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