Hello Freesurfer Developers,

I am brand new to Freesurfer, so I'm just getting acquainted with how to use the program. Our clinic is attempting to run quality control on our imaging data for the last five years. One issue that I've noticed many times in our sample is that the Freesurfer program includes portions of the dura and pia mater in the brain mask volume after running reconstruction. On particularly bad images, it looks like a small part of the skull is included too. I've browsed through the tutorial datasets on Freesurfer, but it seems like there isn't an obvious way to make edits to images to correct for this.

Please let me know what edits I should make if I want to correct for this. In addition, let me know if there is a way to correct for this error that can be quickly applied to a large number of subjects at once. There are at least 150 brains that have this issue, so it would be helpful if there was a way to correct this error quickly.

Best,

Mackenzie

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