the pial curvatures will change, but you probably don't use them anyway
cheers
Bruce
On Tue, 13 May 2014, S.V.Shepherd [work] wrote:
Just to follow up, it looks like mris_thickness needs to be run, but
mris_curvature is unchanged by changes to the pial surface. Thanks again
for the help!
st
Just to follow up, it looks like mris_thickness needs to be run, but
mris_curvature is unchanged by changes to the pial surface. Thanks again
for the help!
stephen
*stephen v. shepherd phd*
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
// 212.327.7620
On Sun, May
don't rerun that as it will rerun the surface deformation. Use
mris_thickness and mris_curvature
On Sun, 11 May 2014, S.V.Shepherd [work]
wrote:
Looking over our scripts, it appears we normally generates the surfaces etc.
through
recon-all -autorecon2-wm <...> -noaseg
despite that ?h.pial
just use mris_thickness. The others should be fine
On Sun, 11 May 2014,
S.V.Shepherd [work] wrote:
Hi Bruce,
How would I go about updating the thickness estimates (?h.thickness, I presume)
after
manually adjusting the pial surface in FreeView? Are the other surfaces
(inflated, sphere,
etc.
Looking over our scripts, it appears we normally generates the surfaces
etc. through
recon-all -autorecon2-wm <...> -noaseg
despite that ?h.pial isn't explicitly listed as an output in the dev table (
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable).
It looks like a step from autorecon
Hi Bruce,
How would I go about updating the thickness estimates (?h.thickness, I
presume) after manually adjusting the pial surface in FreeView? Are the
other surfaces (inflated, sphere, etc.) unaffected by this change, or
should they be recalculated as well?
stephen
*stephen v. shepherd phd*
Hi Stephen
only the thickness estimates should matter, unless you've lost an entire
gyrus or something
Bruce
On Sun, 11 May 2014, S.V.Shepherd
[work] wrote:
Hi Bruce,
This is the manual edit of the pial surface in FreeView, correcting locations
where the grey
matter failed to grow out of
Hi Bruce,
This is the manual edit of the pial surface in FreeView, correcting
locations where the grey matter failed to grow out of the white matter. It
took place after the pipeline had completed, but I'm not sure if I need to
rerun/regenerate steps which are dependent on the pial surface. For
ex
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
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 a
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 sti
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
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
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 up
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
SVSHE
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]"
> wrote:
>
> Greetings,
>
> I've been reconstructing a surface in an NHP using a Kolster T1 scan and
> FS5.3. It we
16 matches
Mail list logo
