Rest_fMRI_使用教程2

严超赣Ph. D.

ycg.yan@gmail.com

State Key Laboratory of Cognitive Neuroscience and Learning,

Beijing Normal University, China

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Outline•Statistical Analysis•Results Viewing•Multiple Comparisons•REST Image Calculator•Other Functions2Statistical AnalysisOne sample T testTwo Sample T testPaired T testANOVA analysis3

One sample T testPreparation•ALFF: mALFF-1

•fALFF: mfALFF-1•ReHo: smReHo-1

•FC: zFC

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One sample T test5One sample T testsmReHomALFFg1-16One sample T test7One sample T testm*-1 imageszFC imagesBrain MaskDirectory for saving SPM.mat8One sample T testThe generatedspm.mat9One sample T testThe generated spm.mat110One sample T testspmT_0001.imgHeightthresholdT = 2.687659{p<0.05(FDR)}Extentthresholdk = 10 voxels11Two sample T testPreparation•ALFF：mALFF

•fALFF: mfALFF•ReHo: smReHo

•FC: zFC•Mask

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Mask•Brain Mask Two sample T testMask=(Patient_1T.img>Thrd)+(CON_1T.img>Thrd)>0Patient_1T.imgCON_1T.imgMask_2T.img(i1>1.96+i2>1.96)>013Two sample T testBrain Mask orMask_2T.imgm* or zFC* imagesfor the two groupsDirectory for saving SPM.mat14Two sample T testThe generatedspm.mat15Two sample T testThe generatedspm.mat1 -116Two sample T testspmT_0001.imgHeightthresholdT = Inf{p<0.05(FDR)}Extentthresholdk = 0 voxels17Paired T test18Paired T testm* or zFC* imagesfor each pairBrain Mask19Paired T test20ANOVA Analysis21ANOVA Analysis3Corresponding levelImages for this group22ANOVA Analysis23Statistical Analysis in REST24One-Sample T-Test0 for m*-1 images1 for m* imagesBrain MaskT Statistic Image25Two-Sample T-TestT Statistic Image: positive corresponds to the mean of Group 1 is greater than the mean of Group 226Two-Sample T-TestTwo-Sample T-Test with covariates: e.g. gray matter proportion images (Oakes et al., 2007, Neuroimage)Please make sure the correspondence between the group Other covariate can be also specified as text images and the covariate images: order and voxel sizefiles. (E.g. age, brain size, IQ etc.)27Paired T-TestSituation 1 –Situation 2Please make sure thecorrespondenceT Statistic Image28ANOVA or ANCOVAANCOVA: e.g. gray matter proportion images (Oakes et al., F Statistic Image2007, Neuroimage)Please make sure the correspondence between the group Other covariate can be also specified as text images and the covariate images: order and voxel sizefiles. (E.g. age, brain size, IQ etc.)29Correlation AnalysisThe imaging measure:ALFF mapsTraits: e.g. MMSE.txt1915231423…30Outline•Statistical Analysis•Results Viewing•Multiple Comparisons•REST Image Calculator•Other Functions31Results Viewing•SPM5•xjview•MRIcroN•REST Slice Viewer

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Results Viewing-SPM533Results Viewing-SPM534Results Viewing-xjview35结果呈现—xjview36Results Viewing -MRIcroN37RESTSliceViewer383940For Voxel size = 3*3*3Voxels are connected if their faces touch rmm=4Voxels are connected if their faces or edges touch rmm=5; SPM_Criterion

