You can try -more or -less when running mri_watershed

You can correct is manually to get a better inner skull. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview After fixing you can run mri_binarize with the --surf option

Not sure about the outerskull if you are doing manual labeling

For the skin, you can run mkheadsurf

On 5/27/2020 7:35 AM, Edoardo Pinzuti wrote:

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Dear Freesurfer community,

using the mri_watershed and -surf to crate inner_skull, outer_skin and outer_skull I get a incorrect inner_skull segmentation, probably due to an erroneous skullstrip. I tried to modify the parameters available but it does not help.  Is there a way to correct this, manually correct or with a mask ?  Any other suggestions will be really appreciated

Thanks Edoardo

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