External Email - Use Caution
I think so.
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Darko Komnenić
<komnen...@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, November 30, 2020 at 6:23 PM
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] arguments to use after pial edits
External Email - Use Caution
Thanks Matt!
Should I also add the -autorecon3 flag, or does that get performed
automatically if I put in "autorecon2"?
Best,
Darko
Message: 4
Date: Mon, 30 Nov 2020 19:16:06 +0000
From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Subject: Re: [Freesurfer] arguments to use after pial edits {Disarmed}
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:
<274fd511-f94f-4bc1-ae0c-804f1a6a3...@wustl.edu<mailto:274fd511-f94f-4bc1-ae0c-804f1a6a3...@wustl.edu>>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
I find the recon-all table to be helpful:
http://secure-web.cisco.com/1rQT1vL5GWrATp5z0Ct2LBj8MsEx75qijDiNOIOc1xsGTqc0VC-s7rH5tRIiUV_kHXR7CsV_-uoWR6y_oPuNxiCAZCmbkgfSfUxHd4oB4gX7XvLCt40MlQR_Ejq0tpN0lnJJt1uO1jl_1XWYZQv92-3NGME0PKZPC51_qjOKHk9cLfcojjN-AssGWAZ7y0t-UJXooxg2G2tzrQqm9emqIASj8_asI8t84TuQRjHEjkEj7KDq8IvfbXNQIT5xDLxB5A7a-aT2IrgX3QZs0Stdt7Q/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllTableStableV6.0
In this case, you probably need to run -autorecon2, as all subsequent steps are
affected by the brainmask.mgz file.
Matt.
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