Thank you Bruce. However, doing the recon-all for both the wm and the cp will have the same result as adding the control points and recon-all in a first step, and then doing the wm edits and recon-all again? I think that if you perform the wm edits in the result of having added the cp, the edits you need may be different than if you have not done the cp step previously. Is this right? Thus, even though it is possible to do an only recon-all step for both edits, is it recommendable to do it?

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

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