If by "total volume within the brain surface contour" you just mean the volume illustrated by the brain extraction mask, then you can take the unnormalised brain volume from sienax and then calculate the volume (in mm^3) of the brain mask that it used and just divide these two values. However, be aware that global brain atrophy may not be well measured by such an index, if the brain surface contour also moves inwards. That's why we normally prefer to normalise by the volume inside the skull, which is what the normalised volume from sienax is representing.
All the best,
> On 8 Aug 2017, at 21:29, Angela Spirou <[log in to unmask]> wrote:
> Hello FSLrs,
> I am trying to find the brain parenchymal fraction (BPF; defined as the ratio of brain parenchymal volume to the total volume within the brain surface contour) by using sienax (using only one time-point/scan). Given the normalized and unnormalized brain volume and the v-scaling factor gained by sienax, how would I calculate the BPF? My end goal is to gain some sort of atrophy percentage. Any help would be most appreciated. Thank you!