Hi Stephen
why do you say it invalidates the morphometry? And we need to know what
pial surface editing you did in order to answer your questions (and what
recon-all steps you rerean)
cheers
Bruce
On Sun, 11 May 2014, S.V.Shepherd [work] wrote:
Hi Bruce,
Thanks again for your help at the FreeSurfer course. I've corrected the pial
surface
manually (knowing that this invalidates the morphometry, but that by restoring
the medial
surface it does let me process functional data). Having done this, do I need
to remake
spheres and patches, or are these unchanged? For example, when using
mri_vol2surf, does
freesurfer know what elements to sample by consulting the ?h.orig and ?h.pial,
or are there
downstream files I should update as well?
Thanks!
stephen
stephen v. shepherd phd
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA //
212.327.7620
On Mon, Apr 21, 2014 at 11:28 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Stephen
no, sorry. There are others on the list that have extensive experience in
using
FS for NHP. Hopefully one of them can answer?
Bruce
On Mon, 21 Apr 2014, S.V.Shepherd [work] wrote:
Hi,
Did you have a chance to take a look at this? The basics shouldn't
be
NHP-specific, so I'd still value your input even though I know you
work only
with humans.
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 10:48 PM, S.V.Shepherd [work]
<stephen.v.sheph...@gmail.com> wrote:
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
<fis...@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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