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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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