MRI date analysis マニュアル
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- ぜんぺい あわび
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1 SPM99/2 fmri MRI event-related SPM2 STEP. image run1 run2 STEP 2 Pre-processing. SPM99. T1 origin EPI origin Slice Timing Realign coregister only Realign reslice Coregister Normalize T1. Normalize EPI Smoothing STEP 3 Statistical Assessment for Individual Subject Default fmri models Result Result STEP 4 Statistical Assessment for Group of Subject Default Basic model Result SPM99/2 Manual, Version 1.4, Feb 16,
2 STEP. image ref1 2 ref1 image SPM analyze analyze 1 *****.img *****.hdr 2 01****.img (hdr) 2 run scout run run run image run1 run2 image 4 run anatomy 2 run1 run2 run3 anatomy run1 run2 fmri run 6 *****1.img *****6.img *****1.hdr *****6.hdr no_use ****7.img STEP 2 Pre-processing SPM slice-timing realignment normalize smoothing SPM99/2 Manual, Version 1.4, Feb 16,
3 . SPM99 MatLab cd d: Return (d) ls Return cd anatomy Return anatomy spm fmri Return SPM window MatLab pwd Return cd.. Return cd../.. Return ls delete Return 1 2. T1 origin MPRAGE 2 EPI SPM99/2 Manual, Version 1.4, Feb 16,
4 axial 256x256 coregister normalize 2 256x256x160 saggital 1 anatomy SPM99 2 Display 2 Done 3 Origin Anterior Commissure AC 4 crosshair position vx 5 HDR edit option set origin Window Option apply to image Done 7 Display 8 voxel size Dimension cross AC point EPI origin EPI 1 6 run cross AC SPM99/2 Manual, Version 1.4, Feb 16,
5 Slice Timing TR slice 1 / slice Block 1 SPM99 2 Slice timing 3 Number of subject / session run 4 Select image to acquisition correct for run Done 2 run 1 run 5 Select sequence type? user specified 26 ( ) first slice = bottom OK 6 Reference slice 26 slice 13 7 TR 8 Acquisition time a Realign coregister only 1 run 000 a img hdr a img (hdr) 2 SPM99 SPM99/2 Manual, Version 1.4, Feb 16,
6 3 Realign 4 number of subject 1 ( 1 1) 5 number of session for subjects run 6 a run run run 7 Which option? coregister only.mat.mat 1.mat.mat Realign reslice 7 coregister and reslice SPM 1 SPM99 2 Realign 3 number of subject 1 ( 1 1) 4 Number of session for subjects run 5 a 6 Which option? reslice only 7 reslice interpolation method? sinc interpolation 8 create what? all image + mean image 9 adjust sampling error yes r mean image 5 display mean image Coregister EPI normalize EPI EPI target T1 1 anatomy SPM99 2 Coregister 3 Number of subject? 1 4 Which option? coregister only 5 Modality of first target image? EPI 6 Modality of first object image? T1 mri 7. select target image realignment mean. img 8. select object image anatomy T1 image 9 Other object image done SPM99/2 Manual, Version 1.4, Feb 16,
7 EPI T1 Check Reg Normalize T1 anatomical normalization T1 1 anatomy SPM99 2 Normalize 3 Which option? Determine parameter & write normalize 4 Number of Subject 1 5 Image to determine parameter T1 done 6. Image to write normalized T1 done 7 Template image T1 image done 8 Bilinear interpolation template T1 image Anatomy ****_sn3d.mat n w. Normalize EPI EPI Realign mean image EPI a) mean image 1 Normalize 2 Which option? write normalize only 3 Number of Subject 1 4 anatomy **** sn3d.mat done 5 mean image mean image done 6 Interpolation method Bilinear interpolation nmean.img b) EPI normalize 1 Normalize 2 Which option? write normalize only 3 Number of Subject 1 4 anatomy **** sn3d.mat done 5 run ra done 6 Interpolation method? Bilinear interpolation nra SPM99/2 Manual, Version 1.4, Feb 16,
8 Smoothing 1 Smooth 2 smoothing {FWHM in mm} 8 mm 6 mm 3 nra*** normalize done snra*** FWHM 8mm run snra ****000.img (hdr) STEP 3 Statistical Assessment for Individual Subject Fixed effects model 1st stage analysis 1 1 result01 SPM99 Default fmri raw event TR 1 Defaults 2 Statistics fmri 3 Upper tail F prob threshold raw 4 Number of Bins/TR 16 5 Sampled bin 8 fmri models voxel time course event hemodynamic response HDR 1 fmri models SPM99/2 Manual, Version 1.4, Feb 16,
9 2 What would you like to do? specify and estimate a model 3 Number of session? run 4 snra*** run 5 Inter scan revel TR 6 Are condition replicated? no run run 7 Number of condition or trial regressor event 1 regressor Task A B 3 8 Name for trial trial1 A_correct trial2 B_correct trial4 miss 9 SOA variable 10 Vector of onset scan no text file 11 Variable duration? no 12 Parametric modulation? none 13 Are these trial? event event block epoch 14 Select basis set hrf with time derivate hrf 2 regressor 15 Interaction among trial? no 16 User specified regressor? no artifact realignment 6 parameter x, y, z, pitch, roll, yaw covariate No. of regressor? 6 6 window 6 run 7 17 Remove global effect scale 18 High pass specify 19 Session cutoff period default 20 Low pass filter hrf 21 Model intrinsic correlation none 22 Set up trial specific F-contrasts no 23 Estimate now later fmri Design data design ISI TR Scan per session Replication yes/no SPM99/2 Manual, Version 1.4, Feb 16,
