Hi Emily,
Assuming the brain stem is indeed included, yes, it would
be prudent to re-run the analysis. Sorry about that! We
will be making some macros to help with this in the future,
which would enable a command like:
3dbucket -prefix SUBJ_WM.nii aparc+aseg.nii'<AFNI_FS_WM>'
That label does not yet exist though.
- rick