Hi Srikanth,
Sorry for being slow, many of us were out of town. Please feel
free to "bump" (reply to) your own message in the future, so that
we see it near the top.
You can use 3dSurf2Vol to create an anatomical mask of the cortical
surface from the standard surface maps.
Note that the surface will not accurately follow the contours of any
subject's brain, and so it does not make for a very good gray matter
mask. See example A from "3dSurf2Vol -help", and consider adding a
'-surf_B' option. You might also consider options '-f_p1_mm' and
'-f_pn_mm' to make the surface thicker.
In any case, it is unlikely that you would be satisfied with such a
mask.
- rick
