afni.nimh.nih.gov

If you are aligning to the template MNI152_2009_template.nii.gz (part of AFNI binaries), then you can use the #4 sub-brick of that as a gray matter plus CSF mask. You can align to that template using the @SSwarper script supplied with AFNI, for example.

In general, a gray matter mask can only be useful if reasonably high-order nonlinear registration (e.g., 3dQwarp) is used to align the brain to a template. Otherwise, there is too much inter-subject variability for this idea to be useful.