AFNI version info (afni -ver): Version AFNI_25.2.12 'Gordian
Dear AFNI team, Gang in particular,
I ran 3dLMEr successfully in which I added 3dClustSim. When I view the results in the GUI, I am unsure how Clusterize is applying the output from 3dClustSim, or if it is at all applying it given my script. Which statistics does Clusterize use, and how is it connected to my 3dClustSim results?
I have not been able to find this in the afni documentation/figure it out. I have attached my script in case it helps, as I am not fully certain I scripted 3dClustsim correctly.
Thank you for your guidance!
Kind regards,,
Aude
3dLMEr -prefix $outp -jobs 12 -mask $group_mask -dbgArgs \
-model "Group*Time+(1|Subj)" -SS_type 3 -bounds -3 3 \
-gltCode main_group "Group : 1*MM -1*BVS" \
-gltCode main_time "Time : 1*post -1*pre" \
-gltCode interaction "Group : 1*MM -1*BVS Time : 1*post -1*pre" \
-gltCode mm_pre "Group : 1*MM Time : 1*pre" \
-gltCode mm_post "Group : 1*MM Time : 1*post" \
-gltCode bvs_pre "Group : 1*BVS Time : 1*pre" \
-gltCode bvs_post "Group : 1*BVS Time : 1*post" \
-gltCode mm_change "Group : 1*MM Time : 1*post -1*pre" \
-gltCode bvs_change "Group : 1*BVS Time : 1*post -1*pre" \
-gltCode mm_vs_bvs_pre "Group : 1*MM -1*BVS Time : 1*pre" \
-gltCode mm_vs_bvs_post "Group : 1*MM -1*BVS Time : 1*post" \
-resid ${outp}_resid \
-dataTable @$table 2>&1 | tee -a $log
if [ $? -ne 0 ]; then
echo "3dLMEr FAILED for $lab" 2>&1 | tee -a $log
((idx++))
continue
fi
# ---------------- smoothness & ClustSim ----------------
resid="${outp}_resid+tlrc"
if [ -e "${resid}.HEAD" ]; then
echo "Estimating smoothness (3dFWHMx)..." 2>&1 | tee -a $log
3dFWHMx -acf -mask $group_mask -input $resid > ${out_dir}/acf_${lab}.1D 2>&1 | tee -a $log
acf_line=$(awk 'NF>=3{l=$0}END{print l}' ${out_dir}/acf_${lab}.1D)
a1=$(echo $acf_line | awk '{print $1}')
a2=$(echo $acf_line | awk '{print $2}')
a3=$(echo $acf_line | awk '{print $3}')
echo "ACF: $a1 $a2 $a3" 2>&1 | tee -a $log
echo "Running 3dClustSim (pthr 0.05,0.01,0.001)..." 2>&1 | tee -a $log
3dClustSim -mask $group_mask -acf $a1 $a2 $a3 -iter 10000 -athr 0.05 -pthr 0.05 0.01 0.001 -prefix ${out_dir}/ClustSim_${lab} 2>&1 | tee -a $log
else ```