Hi Monica
We need a bit more detail to figure out why things are going wrong. Can you
send screenshots or upload a subject? Is the white matter in that region
already 110? Sometimes adding control points in the subjacent wm will bring
intensities up enough to correct the pial. You can also change the intensity
targets in mris_make_surfaces if the control points don’t help, using expert
opts
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Monica Bondy
Sent: Wednesday, September 9, 2020 10:58 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Extending the pial surface
External Email - Use Caution
Hi Freesurfer Developers,
I was hoping to get some advice on fixing pial surface error so we can
calculate cortical thickness. In several patients, although the aseg is fine,
the red outline for the pial surface is missing parts of the cortex (not the
subcortical areas, those are alright). Unfortunately, we cannot use control
points to edit the pial surface because there is no white matter in those parts
of the brain. Is it possible to manually extend the pial surface to include the
excluded cortex?
Also, I looked through the archive and found a similar question and read that
overriding the intensity statistics that mris_make_surfaces computes
automatically may solve my issue. If this is possible could I have some advice
on how to do this?
Otherwise, if you have any advice to fix this problem we would greatly
appreciate it.
Thanks,
Monica
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