Dear FreeSurfer people, I have got a very basic question. I would like to (or better: have to) do some manual tracing on my data. For this, I want my brains to be motion- and nu-corrected and in Talairach. Therefore, I apply the -autorecon1 step to my dataset.
I always assumed that the T1.mgz output is in Talairach space, but 1) when I compare it to the original scan and 2) when I look at the processing flow in the ReconAllDevTable, I doubt this. Do I still need to apply the talairach.xfm to the T1.mgz or something like that?
1) Could you please let me know whether the T1.mgz is indeed the scan I need (thus: is T1.mgz the result of all the autorecon1-steps, accept for skullstripping)? 2) If not: how do I process my scans so that they are motion- and nu- corrected and in Talairach space?
THANK YOU!
Marieke