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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 Group analysis in SPM8

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)

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

FSL: Single Subject

Launch FSL: fsl &

Data tab– First, must select

functional dataset: Select 4D data

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FSL: Single Subject

Click on folder to open file selection dialog

Select fmri12sec… file

Click ok in both boxes

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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

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FSL: Single Subject

Pre-Stats tab– Set spatial

smoothing to 8mm– Other settings ok

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FSL: Single Subject

Stats Tab– Don’t add motion

parameters

Choose full model setup

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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)

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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)

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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

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FSL: Single Subject

Save as design.fsf

Click Go to start analysis

Web browser will open to track progress (takes ~ 10 minutes)

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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

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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 &)

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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!

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FSL: Group Analysis

Click on folders to get to file selection dialog and select the fmri...feat directory for each participant

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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

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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

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FSL: Group Analysis

Contrasts Tab– Only one

contrast (where all subjects show activity)

Click Done to view design

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FSL: Group Analysis

Post-Stats tab– Lower Z

threshold to 1.64 (5%)

– Feel free to repeat analysis later w/ different thresholds..

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FSL: Group Analysis

Save as groupdesign.fsf

Click GO to start analysis (will launch web browser to monitor progress)– Takes about 5 minutes

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FSL: Group Analysis Results

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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…

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

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)

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SPM: Single Subject

Select Realign: Estimate & Reslice from spatial preprocessing bar

Realign: Estimate & Reslice– Click New:Session

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SPM: Single Subject

Realign: Estimate & Reslice– Highlight Session and

click on Select Files to open dialog box

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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

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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

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SPM: Single Subject

Progress shown in lower left window

Results of each step generally displayed in Graphics window

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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

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SPM: Single Subject

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

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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

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SPM: Single Subject

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

Choose Normalize:Write

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SPM: Single Subject

Normalize– Click on New:Subject– Choose parameter

file: T1mpr…

_seg_sn.mat

– Choose Images to Write: all 188 rfmri… files

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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 1 134

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

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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

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SPM: Single Subject

Click Specify 1st-level1st-level

– Highlight Directory and select ./ (current directory) for saving SPM.mat file

– Timing ParametersUnits: SecondsInterscan interval: 2

– Data and Design: New Subject/SessionHighlight Scans and choose all

188 swrfmri… files

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SPM: Single Subject

1st-level– Conditions: New

ConditionName: motorOnsets: can enter as

a list of start times but can also use MATLAB notation 0:24:360

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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

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SPM: Single Subject

Estimate– Choose SPM.mat file– Run (~ 2 minutes)

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SPM: Single Subject

Results– Click on Results

button in Inference bar

Lets define our statistical contrast…– Select SPM.mat – Choose Define new

contrast…

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SPM: Single Subject

Results– Define contrast:

Name: motor>restType: t-contrastContrast: enter 1 and

press SubmitHit OK.Then hit Done in

previous window

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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 voxel43

SPM: Single Subject

Things to try– Overlay activation on

structural image:Overlays: sectionsSelect wT1mprage.. file

– Select max voxel and plot timecourse:Plot: Plot… Fitted ResponsesPredictedAgainst scan or time

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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

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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).

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SPM: Group Analysis

Estimate– Choose SPM.mat from your

group directory– Run (~ 2 min)

Results– Choose SPM.mat from your

group directory

Define new contrastName: group_m>rT-contrastContrast: 1 Hit submit, OK, done

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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…

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