Seed-based Resting State fMRI Analysis in FreeSurfer

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

Task-based Analysis Review

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

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

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

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

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

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

Default Mode Isthmus cingulate seed

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

FS-FAST Configure the seed: Create the seed waveform fcseed-config -segid 1010 -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) https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough

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

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

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

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

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

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

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

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