Hi Rick,

Thanks for your reply. Yes, I'm basically looking for everything within the skull (i.e., brain volume+CSF). We are studying an older population and we want to control for premorbid brain size (i.e., before atrophy), and intra-cranial capacity seems to be the ideal way to do this.

I've done some research, and it seems like many of the programs out there (i.e., Freesurfer, etc..) can easily estimate grey matter volume, white matter volume, and subcortical volume, which, if we sum together, would give us an index of total brain volume. However, it is my understanding that none of these programs provide an estimate CSF volume around the brain (I believe there has been debate about whether one can accurately measure CSF volume around the brain from T1- or T2-weighted BOLD imaging).

I guess the ideal way to do this would be with a proton-density scan (which we don't have). Another option is to trace the cranial cavity on a T1 image, which is labor intensive. From my literature search on the topic there seemed to be a few automated or semi-automated programs out there that can do it, but all of them use software that I am completely unfamiliar with. Before I go down that road, I just wanted to check with you guys to see if there is a way to do it in AFNI.

Hope this makes things more clear!

Thanks again,

Liesel