The output results for q-value of my 3ttest++ on resting state data with two groups (healthy volunteers vs patients), two visits combined, using resting state scans, does not match the results using the afni display.

I used this gen_group_command.py:

# Compare all 100s vs 300s, combined visits, run 2

gen_group_command.py -write_script analysis_script.tt.100s_vs_300s_AllV_R2 -command 3dttest++

-prefix ResultsA.tt.100s_vs_300s_AllV_R2

-dsets CorrZfiles/corr_brain.???_1??.Visit?.2.Z+tlrc.BRIK

-dsets CorrZfiles/corr_brain.???_3??.Visit?.2.Z+tlrc.BRIK

-set_labels 100s 300s

-options

-Clustsim -prefix_clustsim Clust.100s_vs_300s_AllV_R2 -mask TSNR_brainmask_files/clip_count_group_brainTissueMask_tSNR10_Visit1.2+tlrc

and got the following results:

++ Smallest FDR q [1 100s-300s_Zscr] = 0.044138 <==========++++++++ @ p = .001, but q = .7157, L Anterior Cingulate Gyrus (BA 24) size 14 voxels

++ Smallest FDR q [3 100s_Zscr] = 1.13601e-10

++ Smallest FDR q [5 300s_Zscr] = 3.00011e-10

- Added 3 FDR curves to dataset

++ Output dataset ./ResultsA.tt.100s_vs_300s_AllV_R2+tlrc.BRIK

++ Output dataset ./Clust.100s_vs_300s_AllV_R2.resid.nii - 2-sample test: results are 100s - 300s

As noted, the smallest FDR q was 0.044138. However, when I look at the results in afni, there are no significant results at q=.05 (or .04 or .06). The only significant result > 10 voxels at p=.001 (with a q=.7157) is a cluster of 14 voxels which does not meet the clust size min of 38 for alpha = .001 and p= .05.

I’m wondering why the 3dttest++ command found the smallest FDR q = .04413, but I can’t find anything significant at anywhere near that level using the afni display.