I am trying to do a 3dANOVA on some seed connectivity maps. I would like to do the analyses within a specific mask. My understanding is that when one does a 3dANOVA within a mask, the F and t-statistics should change for each voxel because there are fewer voxels tested. I tried to apply the mask by adding – mask to the 3dANOVA command. However, the F and t-statistics for each voxel still exactly matched the whole brain analysis. I know that the mask did work in other respects in that areas outside the mask did go to zero. What then is the correct way to do this analysis?
Under what circumstance are you using 3dANOVA? Could you post the script here?
Masking only hides those voxels you don’t want to see through zeroing, and it does not change anything for those voxels you don’t want to hide.
Okay, so it sounds like when you do a 3dANOVA only considering the voxels in a mask, only the cluster threshold should change? Correct? I had been hearing the opposite. In this analysis, I am looking at connectivity differences in different drug conditions within a mask (all within subject). Here’s the script, it’s in bash
3dANOVA3 -DAFNI_FLOATIZE=YES -type 4 \
-alevels 2 \
-blevels 2 \
-clevels 25 \
-dset .... #### 100 images here
-mask $maskimg \
-fa FSalKet \
-fb FDay12 \
-fab FAB \
-amean 1 SalMean \
-amean 2 KetMean \
-bmean 1 plbMean \
-bmean 2 guaMean \
-abmean 1 1 SalPlbMean \
-abmean 1 2 SalGuaMean \
-abmean 2 1 KetPlbMean \
-abmean 2 2 KetGuaMean \
-adiff 1 2 SalvsKet \
-bdiff 1 2 PlbvsGua \
-aBdiff 1 2 : 1 salPlbvsKetPlb \
-aBdiff 1 2 : 2 SalGuavsKetGua \
-Abdiff 1 : 1 2 SalPlbvsSalGua \
-Abdiff 2 : 1 2 KetPlbvsKetGua \
-bucket $tdir/anova2x2_${seed}_cope_z_${msk}
Both factors are within-subject?
it sounds like when you do a 3dANOVA only considering the voxels in a mask, only the cluster threshold should change? Correct?
Yes, that’s correct.