Although there are many ways to correct for pial, WM, and segmentation defects, it seems common in the literature to forego any edits and simply either accept or reject a subject's FreeSurfer output in order to avoid subjectivity and potential over-editing. Another group rejected subjects if their defects spanned 6 or more slices, for example.

Are there any guide lines on how much editing is too much editing? Should it just be edited enough so it looks tolerable by eye? Maybe by a few different raters?

The defects vary in their severity, so it's difficult to know if a subject should be considered passable or requiring edits based on a minor defect.

My current plan is to conduct my analysis once with excluding subjects with poor segmentation and then again, including  those subjects' edited outputs. Do you agree with this logic?

Thanks for your advice,

Ryan
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