Hi Manuel
-autorecon2-cp runs all the steps that autorecon2-wm does so it is redundant. If you run autorecon2-cp and autorecon3 you will get everything (unless you edit the aseg)
cheers Bruce On Thu, 30 Mar 2017, Manuel Delgado wrote:
Dear list, There is an issue that I have been concerned about since the beginning of my FS learning, as I have found somehow contradictory information in the tutorials. Is there a way to do an only recon-all after all the edits have been made to a subject? For example, if you have edited all the possible steps (skullstrip, control points, wm and pial surface) is it possible to use all the flags for each step in one only step? Something like: recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3 -subjid
<subject>
Or on the other hand each step needs its own recon-all with its appropriate flag? Thank you
-- Manuel Delgado Alvarado, MD Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN