Hello FreeSurfer Gurus,

 

For some reason, I’ve noticed a common issues issue with the autorecon1 skull stripping step in my dataset (see example below – most look quite similar to this). As such, I have been inserting a skull stripped image from AFNI after autorecon1 to circumvent this issue (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12720.html).

 

Should I be concerned that whatever was causing this clipping could be affecting my ICV values?

 

Thanks so much,

Carly