Hello Bruce,

I think this ties to one of my previous questions. Most of the volumes I processed need both wm and pial edits (typically deleting incorrectly added voxels for both). More recently, I was editing wm.mgz for wm and brainmask.mgz for pial. From the wiki, if changes are made for both wm/pia, one can run recon-all -autorecon2 -autorecon3 and both changes would be incorporated, however with some volumes this does not happen: pial edits are incorporated correctly, but wm edits are not, I am not sure why, event though FS6.0.0 sees edits (running recon-all with -showedits points to edits in sm.mgz as well, and those edits propagate into filled.mgz. So next, I plan editing brain.finalsurfs.manedit.mgz for pia ( it turns out one cannot edit this also for wm when that means deleting voxels for wm), wm.mgz for wm, then run -autorecon2-wm -autorecon3. Is this a strategy, and if there are alternatives, please let me know. Also, for some reason, running recon with '-make all'  does not seem to work.

Thank you,

Octavian 
 

On Thu, Mar 30, 2017 at 8:51 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
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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