10 Specify design in scan/second scan hrf time derivative Voltera kernel no Number of condition Vector of onsets event Duration event Parametric modulation none spm.mat fmri Design data data Select data s Global scaling Hi-pass filtering default estimate spm.mat Result voxel T-value Z-value a. 1 F-contrast 1 result01 SPM99 2 Result 3 Select SPM.mat SPM.mat done 4 SPM contrast manager F-contrast 5 Effect of interest done 6 Mask with other contrast No 7 Title for comparison 8 Corrected high threshold no 9 Threshold 1 done SPM template Group 1 b. 1 result01 SPM99 2 Result 3 Select SPM.mat SPM.mat done 4 SPM contrast manager window t-contrast 5 Define new contrast SPM99/2 Manual, Version 1.4, Feb 16,
11 6 Name 7 Contrast 1 run 2 2 Task A B time derivative Task A activation run1 run2 1 0 Task A hrf 1 time derivative 0 8 Submit 1 9 OK con_***.img (hdr) 2 Task A minus Task B run1 Task A minus Task B run2 Task run interaction run1(a B) run2(a B) = run1 ( ) run2 ( ) =( ) ( ) = Task A 2 Task A Task B 3 Task run Group SPM99/2 Manual, Version 1.4, Feb 16,
12 con***.img (hdr) 1 result01 STEP3 Result 1. Mask with other contrast no 2. Title for comparison 3. Corrected high threshold no 4. Threshold voxels STEP 4 Statistical Assessment for Group of Subject 12 Random effects model 2nd stage analysis group SPM99 1 Default statistics fmri 2 Threshold 0.9 raw 3 TR 4 Sample 8 Basic model STEP 3 con***.img (hdr) Task A con_002.img (hdr) 12 Group 1. Basic Model Select design type One sample t-test 2 Select image 12 con_002.img Done 3 GMsca: grand mean scaling no grand mean scaling 4 Explicitly mask images No 5 Global calculation Omit 6 Estimate? now Result SPM99/2 Manual, Version 1.4, Feb 16,
13 1. Group SPM99 2. Result 3. Select SPM.mat SPM.mat done 4. Name ( ) 5. Define new contrast activation 1 deactivation 1 6. Mask with other contrast no 7. Title for comparison 8. Corrected high threshold no 9. Threshold voxels SPM99/2 Manual, Version 1.4, Feb 16,
14 Optimized Voxel-based morphometry VBM Good et. al. NeuroImage 14,21-36,2001 VBM STEP Custom Template T1image T1Template normalize mean image smoothing STEP Segmentation T1 image Custom Template normalize STEP Clean Up GM Template Clean up GM Template mean GM image smoothing STEP Grey Matter Normalize GM image GM Template normalize optimized sn3d.mat optimized STEP Hi-resolution MRI Normalize T1 image sn3d.mat optimized normalize STEP Segmentation T1 image(optimized) Segmentation STEP Clean Up Clean Up STEP Modulation Modulation STEP Smoothing smoothing STEP Global value Global value STEP Statistics SPM99/2 Manual, Version 1.4, Feb 16,
15 STEP Custom Template T1image SPM99 T1Template normalize Default non-linear image voxel-size 1x1x1mm normalize T1image mean image mean image 8mm smoothing Custom Template STEP Segmentation T1 image STEP Custom Template normalize Default non-linear image voxel-size 1x1x1mm Normalize T1 image Segmentation Are they spatially normalized No Homogeneity correction A little homogeneity correction Seg1 Grey Matter /Seg2 White Matter /Seg3 CSF segment STEP Clean Up GM Template ImCalc Seg1 Seg2 **brain i1+i2 brain mask GM WM ImCalc Seg1 Seg2 Seg3 **brain 4 image **GM i1.*i4./(i1+i2+i3+eps) GM image mean image mean image 8mm smoothing GM Template STEP Grey Matter Normalize STEP3 clean up GM image GM Template normalize Default neurological convention R is R non-linear Mask brain when registering No brain mask image voxel-size 1x1x1mm sn3d.mat optimized sn3d.mat optimized STEP Hi-resolution MRI Normalize STEP2 normalize T1 image STEP4 sn3d.mat non-linear normalize Default neurological convention R is R image voxel-size SPM99/2 Manual, Version 1.4, Feb 16,
16 1x1x1mm optimize T1 image optimize STEP Segmentation STEP5 T1 image(optimized) Segmentation Spatially normalized? Yes Homogeneity correction A little homogeneity correction Seg1 Grey Matter /Seg2 White Matter /Seg3 CSF segment Seg1 optimize GM image optimized STEP Clean Up ImCalc Seg1 Seg2 **brain i1+i2 brain mask GM WM ImCalc Seg1 Seg2 Seg3 **brain 4 image **GM i1.*i4./(i1+i2+i3+eps) GM image optimize clean up GM image STEP Modulation SPM99 spm_preserve_quantity mat file script Matlab STEP4 sn3d.mat optimized STEP6 GM image optimized m m**gm image Mats = spm_get(inf,'*_sn3d.mat','select sn3d.mat files'); Images = spm_get(size(mats,1),'*.img','select images to modulate'); for i=1:size(mats,1), spm_preserve_quantity(deblank(mats(i,:)),deblank(images(i,:))); end; STEP Smoothing STEP m**gm image 12mm smoothing sm**gm image optimize modulate GM image STEP Global value GM image GM volume Global value SPM99/2 Manual, Version 1.4, Feb 16,
17 SPM99 get_integrals.mat SPM99 Utility Run File sm**gm image Matlab STEP Statistics SPM99/2 Manual, Version 1.4, Feb 16,
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