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

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Presentation on theme: "1 Data Processing of Resting-State fMRI (Part 2) YAN Chao-Gan Ph. D. State Key Laboratory of Cognitive Neuroscience and Learning, Beijing."— Presentation transcript:

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

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

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

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

5 5 One sample T test

6 6 smReHo mALFF g1-1

7 7 One sample T test

8 8 m*-1 images zFC images Directory for saving SPM.mat Brain Mask

9 9 The generated spm.mat One sample T test

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

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

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

13 13 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 Two sample T test

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

15 15 The generated spm.mat Two sample T test

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

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

18 18 Paired T test

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

20 20 Paired T test

21 21 ANOVA Analysis

22 22 3 Corresponding level ANOVA Analysis Images for this group

23 23 ANOVA Analysis

24 24 Statistical Analysis in REST

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

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

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

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

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

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

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

32 32 Results Viewing SPM5 xjview MRIcroN REST Slice Viewer

33 33 Results Viewing - SPM5

34 34 Results Viewing - SPM5

35 35 Results Viewing - xjview

36 36 xjview

37 37 Results Viewing - MRIcroN

38 38 REST Slice Viewer

39 39

40 40

41 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

42 42

43 43

44 44

45 45

46 46

47 47 This report is based on CUI Xu's xjview. (http://www.alivelearn.net/xjview/) 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: 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: # voxelsstructure 59--TOTAL # VOXELS-- 40Right Cerebrum 33Temporal Lobe 20White Matter 19Temporal_Inf_R (aal) 16Gray Matter 14Superior Temporal Gyrus 13Fusiform_R (aal) 11brodmann area 38 8Inferior Temporal Gyrus 7Middle Temporal Gyrus 7Limbic Lobe 6Uncus 6Temporal_Pole_Mid_R (aal) 5brodmann area 20 3Sub-Gyral Cluster 2 Number of voxels: 98 Peak MNI coordinate:

48 48

49 49

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

51 51 Create Brodmann Mask

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

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

54 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: = =0.774 P=0.05 Probability of not getting a false positive result: = 0.95

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

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

57 57 Let H 1, …, H m be the null hypotheses and P 1, …, P m 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. FDR Theory

58 58 FDR in REST

59 59 FDR in REST

60 60 FDR in REST

61 61 Multiple Comparisons Monte Carlo simulations (AlphaSim) ?

62 62 REST AlphaSim

63 63

64 64 Cl SizeFrequencyCum Propp/VoxelMax FreqAlpha

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

66 66 REST Image Calculator

67 67 REST Image Calculator

68 68 REST Image Calculator Example expressions: (a) g1-1 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>100 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 (f)mean(g1) Calculate the mean image of group 1 (g)(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''.

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

70 70 Power Spectrum

71 71 Power Spectrum

72 72 Power Spectrum

73 73 Power Spectrum

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

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

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

77 77

78 78 NIfTI nii to NIfTI pairs

79 79 NIfTI.nii to NIfTI pairs

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

81 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.

82 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.

83 83 Further Help Further questions:

84 84 Thanks to 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! SPM Team: Wellcome Department of Imaging Neuroscience, UCL MRIcroN Team: Chris RORDEN Xjview Team: CUI Xu ……

85 85 Thanks for your attention!


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