Jenni:
Thanks for your reply and explanation of the brainmask logic and rationale.
As for this:
Question 1: Is there a rationale for 255 values? (in the brainmask volume)
I'm not sure where these are coming from in your volume - I assume you havent done any editting on this one.
These subjects' data may well have been edited (not by me, hence my not knowing exactly what's what here). And I suppose it's the brainmask.mgz volume that would have been edited, and the act of editing it sets voxels to 255 perhaps? (The 255's are in the appropriate locations to add additional grey matter to the edges.)
That leads me to believe that the answer to this:
Question 0: Is the detailed image data in brainmask.mgz ever used, or is it simply a zero/not-zero mask? Ie: is the meaning "masked brain", or "mask using non-zero values to show where brain is".
... is that brainmask.mgz is used by subsequent steps as a mask in combination with some other image volume providing the actual image. In that case the actual intensities of brainmask.mgz are ignored.
And I now see in the script that mri_ca_normalize does indeed use brainmask.mgz with the mask flag, so I guess I'm probably right that the actual intensities are unimportant. (And nu.mgz provides the actual image).
Phew, I think I now have that straight... for this week :-)
Graham