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Seed-based Resting State fMRI Analysis in FreeSurfer

Seed-based Resting State fMRI Analysis in FreeSurfer. Remember to do evaluations!. 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 ’

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Seed-based Resting State fMRI Analysis in FreeSurfer

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  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. +3% 0% -3% Statistical Parametric Map (SPM) 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 *b • 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: • 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

  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

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