A: If your skull-stripped volume does not have the cerebellum, then no. If it does, then yes, however you will have to run the data a bit differently.
First you must run only -autorecon1 like this:
recon-all -autorecon1 -noskullstrip -s <subjid>
Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this brainmask.mgz file and check that it looks okay (there is no skull, cerebellum is intact; use the sample subject bert that comes with your FreeSurfer installation to make sure it looks comparable). From there you can run the final stages of recon-all:
recon-all -autrecon2 -autorecon3 -s <subjid>
I tried to process recon-all -autrecon2 -autorecon3 -s <subjid>.
But I have a problem.
Error message: Flag -autrecon2 unrecognized.
What is the problem?
1) FreeSurfer version: 6.0
2) Platform: CentOS release 6.8