
Other Functions 53

54. Multiple Comparisons P=0.05
Probability of not getting a false positive result:
= 0.95
P=0.05
Probability of not getting a false positive result:
= 0.95
P=0.05
Probability of not getting a false positive result:
= 0.95
P=0.05
Probability of not getting a false positive result:
= 0.95
P=0.05
Probability of not getting a false positive result:
= 0.95
0.955=0.774 54

55. Multiple Comparisons Bonferroni correction: 0.05/5=0.01
Family-Wise Error (FWE) correction
False Discovery Rates (FDR) correction
Monte Carlo simulations (AlphaSim) 55

56. FDR Theory False discovery rate Qe=E(V/(V+S))=E(V/R)
Benjamini and Hochberg, 1995, Journal of the Royal Statistical Society 56 56 56

57. FDR Theory
Let H1, …, Hm be the null hypotheses and P1, …, Pm their corresponding p-values. Order these values in increasing order and denote them by P(1), …, P(m). For a given q, find the largest k such that P(k) ≦ kq/m.
Then reject (i.e. declare positive) all H(i) for i = 1, …, k. 57 57 57

58. FDR in REST 58 58 58

59. FDR in REST 59 59 59

60. FDR in REST 60 60 60

61. Multiple Comparisons
Monte Carlo simulations (AlphaSim) ? 61

62. REST AlphaSim 62

63. 63

64. Cl Size Frequency Cum Prop p/Voxel Max Freq Alpha 64

65. Outline Statistical Analysis Results Viewing Multiple Comparisons
REST Image Calculator
Other Functions 65

66. REST
Image
Calculator 66

67. REST Image Calculator 67

68. REST Image Calculator Example expressions:
(a) g Subtract 1 from each image in group 1
(b) g1-g2 Subtract each image in group 2 from each corresponding image in group1
(c) i1-i2 Subtract image 2 from image 1
(d) i1> Make a binary mask image at threshold of 100
(e) g1.*(i1>100) Make a mask and then apply to each image in group 1
mean(g1) Calculate the mean image of group 1
(i1-mean(g1))./std(g1) Calculate the z value of i1 related to group 1
(g) corr(g1,g2,''temporal'') Calculate the temporal correlation between two groups, i.e. one correlation coefficient between two ''time courses'' for each voxel.
(h) corr(g1,g2,''spatial'') Calculate the spatial correlation between two groups, i.e. one correlation coefficient between two images for each ''time point''. 68

69. Outline Statistical Analysis Results Viewing Multiple Comparisons
REST Image Calculator
Other Functions 69

70. Power Spectrum 70

71. Power Spectrum 71

72. Power Spectrum 72

73. Power Spectrum 73

74. Granger Causality Analysis Contributed by Mr. ZANG Zhen-Xiang74

75. Theory of Granger Causality
Signed path coefficient
Chen et al, 2009, ISMRM
Granger 1969; Ding et al., 2006 75

76. Theory of Granger Causality
Residual based
Granger 1969; Ding et al., 2006 76

77. 77

78. NIfTI nii to NIfTI pairs78

79. NIfTI .nii to NIfTI pairs79

80. Reading and Writing functions
[Data Vox Head]=rest_readfile('brodmann.nii');
Data – 181*217*181 double
Vox – 1 1 1
Head - Structure
Processing:
BA20Data=(Data==20);
Writing:
rest_WriteNiftiImage(BA20Data,Head,'BA20.img'); 80

81. Solve Problem "Out Of Memory"
1. Reboot your computer and do not run any other programs.
2. Enlarge your memory.
3. MATLAB Version 7.1 or above is suggested.
4. You can turn on the 3GB switch of Windows XP!!! Please see more details in
5. If this problem remains, please install Linux, especially 64 bit Linux and Matlab. 81

82. Solve Problem "Out Of Memory"
Enable the 3GB switch on Windows XP
* Right-click My Computer -> Properties -> Advanced -> Startup and Recovery -> Settings -> Edit.
Modify the following line (maybe not exactly same) in the boot.ini file:
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="WinXP Pro 3GB" /noexecute=optin /fastdetect /3GB
* Save and close -> Restart your computer.
Enable the 3GB switch on Windows Vista and Windows 7 (32-bit)
* Right-click Command Prompt in the Accessories program group of the Start menu. Click Run as Administrator.
* At the command prompt, enter "bcdedit /set IncreaseUserVa 3072"
* Restart the computer. 82

83. Further Help
Further questions: 83

84. All the group members! Thanks to
SPM Team: Wellcome Department of Imaging Neuroscience, UCL
MRIcroN Team: Chris RORDEN
Xjview Team: CUI Xu ……
DONG Zhang-Ye
GUO Xiao-Juan
HE Yong
LONG Xiang-Yu
SONG Xiao-Wei
YAO Li
ZANG Yu-Feng
ZHANG Han
ZHU Chao-Zhe
ZOU Qi-Hong
ZUO Xi-Nian ……
All the group members! 84

85. Thanks for your attention!85