Dear experts, I would like to run a for-loop in FreeSurfer 5.1. so that I can have multiple subjects analyzed over the holiday, without having to come to the lab and start each of them myself. I searched the previous emails in this list and know that I can make a file with a subject list, and then have the loop go through that file. I was wondering, however, how to handle the -i part of recon-all command? Each subject in a loop needs to have one brain image assigned - I don't think FreeSurfer will know where to look for images just by telling it what the subject name is. Thanks in advance for any help!
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