Hi Ed

just run them once - it will detect the manual interventions and preserve them.

cheers Bruce On Mon, 29 Feb 2016, Ed Gronenschild wrote:

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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