Hi Tim,
The default for afni_proc.py is not to mask the data.
Note that afni_proc.py should warn you of this. So if
you do want to mask it, add the -mask_apply option.
---
One main reason is that intersecting the masks across
all subjects tends to remove a lot of brain from the
result. The other main reason is that you lose some
ability to trouble-shoot.
It is recommended instead that you apply a group mask
in standard space.
See the 'MASKING NOTE' section from "afni_proc.py -help"
for more details.
- rick
