Hi Bruce,

I'm confused about this.
The manual-intervention workflow directives listed in recon-all (6 beta)
tell that the series of commands should be:
-autorecon2
-autorecon2-cp
-autorecon3

-autorecon2 processes stages 6-23
and
-autorecon2-cp process stages 12-23

So it seems to be a waste of time to process stages 12-23 twice.

My question is: how to run stages 6-23 with control points?

Cheers,
Ed

On 26 Feb 2016, at 14:13, <freesurfer-request@nmr.mgh.harvard.edu> <freesurfer-request@nmr.mgh.harvard.edu> wrote:

Hi Ed

if you run the skull stripping the autorecon2 and autorecon3 it should 
detect and preserve your manual interventions

cheers
Bruce


On Thu, 25 Feb 2016, Gronenschild Ed (NP) wrote:

Hi,

I have made some manual skullstrip adjustments and added a
number of control points in the white matter.
How should I proceed with recon-all to incorporate both adjustments?

Cheers,
Ed

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