1 Hands-On Data Analysis Kate Pirog Revill and Chris Rorden Data from safety training –9 subjects...
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Transcript of 1 Hands-On Data Analysis Kate Pirog Revill and Chris Rorden Data from safety training –9 subjects...
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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
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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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
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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