Hi Bruce,

As requested, I'm transferring over the entire folder. It's saved as 140107OTIS_from_Shepherd_attn_Fischl.tar.gz

Our pipeline appears to sidestep aseg (I'm not precisely sure why or how). I have what I think are a reasonable brainmask.mgz and wm.mgz, which appear to be the two key files to target for manual edits. But when I proceed to the next step:

   recon-all -autorecon2-wm -subjid 140107OTIS -cc-crs 128 108 168 -pons-crs 128 255 128 -noaseg

there are divots in the grey matter in the ACC just anterior and dorsal to the genu and in middle OFC. I'm not sure why. Additionally, the wm edits in occipital do not appear to be helping. This is easiest to see if I run

   tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs

select a point just to the side of midline (e.g. 125 103 128) and switch to a sagittal view.

Thanks for your help.

stephen

stephen v. shepherd   phd
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620

On Wed, Apr 16, 2014 at 10:05 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

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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