Hi,

You can simply rerun 'recon-all -all’ on top of your already processed/edited subject, and it will respect your previous edits.  Of course, it is a good idea to still review/QC the results afterwards, to make sure that the outcome of those edits is satisfactory under the new FS version.

And, if you want to preserve your results under FS 5.3, then you should make a copy of those results before rerunning recon-all.

cheers,

-MH

-- 

Michael Harms, Ph.D.

-----------------------------------------------------------

Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave. Tel: 314-747-6173

St. Louis, MO  63110 Email: mharms@wustl.edu

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Kirstie Whitaker <kw401@cam.ac.uk>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, June 22, 2016 at 1:28 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Quality control with different pipelines

Hi everyone,

I processed and edited 300 participants for our study using Freesurfer 5.3 and I'd like to move to using the dev version that's currently available because we have a bunch more data that's been collected and I think it does a better job. (This question also applies to moving to v 6 when it is released).

If I run the dev version of recon-all and then copy over the control points and wm.mgz files that we edited in the original run, and run recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very good approximation for the edits we conducted? Or does this "shortcut" not do what I think it does?

Does anyone have any experience moving from one version of freesurfer to another without having to start from square one with the edits?

Thank you again for the fantastic tools!

Kx

--

Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

Phone: +44 7583 535 307

Website: www.kirstiewhitaker.com

 

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