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.) 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 <[email protected]>
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
<[email protected]> 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
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