[Freesurfer] Longitudinal Stream: Recon-all and Base template

Hello All,

I am planning to run the longitudinal stream on my data set and I have a few questions:

1) When I run the data cross sectionally using "recon-all -all" should I specify all my subject's T1 volumes (using the -file1.nii -1file2.nii) or can I run each of my subject's T1 volumes individually through recon-all? My understanding is that some motion correction will occur if I specify more than one T1 which may alter the results versus if I specify one T1?

2) What input files should I use to create my base templates? Are the input files the norm.mgz files from each subject?

Thank you in advance for your help!

Best, Tamara