Hi Allison,
seems like autorecon2-pial has been removed from FreeSurfer (also in the
cross sectional stream). I don't know when, why and what would be the
equivalent command, but someone on the list will know.
About brainmask edits, they are described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits
The brainmask in the base is the union of all mask from cross (after
registration) and is fixed for all time points. If the mask is correct,
this is usually OK. So it makes sense to edit the brainmask in the base
and not in the individual time points. In the base you would re-run
autorecon2 and autorecon3 as the edited brainmask affects not just the
surfaces, but also aseg etc.
If edits are really needed in the long runs, then edit it there and also
run autorecon2 and autorecon3.
Best, Martin
On 07/14/2017 07:28 PM, Allison Rainford wrote:
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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