1. 1 Data Processing of Resting-State fMRI (Part 2) YAN Chao-Gan Ph. D. ycg.yan@gmail.com 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 = 2.687659 {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 + CON_1T.img>0 Patient_1T.img CON_1T.img Mask_2T.img i1+i2>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 Outline Statistical Analysis Results Viewing Multiple Comparisons REST Image Calculator Other Functions

25. 25 Results Viewing SPM5 xjview MRIcroN REST Slice Viewer

26. 26 Results Viewing - SPM5

27. 27 Results Viewing - SPM5

28. 28 Results Viewing - xjview

29. 29 xjview

30. 30 Results Viewing - MRIcroN

31. 31 REST Slice Viewer

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34. 34 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

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40. 40 This report is based on CUI Xu's xjview. (http://www.alivelearn.net/xjview/) Revised by YAN Chao-Gan and ZHU Wei-Xuan 20091108: 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: 27 6 -45 Peak MNI coordinate region: // Right Cerebrum // Temporal Lobe // Superior Temporal Gyrus // White Matter // undefined // Temporal_Inf_R (aal) Peak intensity: 3.5023 # 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: -9 -78 -51

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43. 43 Create Brodmann Mask Template\brodmann.nii Or Template\Brodmann_61x73x61.nii

44. 44 Create Brodmann Mask

45. 45 Data Resample 0 – Nearest Neighbor 1 – Trilinear 2- 2nd degree b-spline

46. 46 Outline Statistical Analysis Results Viewing Multiple Comparisons REST Image Calculator Other Functions

47. 47 Multiple Comparisons P=0.05 Probability of not getting a false positive result: 1 - 0.05 = 0.95 P=0.05 Probability of not getting a false positive result: 1 - 0.05 = 0.95 P=0.05 Probability of not getting a false positive result: 1 - 0.05 = 0.95 P=0.05 Probability of not getting a false positive result: 1 - 0.05 = 0.95 0.95 0.95 0.95 0.95 0.95 0.95 5 =0.774 P=0.05 Probability of not getting a false positive result: 1 - 0.05 = 0.95

48. 48 Multiple Comparisons Bonferroni correction: 0.05/5=0.01 False Discovery Rates (FDR) correction Family-Wise Error (FWE) correction Monte Carlo simulations (AlphaSim)

49. 49 Multiple Comparisons Monte Carlo simulations (AlphaSim) ?

50. 50 REST AlphaSim

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52. 52 Cl SizeFrequencyCum Propp/VoxelMax FreqAlpha 12359710.6198980.00961301.000000 2761500.8199450.00628201.000000 3322970.9047890.00413101.000000 4159400.9466640.00276301.000000 584760.9689300.00186301.000000 647860.9815030.00126511.000000 727670.9887720.000860190.999000 816060.9929910.000586510.980000 910110.9956470.0004051270.929000 105850.9971840.0002761320.802000 113910.9982110.0001941720.670000 122360.9988310.0001331460.498000 131640.9992620.0000931070.352000 14980.9995190.000063780.245000 15690.9997010.000043610.167000 16370.9997980.000029300.106000 17220.9998560.000020220.076000 18220.9999130.000015210.054000 19110.9999420.000010110.033000 2070.9999610.00000770.022000 2150.9999740.00000550.015000 2250.9999870.00000350.010000 2340.9999970.00000240.005000 2411.0000000.00000010.001000

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

54. 54 REST Image Calculator

55. 55 REST Image Calculator

56. 56 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) 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''.

57. 57 Outline Statistical Analysis Results Viewing Multiple Comparisons REST Image Calculator Other Functions

58. 58 NIfTI nii to NIfTI pairs

59. 59 NIfTI.nii to NIfTI pairs

60. 60 Reading and Writing functions Reading: [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');

61. 61 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 http://www.microsoft.com/whdc/system/platform/server/PAE/PAEmem.mspx. 5. If this problem remains, please install Linux, especially 64 bit Linux and Matlab.

62. 62 www.restfmri.net Further Help Further questions: Further professional data analysis service: Brain Imaging Data Analysis and Consultation Section (BIDACS) bidacs@gmail.com

63. 63 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 ……

64. 64 Thanks for your attention!