From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Thursday, February 17, 2022 6:06 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)

The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the the white.preaparc is where the problem starts.

When you say that v6 did better, do you mean on this same data or on different data? The surface placement has not changed that much since v6.

On 2/14/2022 12:50 PM, Edan Daniel wrote:

External Email - Use Caution

We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6.
After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1):

recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)

The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on?

Would love to hear your thoughts about this.

Many thanks!!

Edan, Braindevlab@Princeton
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