Hi Antonio,

You only need to run autorecon2 once, and you should choose the option that starts the farthest back in the stream for the edits you did.

For example, autorecon2-cp starts farthest back, then autorecon2-wm, and then autorecon2-pial runs the fewest steps.  So, if you’ve added control points and done any of the additional edits you will need to run autorecon2-cp.  If you’ve done wm edits and pial edits you will need to run autorecon2-wm, and if all you’ve done are pial edits you will need to run autorecon2-pial.

I hope this makes sense.

Jenni

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From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Gallo, Antonio (NIH/NINDS) [F]
Sent: Tuesday, November 21, 2006 4:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] more than one edit in the same subject

Dear All,

Since I sometimes need to fix more than one output in the same subject (for example, editing the WM, correcting the pial surface, and adding some control points), I was wondering whether

1) I had to run autorecon2 after each correction;

2) If yes (to the above), should I run autorecon2 in any specific order?

Thanks,

Antonio

Antonio Gallo, MD

NIB-NINDS-NIH

10 Center Drive

Building 10, Room 5B16

Bethesda, MD, 20892 - USA

ph #: 001-301-402.6391

fax #: 001-301-402.0373

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