1. 1 Hands-On Data Analysis Kate Pirog Revill and Chris Rorden Data from safety training –9 subjects –Finger-tapping task (12s tapping, 12s rest) –188 scans acquired over 6:16 (TR = 2) –Hi-res structural image Single-subject analysis in FSL Single-subject analysis in SPM8 Group analysis in FSL Group analysis in SPM8

2. Finding the Data Open terminal window –Navigate to directory home/public/coursedemo –Choose analysis technique (/spm or /fsl) –Choose subject (/subj1 through /subj9) Data already converted from dicom format –Hi-res structural: T1mprages002a1001… –Functional: fmri12secon12secoff… –timing.txt (fsl folders only) 2 Get it from the web http://www.cabiatl.com/Resources/FSL/subj9.zip

3. FSL: Single Subject Launch FSL: fsl & Data tab –First, must select functional dataset: Select 4D data 3

4. FSL: Single Subject Click on folder to open file selection dialog Select fmri12sec… file Click ok in both boxes 4

5. FSL: Single Subject Data tab: –Set TR = 2 –Set high-pass cutoff to 48 (2 x block size) –Delete 0 volumes –Total volumes and output directory set automatically 5

6. FSL: Single Subject Pre-Stats tab –Set spatial smoothing to 8mm –Other settings ok 6

7. FSL: Single Subject Stats Tab –Don’t add motion parameters Choose full model setup 7

8. FSL: Single Subject One explanatory variable: motor –Custom format Choose timing.txt (3 column file with block onsets, durations, and strengths) –Uncheck temporal derivative (block design) 8

9. FSL: Single Subject Contrasts tab –One contrast: areas more active during the motor task than during rest –Name it motor>rest Click Done, model will appear: does it make sense? – (click on it to make it disappear) 9

10. FSL: Single Subject Registration –Make sure Normal search, 12 DOF are selected –Could add hi-res structural here, but won’t to save time & preprocessing steps 10

11. FSL: Single Subject Save as design.fsf Click Go to start analysis Web browser will open to track progress (takes ~ 10 minutes) 11

12. FSL: Single Subject Done? Check it out… Click on blue links to view results: –Pre-stats: motion parameters –Stats: model design –Post-stats: activation map and voxel fits –Registration: alignment of functional image to template 12

13. FSL: Group Analysis All individual subject analyses must be completed first Navigate to /home/public/coursedemo/fsl and create your own folder for group analysis (name it after yourself). Enter this folder and launch FSL (fsl &) 13

14. FSL: Group Analysis Set tab at top left to Higher- level analysis Data Tab: –Inputs are FEAT directories –9 inputs –Output directory should be ok if you launched FSL from the directory I told you to create for yourself! 14

15. FSL: Group Analysis Click on folders to get to file selection dialog and select the fmri...feat directory for each participant 15

16. FSL: Group Analysis Stats Tab –Make sure to choose Mixed effects: Simple OLS MUCH faster- doesn’t take subject variability into account –Choose Full model setup 16

17. FSL: Group Analysis EVs Tab –Only 1 group of subjects –Want to see motor activity for all subjects, so set EV to 1 for each input 17

18. FSL: Group Analysis Contrasts Tab –Only one contrast (where all subjects show activity) Click Done to view design 18

19. FSL: Group Analysis Post-Stats tab –Lower Z threshold to 1.64 (5%) –Feel free to repeat analysis later w/ different thresholds.. 19

20. FSL: Group Analysis Save as groupdesign.fsf Click GO to start analysis (will launch web browser to monitor progress) –Takes about 5 minutes 20

21. FSL: Group Analysis Results 21

22. Finding the Data SPM pipeline –Preprocess: realign (motion correct), coregister (align T1 to fMRI), normalize (warp to standard space), smooth –Conduct statistics. Data already converted from dicom using dcm2nii –File in /home/public/coursedemo/subj1...subj9 –Hi-res structural: T1mprage… –Functional: fmri12secon12secoff… 22 Get it from the web http://www.cabiatl.com/Resources/SPM/subj9.zip

23. SPM: Single Subject Again, get into proper directory: cd /home/public/coursedemo/spm/subj9 Launch MATLAB matlab & At prompt, launch SPM8 spm8 (“spm fmri” outside CABI) 23

24. SPM: Single Subject Select Realign: Estimate & Reslice from spatial preprocessing bar Realign: Estimate & Reslice –Click New:Session 24

