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
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