You can also register your subjects to the new average subject (creates a new spherical registragtion). Use the surfreg script (run with --help for more info).
doug

On 2/15/13 8:55 AM, Bruce Fischl wrote:

Hi Sophie

what template do you mean? You can't rerun the subcortical segs or parcellations since they depend on manual labelings. You could regenerate our cortical folding patterns atlas, but I don't think that buys you much since the atlas you would build is by definition in register with our current one (if it wasn't you wouldn't be able to use our cortical parcellations)

cheers
Bruce

On Fri, 15 Feb 2013, Sophie Maingault wrote:

Hello Freesurfer experts !

I created a new template with make_average_subject called 80tvs and I would
like to re-run some of my subjects with this new template. I can?t find the
command line in FAQ. Is it for example : recon-all ?all ?s t0001 ?target
80tvs ?? So I need the repertory of this new template in the subject_dir ?

Thank you for the answer !

Sophie
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