I have been working for a while now trying to get cluster thresholds by using 3dClustSim for a 3dLME group analysis I ran, but the thresholds I am getting still seem strangely low. For a wholebrain with functional data smoothed at 6 with 3dBlurToFWHM, at p threshold of .005, alpha of .05, NN2, bi-sided, it recommends a threshold of 16.3 (voxel size 3.125 mm x 3.125 mm x 3.125 mm). I am calculating my ACF values using 3dFWHMx and the input file is the residuals I collected from the 3dLME analysis I ran (which was supported as an option here: https://afni.nimh.nih.gov/afni/community/board/read.php?1,156149,156170). Below are the ACF values output:
0 0 0 0
0.572146 2.46819 7.35051 6.73157
Do you have any ideas about what I might be missing? Please know if I can add additional information to help get to the bottom of this.
After pondering for a while, those numbers do not seem out of the realm of reasonableness. Your blur level is pretty low: 3.125 mm voxels, with a final blur (not an added blur) of FWHM = 6 mm.
That would be akin to adding a blur of FWHM = 3 mm, or so, which is very small.
So if the final FWHM is supposed to be 6 mm (and that is estimated with a standard, Gaussian ACF), you are getting a mixed-model ACF FWHM estimate of 6.7 mm, which seems to be in the correct ballpark.
To be sure, note what the 4 parameters are. The first is the fraction of the Gaussian term in the ACF model (so the linear fraction is .43 = 1-.57). The Gaussian term is 2.5 mm (small), and the linear term is 7.35. But that leads to a reasonable FWHM of 6.73 mm.
Also to be sure, are you applying a brain mask in this computation?
Ok, great! Yes, I was using a wholebrain mask.