Hi, Is it possible to run recon-all on a series of scans?
I have multiple scans that I want to process longitudinally. The .nii files have all been converted to .mgz files and labelled sequentially (i.e., 001.mgz, 002.mgz, etc.) in /Applications/freesurfer/subjects/<subjid>/mri. I've tried running recon-all on this whole folder with the command line: recon-all -subjid <subjid> -all, but it does not execute properly. Do I have to run each of these scans separately using recon-all (i.e., do I need to use a separate terminal for each scan)? Thank you in advance for your time and help.
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