Folks:
I'd appreciate if someone could explain the brainmask.auto.mgz, and brainmask.mgz logic?
Somewhat alarming is that in a brainmask volume, I'm seeing some full-brightness (255) values on the edge of the mask (border of brain and nothing), which are certainly not in the input volume T1.mgz volume.
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".
Question 1: Is there a rationale for 255 values?
That led me to look at the brainmask.auto volume, and the "bad" values are not there either.
The recon-all script is a bit puzzling and convoluted in this area --
Question 2: It appears that the Skull Stripping section of the script uses a "-keep" flag on mri_watershed. This isn't explained on the wiki doc page -- what does it do? (And why does mri_watershed get BMA and two BM's?)
Question 3: In the normal case, does brainmask.auto.mgz just get copied to brainmask.mgz? If so it's a puzzle to me how these wind up different (in the cases I looked at the mgz files are not the same size).
<more scratching of head>
Thanks,
Graham