Hi Stephen Are the ventricles and callosum correctly labeled? If you upload a subject I'll try to take a look Cheers Bruce
> On Apr 7, 2014, at 8:38 PM, "S.V.Shepherd [work]" > <stephen.v.sheph...@gmail.com> wrote: > > 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 > > <Capture1.PNG><Capture2.PNG> > > > stephen v. shepherd phd > The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // > 212.327.7620 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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