Yes, that is expected with your command line. The issue is that you are using a positive (pos) a priori hypothesis about the sign of the effect. By default, freesurfer generates unsigned statistics (this is what you see when you just view the stats map). When you specify pos, it adjusts the voxel-wise sig value to that of the (lower) signed test, so you see more voxels.

btw, the cluster forming threshold that you are using (1.3 = p<.05) is too small for GRF. Probably you need something like 3 (p<.001). If you want to use 1.3, then use permutation.

Dear Freesurfer experts,

I'm trying to run multiple comparisons correction using mri_glmfit-sim. Since I'm working with volume data, I used -grf instead of -cache. The resulting map has bigger clusters with higher significance values than the original sig.mgh map from mri_glmfit. Is this normal? Is there anything I should change in my command?

Here is the command:
mri_glmfit-sim --glmdir r_PCC_glm --grf 1.3 pos --cwp 0.05 --2spaces

Thanks,

Jiahe

--

Jiahe Zhang

Ph.D. Candidate

Department of Psychology

Northeastern University

617-373-4789

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