3dClustSim: small cluster size, almost all brain covered by significant clusters (?)

Also Stimulus_type is a within-subject factor (for all participants).

In that case, consider the following model (see more discussion about model specification here):

3dLMEr -prefix LMEr -jobs 12 \
...
 -model  'Group*Propofol_Concentration*Stimulus_type+Gender+Session+(1|Subj)+(1|Subj:Stimulus_type)+(1|Subj:Session)' \
 -qVars 'Propofol_Concentration' \
...

If I want to show the chi square results, which threshold should I use?

In general, I suggest a voxel-level p-value of 0.01 and a cluster-level threshold (e.g., 20 voxels). Then, adopt a highlight, but don't hide approach in result reporting.

Gang Chen