Hi Liana,

The mask block is needed for some computations, but it is not
actuallly applied to the single subject results (since we think
that is a bad idea).

If you really want it applied to the single subject results, add
the -mask_apply option, with one of the paramters: epi, anat,
group, extents, e.g. to apply the EPI mask:

-mask_apply epi

But we suggest making your own group mask to apply at the group
analysis level. If you want to do that, consider using 3dmask_tool,
e.g.

3dmask_tool -input group.*/subj.*/*.results/full_mask*.HEAD \
-frac 0.7 -prefix ./group_EPI_mask

That would make a mask from all subjects' EPI masks, but where at
least 70% of the subjects are in the mask.

- rick