The error that you have there is probably an incorrectly fixed defect and should be fixed by editing the wm.mgz (ie, probably not control points for now). There are no edits specifically for FLAIR (which will only affect the pial surface -- here the white surface is off)

On 1/23/2020 2:34 PM, Swanson,Clayton wrote:

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Hi FreeSurfer Developers,
After looking through the archives my question still remains. I am wondering if the same rules apply for editing/correcting FLAIR images as it does for T1 images. For example, can I add control points to the WM.mgz then re-run recon-all using the command recon-all - s <subject> -autorecon2-cp -autorecon3. For visualization I have attached a screenshot of what I am attempting to correct.

Thank you for your help,

Clayton
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