In theory you could, but you'd have to map the tp1 brainmask to tp2. Note that it might not matter that much because the cross surfaces are not used during the base creation. I would see how things look in the base, then edit the brainmask in the base if needed. The base brainmask will then be propagated to the long time points, so maybe you only have to edit it once, if at all.

On 3/16/2023 3:16 PM, KennethSPrice wrote:

External Email - Use Caution

Hello all,

I'm wondering if I can use brainmask or pial surface of timepoint1 as a reference for the skullstrip of timepoint2. TP2 is being problematic during skullstrip. I've tried -wsthresh and -gcut. Any option to use brainmask1 as a reference point for brainmask2?

Sent with Proton Mail secure email.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer