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Hi,
I ran a functional connectivity analysis according to the walkthrough in the Freesurfer Wiki. After the group analysis (with mri_glmfit using ces and cesvar), I plotted the results (sig.nii.gz of the GLM) with freeview, but the distribution seems off. I'll attach a screenshot, but in case someone cannot access it: There are only few negative data points, the majority seems to be in two (!) approx. gaussian distributions centered at ~5 (the smaller one) and ~8, so most points have values between 5 and 10. Running an FDR correction suggested that the threshold should be 1.3
Because the seems highly unlikely, I search the mailing list archive and found out about the bug in the functional connectivity analysis. Therefore, I repeated the group analysis with the pcc instead of the ces, but that didn't really change anything. Side note/question here: There is no variance corresponding to cesvar I could use in that case, right?
Any suggestions on what could've gone wrong?
Here are the exact steps I used:
# Create nuisance variables for white matter: fcseed-config -wm -fcname wm.dat -fsd bold -pca -cfg wm.config fcseed-sess -sf Part3HR -cfg wm.config # Create nuisance variables for ventricles + CSF: fcseed-config -vcsf -fcname vcsf.dat -fsd bold -pca -cfg vcsf.config fcseed-sess -sf Part3HR -cfg vcsf.config
# Auditory cortex ################## # configure parameters fcseed-config -roi AC-rh -fcname AC-rh.dat -fsd bold -mean -cfg AC-rh.config
# create FC seeds fcseed-sess -sf Part3HR -cfg AC-rh.config
# FC analysis mkanalysis-sess -analysis fc.AC.surf.rh -surface fsaverage rh -fwhm 5 -notask -taskreg AC-rh.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run
selxavg3-sess -sf Part3HR -a fc.AC.surf.rh
isxconcat-sess -sf Part3HR -analysis fc.AC.surf.rh -o AverageFC_AC -all-contrasts -map pcc mri_glmfit --y ./AverageFC_AC/fc.AC.surf.rh/AC-rh/pcc.nii.gz \ --osgm \ --surface fsaverage rh \ --glmdir ./AverageFC_AC/fc.AC.surf.rh/GLM_AC-rh \ --save-eres \ --nii.gz
I'd appreciate any input. Thanks in advance!
Best regards, Laura
