Hi Doug, I was trying to run functional connectivity analysis following instructions on the FreeSurferWiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough). I was able to successfully run the following commands (nothing errored as far as I can tell) but the resulting partial correlation and significance maps turned out to be empty. Could you take a look at the commands and let me know if anything can be improved?
1. PREPROC preproc-sess -s subject_001 -fwhm 6 -surface fsaverage lhrh -mni305-2mm -fsd bold -per-run -stc up 2. SEED CONFIG fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg mean.L_Posteriorcingulate.config 3. SEED TIMECOURSE fcseed-sess -s subject_001 -cfg mean.L_Posteriorcingulate.config (wm.dat and vcsf.dat were similarly created) 4. ANALYSIS CONFIG mkanalysis-sess -analysis fc.lpccseed.surf.lh.lpf -surface fsaverage lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 5 -per-run -lpf .1 5. ANALYSIS selxavg3-sess -analysis fc.lpccseed.surf.lh.lpf -s subject_001 Thanks, Jiahe -- Jiahe Zhang Ph.D. Student Department of Psychology Northeastern University 617-373-4789
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