1. Seed-based Resting State fMRI Analysis in FreeSurfer

2. Remember to do evaluations!

3. Overview Task-based fMRI Review
Seed-based Functional Connectivity Overview
FS-FAST Commands

4. Task-based Analysis Review

5. Visual/Auditory/Motor Activation Paradigm
15 sec ‘ON’, 15 sec ‘OFF’
Flickering Checkerboard

6. Task-based fMRI Analysis
y = X * b
bOdd
bEven
bbase =
Raw fMRI Waveform
Contrast C = [1 -1 0]
Design Matrix
Regressors
Data from
one voxel

7. Statistical Parametric Map (SPM)
+3% 0%
-3%
H0 Significance
t-Map (p,z,F)
(Thresholded p<0.01)
sig = −log10(p)
Contrast Amplitude
bON - bOFF
CON, COPE, CES
Variance of Contrast
(Error Bars)
VARCOPE, CESVAR
“Massive Univariate Analysis”
-- Analyze each voxel separately

8. Resting State Correlations
Biswal, et al, 1995, noticed that many voxels had a similar waveform even after removing task
Were these waveforms being driven by endogenous neural activation?
Resting state scan: subject just lies there, no explicit task

9. Functional Connectivity: Seed-based=
GLM
Voxel = weighted Seed
Fit for the weight (b)
Contrast = [1]
Pass to higher group analysis
Can use correlation coeff
Voxel
Seed

10. Seed Regions Average across ROI Any ROI in FS
Define your own in conformed space
For default mode:
Isthmus cingulate
Precuneus

11. Default Mode
Isthmus cingulate seed

12. FC Analysis No task, subject just lies there, usually eyes open
Standard preprocessing operations
Motion correction
Slice-timing correction (usually less important)
Smoothing, etc
Nuisance regressor removal
Global signal removal?
Motion (derivatives, powers)
Low frequency (<.01Hz)
Physiology (respiration, heart rate, blood pressure, etc)
White matter, CSF

13. FS-FAST Configure the seed: Create the seed waveform
fcseed-config -segid fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg mean.L_Posteriorcingulate.config
1010 = left isthmus cingulate ($FREESURFER_HOME/FreeSurferColorLUT.txt)
Configuration done once
Create the seed waveform
fcseed-sess -s SessId –cfg L_Posteriorcingulate.config
Done for each session
Nuisance Waveforms (eg, WM)
fcseed-config -wm -fcname wm.dat -fsd bold -pca -cfg wm.config
“-wm” flag indicates to use white matter (also –vcsf for ventricles)

14. FS-FAST Configure the analysis:
mkanalysis-sess -analysis fc.lpccseed.surf.lh
-surface fsaverage lh
-fwhm 5
-notask
-taskreg L_Posteriorcingulate.dat 1
-nuisreg vcsf.dat 1
-nuisreg wm.dat 1
-mcextreg
-polyfit 5

15. FS-FAST Configure the analysis:
mkanalysis-sess -analysis fc.lpccseed.surf.lh
-surface fsaverage lh
-fwhm 5
-notask
-taskreg L_Posteriorcingulate.dat 1
-nuisreg vcsf.dat 1
-nuisreg wm.dat 1
-mcextreg
-polyfit 5
Do this instead of specifying a paradigm file

16. FS-FAST Configure the analysis:
mkanalysis-sess -analysis fc.lpccseed.surf.lh
-surface fsaverage lh
-fwhm 5
-notask
-taskreg L_Posteriorcingulate.dat 1
-nuisreg vcsf.dat 1
-nuisreg wm.dat 1
-mcextreg
-polyfit 5
Seed waveform
Created by fcseed-sess
“1” – use single waveform
Does not make sense to use more for a seed

17. FS-FAST Configure the analysis:
mkanalysis-sess -analysis fc.lpccseed.surf.lh
-surface fsaverage lh
-fwhm 5
-notask
-taskreg L_Posteriorcingulate.dat 1
-nuisreg vcsf.dat 1
-nuisreg wm.dat 1
-mcextreg
-polyfit 5
Nuisance waveforms
Created by fcseed-sess
“1” – use single waveform
Possible to use more than one for nuisance

18. FS-FAST Configure the analysis:
mkanalysis-sess -analysis fc.lpccseed.surf.lh
-surface fsaverage lh
-fwhm 5
-notask
-taskreg L_Posteriorcingulate.dat 1
-nuisreg vcsf.dat 1
-nuisreg wm.dat 1
-mcextreg
-polyfit 5
Motion correction nuisance waveforms

19. FS-FAST Configure the analysis:
mkanalysis-sess -analysis fc.lpccseed.surf.lh
-surface fsaverage lh
-fwhm 5
-notask
-taskreg L_Posteriorcingulate.dat 1
-nuisreg vcsf.dat 1
-nuisreg wm.dat 1
-mcextreg
-polyfit 5
Polynomial regressors. Larger order increases the bandwidth of the high-pass filter.
Could also use –hpf .01

20. FS-FAST Summary
Configure the analysis: mkanalysis-sess -analysis fc.lpccseed.surf.lh …
No need to create a contrast (mkcontrast), one called “L_Posteriorcingulate” will be made for you
selxavg3-sess -s sessionid -a fc.lpccseed.surf.lh
isxconcat-sess –c L_Posteriorcingulate …
mri_glmfit, etc
lh, rh, and subcortical

21. End of Presentation 21