Hi Stephen
can you upload the whole subject dir? Also, why is there no aseg for this
subject?
Bruce
On Tue, 8 Apr 2014, S.V.Shepherd [work] wrote:
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.
>
> 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>
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