Data Processing of RestingState f MRI Part 2

Data Processing of Resting-State f. MRI (Part 2) YAN Chao-Gan 严超赣 Ph. D. ycg. yan@gmail. com State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, China 1

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

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

One sample T test Preparation • ALFF: m. ALFF-1 • f. ALFF: mf. ALFF-1 • Re. Ho: sm. Re. Ho-1 • FC: z. FC 4

One sample T test 5

One sample T test sm. Re. Ho m. ALFF g 1 -1 6

One sample T test 7

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

One sample T test The generated spm. mat 9

One sample T test The generated spm. mat 1 10

One sample T test spm. T_0001. img Heightthreshold. T = 2. 687659 {p<0. 05(FDR)} Extentthresholdk = 10 voxels 11

Two sample T test Preparation • ALFF：m. ALFF • f. ALFF: mf. ALFF • Re. Ho: sm. Re. Ho • FC: z. FC • Mask 12

Mask Two sample T test • Brain Mask=(Patient_1 T. img>Thrd)+(CON_1 T. img>Thrd) >0 Patient_1 T. img CON_1 T. img Mask_2 T. img (i 1>1. 96+i 2 >1. 96)>0 13

Two sample T test Brain Mask or Mask_2 T. img m* or z. FC* images for the two groups Directory for saving SPM. mat 14

Two sample T test The generated spm. mat 15

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

Two sample T test spm. T_0001. img Heightthreshold. T = Inf {p<0. 05(FDR)} Extentthresholdk = 0 voxels 17

Paired T test 18

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

Paired T test 20

ANOVA Analysis 21

ANOVA Analysis 3 Corresponding level Images for this group 22

ANOVA Analysis 23

Statistical Analysis in REST 24

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

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

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

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

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

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

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

Results Viewing • SPM 5 • xjview • MRIcro. N • REST Slice Viewer 32

Results Viewing - SPM 5 33

Results Viewing - SPM 5 34

Results Viewing - xjview 35

结果呈现—xjview 36

Results Viewing - MRIcro. N 37

REST Slice Viewer 38

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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

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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 # 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 47

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Create Brodmann Mask Templatebrodmann. nii Or TemplateBrodmann_61 x 73 x 61. nii 50

Create Brodmann Mask 51

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

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

Multiple Comparisons P=0. 05 0. 95 Probability of not of Probability not Probability of not 0. 955=0. 774 getting a false getting a false positive result: positive result: 1 - 0. 05 = 0. 95 1 - 0. 05 = 10. 95 - 0. 05 = 0. 95 1 - 0. 05 = 0. 95 54

Multiple Comparisons • Bonferroni correction: 0. 05/5=0. 01 • Family-Wise Error (FWE) correction • False Discovery Rates (FDR) correction • Monte Carlo simulations (Alpha. Sim) 55

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

FDR Theory • Let H 1, …, Hm be the null hypotheses and P 1, …, 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

FDR in REST 58

FDR in REST 59

FDR in REST 60

Multiple Comparisons Monte Carlo simulations (Alpha. Sim) ? 61

REST Alpha. Sim 62

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Cl Size 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Frequency 235971 76150 32297 15940 8476 4786 2767 1606 1011 585 391 236 164 98 69 37 22 22 11 7 5 5 4 1 Cum Prop p/Voxel 0. 619898 0. 819945 0. 904789 0. 946664 0. 968930 0. 981503 0. 988772 0. 992991 0. 995647 0. 997184 0. 998211 0. 998831 0. 999262 0. 999519 0. 999701 0. 999798 0. 999856 0. 999913 0. 999942 0. 999961 0. 999974 0. 999987 0. 999997 1. 000000 Max Freq 0. 009613 0. 006282 0. 004131 0. 002763 0. 001863 0. 001265 0. 000860 0. 000586 0. 000405 0. 000276 0. 000194 0. 000133 0. 000093 0. 000063 0. 000043 0. 000029 0. 000020 0. 000015 0. 000010 0. 000007 0. 000005 0. 000003 0. 000002 0. 000000 Alpha 0 0 0 1 19 51 127 132 172 146 107 78 61 30 22 21 11 7 5 5 4 1 1. 000000 0. 999000 0. 980000 0. 929000 0. 802000 0. 670000 0. 498000 0. 352000 0. 245000 0. 167000 0. 106000 0. 076000 0. 054000 0. 033000 0. 022000 0. 015000 0. 010000 0. 005000 0. 001000 64

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

REST Image Calculator 66

REST Image Calculator 67

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

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

Power Spectrum 70

Power Spectrum 71

Power Spectrum 72

Power Spectrum 73

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

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

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

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NIf. TI nii to NIf. TI pairs 78

NIf. TI. nii to NIf. TI pairs 79

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

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 3 GB switch of Windows XP!!! Please see more details in http: //msdn. microsoft. com/en-us/library/ff 556232. aspx. 5. If this problem remains, please install Linux, especially 64 bit Linux and Matlab. 81

Solve Problem "Out Of Memory" Enable the 3 GB 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="Win. XP Pro 3 GB" /noexecute=optin /fastdetect /3 GB * Save and close -> Restart your computer. Enable the 3 GB 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 Increase. User. Va 3072" * Restart the computer. 82

Further Help Further questions: www. restfmri. net 83

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 …… SPM Team: Wellcome Department of Imaging Neuroscience, UCL MRIcro. N Team: Chris RORDEN Xjview Team: CUI Xu …… All the group members! 84

Thanks for your attention! 85