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 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 autorecon3 might be useful:
mris_make_surfaces <subjID> ?h -orig_white ?h.orig orig_pial ?h.pial
to update the curvature and thickness files without changing the wm and pial --
but I'm not
sure this is how it works.
stephen
stephen v. shepherd phd
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA //
212.327.7620
On Sun, May 11, 2014 at 5:22 PM, S.V.Shepherd [work]
<stephen.v.sheph...@gmail.com> 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.) unaffected by this change, or should they be
recalculated as well?
stephen
stephen v. shepherd phd
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA //
212.327.7620
On Sun, May 11, 2014 at 3:51 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
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 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 example, are mris_sphere, mris_curvature,
and mris_flatten dependent upon
the pial surface or cortical thickness, or do they work
directly off the wm/orig surface?
If the former, I should rerun them; if the latter I don't need
to do anything but just
repaint the functional statistics of interest using
mri_vol2surf and the updated cortical
bounds (which I presume happens automatically, having
corrected ?h.pial).
My comment about morphometry was meant to note that, since I'm
manually changing the
distance between the wm and pial surface in places where there
were medial surface
artifacts, it would be unwise to try to draw any conclusions
from comparing
manually-adjusted and automatically-calculated cortical
thicknesses.
stephen
stephen v. shepherd phd
The Rockefeller University / 1230 York Avenue / New York
NY 10065-6307 USA // 212.327.7620
On Sun, May 11, 2014 at 9:50 AM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
