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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

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Hands-On Data Analysis


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hands on data analysis
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
finding the data
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)

Get it from the web http://www.cabiatl.com/Resources/FSL/subj9.zip

fsl single subject
FSL: Single Subject
  • Launch FSL: fsl &
  • Data tab
    • First, must select functional dataset: Select 4D data
fsl single subject4
FSL: Single Subject
  • Click on folder to open file selection dialog
  • Select fmri12sec… file
  • Click ok in both boxes
fsl single subject5
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
fsl single subject6
FSL: Single Subject
  • Pre-Stats tab
    • Set spatial smoothing to 8mm
    • Other settings ok
fsl single subject7
FSL: Single Subject
  • Stats Tab
    • Don’t add motion parameters
  • Choose full model setup
fsl single subject8
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)
fsl single subject9
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)
fsl single subject10
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
fsl single subject11
FSL: Single Subject
  • Save as design.fsf
  • Click Go to start analysis
  • Web browser will open to track progress (takes ~ 10 minutes)
fsl single subject12
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
fsl group analysis
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 &)
fsl group analysis14
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!
fsl group analysis15
FSL: Group Analysis
  • Click on folders to get to file selection dialog and select the fmri...feat directory for each participant
fsl group analysis16
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
fsl group analysis17
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
fsl group analysis18
FSL: Group Analysis
  • Contrasts Tab
    • Only one contrast (where all subjects show activity)
  • Click Done to view design
fsl group analysis19
FSL: Group Analysis
  • Post-Stats tab
    • Lower Z threshold to 1.64 (5%)
    • Feel free to repeat analysis later w/ different thresholds..
fsl group analysis20
FSL: Group Analysis
  • Save as groupdesign.fsf
  • Click GO to start analysis (will launch web browser to monitor progress)
    • Takes about 5 minutes
finding the data22
Finding the Data

Get it from the web http://www.cabiatl.com/Resources/SPM/subj9.zip

  • 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

spm single subject
SPM: Single Subject

Again, get into proper directory: cd /home/public/coursedemo/spm/subj9

Launch MATLAB matlab &

At prompt, launch SPM8spm8

(“spm fmri” outside CABI)

23

spm single subject24
SPM: Single Subject
  • Select Realign: Estimate & Reslice from spatial preprocessing bar
  • Realign: Estimate & Reslice
    • Click New:Session

24

spm single subject25
SPM: Single Subject
  • Realign: Estimate & Reslice
    • Highlight Session and click on Select Files to open dialog box

25

spm single subject26
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

spm single subject27
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

spm single subject28
SPM: Single Subject

Progress shown in lower left window

Results of each step generally displayed in Graphics window

28

spm single subject29
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

spm single subject30
SPM: Single Subject

Segmentation: find grey and white matter in hi-res structural image (improves normalization)

30

spm single subject31
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

spm single subject32
SPM: Single Subject

Normalize: warp images to standard space (functionals and structural)

Choose Normalize:Write

32

spm single subject33
SPM: Single Subject
  • Normalize
    • Click on New:Subject
    • Choose parameter file:
      • T1mpr…_seg_sn.mat
    • Choose Images to Write:
      • all 188 rfmri… files

33

spm single subject34
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

spm single subject35
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

spm single subject36
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

spm single subject37
SPM: Single Subject
  • Click Specify 1st-level
  • 1st-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

spm single subject38
SPM: Single Subject
  • 1st-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

spm single subject39
SPM: Single Subject
  • 1st-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

spm single subject40
SPM: Single Subject
  • Estimate
    • Choose SPM.mat file
    • Run (~ 2 minutes)

40

spm single subject41
SPM: Single Subject
  • Results
    • Click on Results button in Inference bar
  • Lets define our statistical contrast…
    • Select SPM.mat
    • Choose Define new contrast…

41

spm single subject42
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

spm single subject43
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

spm single subject44
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

spm group analysis
SPM: Group Analysis

Navigate to /home/public/spm and make your own group directory (i.e. kategroup)

Launch MATLAB and spm8.

Choose Specify 2nd-Level

45

spm group analysis46
SPM: Group Analysis

2nd-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

spm group analysis47
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

spm group analysis48
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