25. SPM: Single Subject Realign: Estimate & Reslice –Highlight Session and click on Select Files to open dialog box 25

26. SPM: Single Subject Select all fmri12sec… images (hold down shift) –Hint: type ^f.* in filter box to only show files starting with f –188 files selected –Click Done 26

27. SPM: Single Subject Realign: Estimate & Reslice –Leave all options as defaults –Save as realign.mat –Press green arrow to run (2 min) –Close batch editor 27

28. SPM: Single Subject Progress shown in lower left window Results of each step generally displayed in Graphics window 28

29. SPM: Single Subject Select Coregister: Estimate Coregistration –Choose reference image: meanfmri12secon… –Choose source image: T1mprages… –Save as coreg.mat –Click green arrow to run (2 min) –Click around results to check alignment 29

30. SPM: Single Subject Segmentation: find grey and white matter in hi-res structural image (improves normalization) 30

31. SPM: Single Subject Segment –Highlight Data and select file T1mprages… –Save as segment.mat –Run (~ 5 minutes) To view results, click Display “c1T1mpr” is gray matter, “c2T1mpr” is white matter 31

32. SPM: Single Subject Normalize: warp images to standard space (functionals and structural) Choose Normalize:Write 32

33. SPM: Single Subject Normalize –Click on New:Subject –Choose parameter file: T1mpr…_seg_sn.mat –Choose Images to Write: all 188 rfmri… files 33

34. SPM: Single Subject Normalize –Set Voxel Sizes to 3 3 3 –Save as func_norm.mat –Run (~ 1 min) Also normalize structural image –Same procedure except Images to Write = T1mprages Voxel Sizes = 1 1 1 34

35. SPM: Single Subject To check results of normalization, choose Check Reg, then select wT1mprage… and one of the wrfmri… images and see if they match up well 35

36. SPM: Single Subject Smoothing –Highlight Images to Smooth and select all 188 wrfmri… files –Check that FWHM = [8 8 8] –Save as smooth.mat –Run (~ 3 min) No display 36

37. SPM: Single Subject Click Specify 1 st -level 1 st -level –Highlight Directory and select./ (current directory) for saving SPM.mat file –Timing Parameters Units: Seconds Interscan interval: 2 –Data and Design: New Subject/Session Highlight Scans and choose all 188 swrfmri… files 37

38. SPM: Single Subject 1 st -level –Conditions: New Condition Name: motor Onsets: can enter as a list of start times but can also use MATLAB notation  0:24:360 38

39. SPM: Single Subject 1 st -level –Durations: 12 (all blocks are 12s long, so only one value needed) –High Pass Filter: 48 –Save as design.mat –Run (1min) You will see a design matrix when completed 39

40. SPM: Single Subject Estimate –Choose SPM.mat file –Run (~ 2 minutes) 40

41. SPM: Single Subject Results –Click on Results button in Inference bar Lets define our statistical contrast… –Select SPM.mat –Choose Define new contrast… 41

42. SPM: Single Subject Results –Define contrast: Name: motor>rest Type: t-contrast Contrast: enter 1 and press Submit Hit OK. Then hit Done in previous window 42

43. SPM: Single Subject Results –Mask with other contrasts: no –Title: motor>rest –P value adjustment: FWE –P value: 0.05 –Extent threshold: 0 –Will run for < 1 min… View Results –Right-click on glass brain to find global maximum voxel 43

44. SPM: Single Subject Things to try –Overlay activation on structural image: Overlays: sections Select wT1mprage.. file –Select max voxel and plot timecourse: Plot: Plot… Fitted Responses Predicted Against scan or time 44

45. SPM: Group Analysis Navigate to /home/public/spm and make your own group directory (i.e. kategroup) Launch MATLAB and spm8. Choose Specify 2 nd - Level 45

46. SPM: Group Analysis 2 nd -Level –Choose a results directory (the one you just made) –Scans: navigate to each subject’s directory and choose con_0001.img Don’t hit OK until you’ve completed all 9 subjects –Save as groupdesign.mat –Run (~2 min) The resulting matrix is a white box (same effect for all subjects). 46

47. SPM: Group Analysis Estimate –Choose SPM.mat from your group directory –Run (~ 2 min) Results –Choose SPM.mat from your group directory Define new contrast Name: group_m>r T-contrast Contrast: 1 Hit submit, OK, done 47

48. SPM: Group Analysis Results –Mask with other contrasts: no –Title: motor>rest –P value adjustment: FWE –P value: 0.05 –Extent threshold: 0 –Will run for < 1 min… 48