I believe I've taken care of that by masking non-brain voxels using a group intersection mask. Here's my code for these three steps:
#Neutral cues
3dttest -prefix tmp.ds_neutral_tvs0 -base1 0 \
-set2 \
../s01/s01_ds_CR.buc_norm+tlrc'[1]' \
../s02/s02_ds_CR.buc_norm+tlrc'[1]' \
../s03/s03_ds_CR.buc_norm+tlrc'[1]' \
../s05/s05_ds_CR.buc_norm+tlrc'[1]' \
../s06/s06_ds_CR.buc_norm+tlrc'[1]' \
../s07/s07_ds_CR.buc_norm+tlrc'[1]' \
../s08/s08_ds_CR.buc_norm+tlrc'[1]' \
../s09/s09_ds_CR.buc_norm+tlrc'[1]' \
../s11/s11_ds_CR.buc_norm+tlrc'[1]' \
../s12/s12_ds_CR.buc_norm+tlrc'[1]' \
../s13/s13_ds_CR.buc_norm+tlrc'[1]' \
../s14/s14_ds_CR.buc_norm+tlrc'[1]' \
../s15/s15_ds_CR.buc_norm+tlrc'[1]' \
../s16/s16_ds_CR.buc_norm+tlrc'[1]' \
../s17/s17_ds_CR.buc_norm+tlrc'[1]' \
#Apply intersection (group) mask
3dcalc \
-a tmp.ds_neutral_tvs0+tlrc \
-b ${stdir}/masks/CR_group_mask+tlrc \
-expr "a*b" \
-prefix all_ds_neutral_tvs0_masked+tlrc
#Add FDR curves to output datasets
foreach dset (`ls -1 all*BRIK`)
3drefit -addFDR $dset
