Hi FSL experts,

I have a 2 (between sub) x3(within sub) mixed effects model that I ran using FLAMEO from the command line.

 flameo --cope=all_copes_angry_happy_neutral --varcope=all_varcopes_angry_happy_neutral --mask=mask.nii.gz --dm=design.mat --tc=design.con --cs=design.grp --runmode=flame1

I am trying to perform standard cluster correction (whole-brain) on the resulting zstat images. To my best knowledge, I should use smoothest to calculate the smoothness of the images, and then use cluster to perform the cluster correction.

smoothest -d 140 -r res4d.nii.gz -m mask.nii.gz >> cluster_correction/smoothness_output

cluster -i cluster_correction/zstat5.nii.gz -t 2.3 -o cluster_correction/cluster_zstat5_PI_COMP_H_A_clust -d 0.43451 --volume=234519 -p .05 --othresh=cluster_zstat5_PI_COMP_H_A.nii.gz


However, when I ran that cluster correction for my model, i am getting HUGE clusters that cover half of the brain, so they are absolutely not correctly thresholded. (Whereas when I open the raw z-stats image and threshold manually, I do not get such large clusters). I suspect something is wrong either with the original model (see design files attached) or the smoothest/cluster correction.

For smoothest, the input requires DF. degrees of freedom are unknown in a mixed effects model, but since flame 1 uses number of copes - all of the predictors including conditions, subjects, confounds, I calculated the DF from the number of rows - number of columns in the design matrix. Is the appropriate degrees of freedom for this analysis?

Thanks!
Michelle