afni.nimh.nih.gov

Hi Ranjan,

We do not generally apply masks at the subject level.
But you want to, use 3dcalc to multiply the stats
dataset (or particular sub-bricks) by the full_mask
dataset, for example. Then run 3drefit -addFDR, e.g.

3dcalc -a stats+tlrc -b full_mask+tlrc -expr a -prefix stats.masked
3drefit -addFDR stats.masked+tlrc

- rick