Have you looked at the individual subjects? This will sometimes happen when there are strong global signals as the global signal (by definition) gets into the regressor and is everywhere, so you end up with these large swaths of positive activation. You're already doing the things I would suggest. You can try doing more of it (eg, increase the number of components or the number of polynomials). You can also try something like the ithsmus cingulate to generate a default mode map to see if that looks typical.

On 7/9/2024 3:56 AM, Doll, Laura wrote:

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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
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