Hello,

When running afni_proc.py I included the following lines (I mention only the ones relevant to this question):

-blocks tshift align tlrc volreg blur mask scale regress \
-volreg_align_e2a \
-volreg_tlrc_warp \
-regress_apply_mask \

Subsequent to running afni_proc.py, I ran a second level analysis with 3dttest++. However, when I look at the 2nd level results as an overlay (with talairach template as an underlay), there are definitely some clusters of voxels outside of the brain. Otherwise, everything else looks pretty good and I got expected results. However, why doesn't the masking carry through to the 2nd level analysis?

Thanks,
Liana