When I run the first portion of the recon-all script according to the instructions in RecommendedReconstruction, the command I am instructed to use is:

recon-all -i invol1  -i invol2 -autorecon1 -subjid your_subject_name

This command allows me to specify the input files and assign them a name.

When I try to run the entire recon-all script according to the instructions in FSTutorial/MorphAndRecon, I am instructed to use this command:

recon-all -autorecon-all -s <subjid>

However, unlike the script for the first portion of the recon-all script, there does not appear to be anything in this command that allows me to specify my input files and assign them a name.  Because my subject name is not specified, I cannot get the recon-all script to run.  How do I assign a subject name without having to run the first portion of the recon-all script?  Any help will be greatly appreciated.