Greetings,
I've been reconstructing a surface in an NHP using a Kolster T1 scan and FS5.3. It went very well, at first, but I've hit a wall. I have trouble in occipital (due to poor signal strength/constrast) and some typical-with-NHP problems in ACC and OFC. I think there are three related questions.
1) I lose parts of the ACC near the genu of the corpus callosum. I have attached a screen shot -- the white matter and gray matter both look decent. I wondered if the corpus callosum might be handled specially, and if differences between human and nhp callosi might prevent the ACC from growing normally?
2) In trying to deal with this, I greyed out the ACA, which was bright and potentially confounding. I wasn't sure how to do this in brain.finalsurfs.manedit, since my understanding is that only 1s (nonbrain) and 255s (wm) were preserved. I tried brain, which got overwritten, but ultimately succeeded by editing brainmask and rerunning -autorecon2-wm. Is there a way to repain gray matter in brain.finalsurfs.manedit? Alternately, if I continue editing brainmask (or equivalent) directly, should I be darkening or lightening the gray matter in the excluded section of the ACC? I would assume lighten -- but in the OFC, some gray matter (not shown) appears to be excluded for being too bright.
3) In some places I've specified wm (e.g. in the ACC, here) but it hasn't stuck. I assume this is because autorecon isn't convinced by the wm specification after looking at brain.finalsurfs -- how might I (gently!) override this?
Thanks very much for your time and patience.
stephen
[image: Inline image 2][image: Inline image 1]
*stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
