afni.nimh.nih.gov

If you just want to save disk space, a mask can me made
as part of most AFNI commands by naming the dataset
starting with 3dcalc, as in:

3dmaskave -mask '3dcalc -a ROIs+tlrc -expr amongst(a,13,19)' INPUT+tlrc

Putting the entire 3dcalc expression in quotes is important.

Does that seem like what you might want?

- rick