The edits you are making only change the initial surface; the surface
placement then refines the placement. Sometimes the surface placement
can be quite stubborn. If this is the case, the ?h.orig.nofix and
?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent).
Also check the the white.preaparc is where the problem starts.
When you say that v6 did better, do you mean on this same data or on
different data? The surface placement has not changed that much since v6.
On 2/14/2022 12:50 PM, Edan Daniel wrote:
External Email - Use Caution
We have been having issues with recreating the final surfaces after
editing the white matter segmentation, which used to work smoothly in
version 6.
After running a subject through recon-all (version 7.1.1 *without* the
parallel flag) and then editing the white matter, we run the following
command (w v7.1.1):
recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername '
-cc-crs ' num2str(corpus_point)
The ribbon file and surfaces do update *very slightly* but it’s
largely ignoring our (sometimes large) edits. This pipeline worked
well for us in version 6- do you have any idea what might be going on?
Would love to hear your thoughts about this.
Many thanks!!
Edan, Braindevlab@Princeton
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