I believe ventricles and callosum are correctly labeled. I've been viewing with ''' tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs '''. I've uploaded ( as per the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange ) the file contents of my Otis's mri/ directory, as SVSHEPHERD_subj_OTIS_for_DOUG_on_20140408.tar.gz. I hope this will be enough?
Ares of concern are * ACC (e.g. 123 105 208) - maybe misses a thin wm bundle? or won't grow grey from CC? * OFC (e.g. 123 133 218) - may be excluded as Olfactory Bulb, or bc too bright. * Occ (e.g. 115 109 97) - mostly poor scan quality; may require manual overpaint.
stephen
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.
- 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?
- 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.
- 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
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