Hi FreeSurfer Team, My lab has recently begun editing longitudinal data in version 6 and have found that we cannot use the same flags for -autorecon2 as we did when running longs in version 5.1. Typically, after making any necessary edits to a long, we run -autorecon2-pial -autorecon3. This flag hasn't been successful in version 6, producing an error message that the flag is unrecognized. Because we still only require some brainmask edits on the longs, we would like to know how we can continue to run these to process only pial.
All help is greatly appreciated! Allison
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