Seedbased Resting State f MRI Analysis in Free

Seed-based Resting State f. MRI Analysis in Free. Surfer

Remember to do evaluations! 2

Overview • Task-based f. MRI Review • Seed-based Functional Connectivity Overview • FS-FAST Commands 3

Task-based Analysis Review 4

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

Raw f. MRI Waveform Task-based f. MRI Analysis y = X * b b. Odd b. Even bbase = Contrast C = [1 -1 0] Data from one voxel Design Matrix Regressors 6

Statistical Parametric Map (SPM) +3% 0% -3% Contrast Amplitude b. ON - b. OFF CON, COPE, CES “Massive Univariate Analysis” -- Analyze each voxel separately Variance of Contrast (Error Bars) VARCOPE, CESVAR H 0 Significance t-Map (p, z, F) (Thresholded p<0. 01) sig = −log 10(p) 7

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 8

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

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

Default Mode • Isthmus cingulate seed 11

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 (<. 01 Hz) – Physiology (respiration, heart rate, blood pressure, etc) – White matter, CSF 12

FS-FAST • Configure the seed: – fcseed-config -segid 1010 -fcname L_Posteriorcingulate. dat -fsd bold -mean -cfg mean. L_Posteriorcingulate. config – 1010 = left isthmus cingulate ($FREESURFER_HOME/Free. Surfer. Color. LUT. txt) – Configuration done once • Create the seed waveform – fcseed-sess -s Sess. Id –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/Fs. Fast. Functional. Connectivity. Walkthrough 13

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 14

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

FS-FAST • Configure the analysis: mkanalysis-sess -analysis fc. lpccseed. surf. lh -surface fsaverage lh -fwhm 5 -notask -taskreg L_Posteriorcingulate. dat 1 Nuisance waveforms Created by fcseed-sess -nuisreg vcsf. dat 1 “ 1” – use single waveform -nuisreg wm. dat 1 Possible to use more than -mcextreg one for nuisance -polyfit 5 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 Motion correction -mcextreg nuisance waveforms -polyfit 5 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 Polynomial regressors. -mcextreg Larger order increases the -polyfit 5 bandwidth of the highpass filter. Could also use –hpf. 01 19

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 • selxavg 3 -sess -s sessionid -a fc. lpccseed. surf. lh • isxconcat-sess –c L_Posteriorcingulate … • mri_glmfit, etc • lh, rh, and subcortical 20

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