Voxels are connected if their faces, edges, or corners touchrmm=641

4243444546This 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 1Number of voxels: 59Peak MNI coordinate: 27 6 -45Peak MNI coordinate region: // Right Cerebrum // Temporal Lobe // Superior Temporal Gyrus // White Matter // undefined // Temporal_Inf_R (aal)Peak intensity: 3.5023# voxelsstructure59--TOTAL # VOXELS--40Right Cerebrum33Temporal Lobe20White Matter19Temporal_Inf_R (aal)16Gray Matter14Superior Temporal Gyrus13Fusiform_R (aal)11brodmann area 388Inferior Temporal Gyrus7Middle Temporal Gyrus7Limbic Lobe6Uncus6Temporal_Pole_Mid_R (aal)5brodmann area 203Sub-Gyral----------------------Cluster 2Number of voxels: 98474849Create Brodmann MaskTemplate\\brodmann.niiOrTemplate\\Brodmann_61x73x61.nii50Create Brodmann Mask51Data Resample0 –Nearest Neighbor1 –Trilinear2-2nd degree b-spline52Outline•Statistical Analysis•Results Viewing•Multiple Comparisons•REST Image Calculator•Other Functions5321.5Multiple Comparisons10.50-0.512345P=0.05P=0.05P=0.05P=0.05P=0.050.95 0.95 0.95 0.95 0.95Probability of not Probability of not Probability of not Probability of not Probability of not 0.955=0.774getting a false getting a false getting a false getting a false getting a false positive result:positive result:positive result:positive result:positive result:1 -0.05 = 0.951 -0.05 = 0.951 -0.05 = 0.951 -0.05 = 0.951 -0.05 = 0.9554Multiple Comparisons•Bonferroni correction: 0.05/5=0.01•Family-Wise Error (FWE) correction•False Discovery Rates (FDR) correction •Monte Carlo simulations (AlphaSim)

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FDR Theory•False discovery rate Qe=E(V/(V+S))=E(V/R)Benjamini and Hochberg, 1995, Journal of the Royal Statistical Society56FDR Theory•Let H1, …, Hmbe the null hypotheses and P1, …, Pmtheir 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 REST58FDR in REST59FDR in REST60Multiple ComparisonsMonte Carlo simulations (AlphaSim)1110987654321123456789101111109876543211234567891011?61REST AlphaSim6263Cl Size123456789101112131415161718192021222324Frequency2359717615032297159408476478627671606101158539123616498693722221175541Cum Propp/Voxel0.6198980.8199450.9047890.9466640.9689300.9815030.9887720.9929910.9956470.9971840.9982110.9988310.9992620.9995190.9997010.9997980.9998560.9999130.9999420.9999610.9999740.9999870.9999971.000000Max Freq0.0096130.0062820.0041310.0027630.0018630.0012650.0008600.0005860.0004050.0002760.0001940.0001330.0000930.0000630.0000430.0000290.0000200.0000150.0000100.0000070.0000050.0000030.0000020.000000Alpha0000011951127132172146107786130222111755411.0000001.0000001.0000001.0000001.0000001.0000000.9990000.9800000.9290000.8020000.6700000.4980000.3520000.2450000.1670000.1060000.0760000.0540000.0330000.0220000.0150000.0100000.0050000.00100064Outline•Statistical Analysis•Results Viewing•Multiple Comparisons•REST Image Calculator•Other Functions65REST Image Calculator66REST Image Calculator67REST Image CalculatorExample 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''.

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Outline•Statistical Analysis•Results Viewing•Multiple Comparisons•REST Image Calculator•Other Functions69Power Spectrum70Power Spectrum71Power Spectrum72Power Spectrum73Granger Causality AnalysisContributed by Mr. ZANG Zhen-Xiang74Theory of Granger CausalitySigned path coefficientChen et al, 2009, ISMRMGranger 1969; Ding et al., 200675Theory of Granger CausalityResidual basedGranger 1969; Ding et al., 20067677NIfTI nii to NIfTI pairs78NIfTI .nii to NIfTI pairs79Reading and Writing functionsReading:

[Data Vox Head]=rest_readfile('brodmann.nii');Data –181*217*181 doubleVox –1 1 1Head -StructureProcessing:

BA20Data=(Data==20);Writing:

rest_WriteNiftiImage(BA20Data,Head,'BA20.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 3GB switch of Windows XP!!! Please see more details in http://msdn.microsoft.com/en-us/library/ff556232.aspx.5. If this problem remains, please install Linux, especially 64 bit Linux and Matlab.81

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

Further HelpFurther questions:www.restfmri.net

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Thanks toDONG Zhang-YeGUO Xiao-JuanHE Yong

LONG Xiang-YuSONG Xiao-WeiYAO Li

ZANG Yu-FengZHANG HanZHU Chao-ZheZOU Qi-HongZUO Xi-Nian……

SPM Team: Wellcome Department of Imaging Neuroscience, UCLMRIcroN Team: Chris RORDENXjview Team: CUI Xu……

All the group members!

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Thanks for your attention!85