You only need to do:
recon-all -autorecon2-cp -autorecon3 -subjid subject3_before
-autorecon2-cp will do all the steps in -wm and -pial
doug
Matt Clarkson wrote:
Hi there,
If you run recon-all, and then do some edits, for example control points, then the tutorial says you do: recon-all -autorecon2-cp -autorecon3 -subjid subject4_before
Similarly for white matter: recon-all -autorecon2-wm -autorecon3 -subjid 111_manual_edits_before
and similarly for brain mask: recon-all -autorecon2-pial -autorecon3 -subjid subject3_before
So, if I have done all 3 types of edits, would it be better to do:
recon-all -autorecon2-cp -autorecon3 -subjid subject3_before recon-all -autorecon2-wm -autorecon3 -subjid subject3_before recon-all -autorecon2-pial -autorecon3 -subjid subject3_before
or would I do: recon-all -autorecon2-cp -autorecon2-wm -autorecon2-pial -autorecon3 -subjid subject3_before
While the second option is more than likely quicker, will it make any difference to the results?
Many thanks in advance.