Hi,
The missing sulcus may be a consequence of the topology correction going awry.  Check the “nofix” surface to see the surface before topology correction.  If the topology correction is the problem, you’ll need to edit the wm.mgz.  There is an example on the FS tutorials.

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 Barbara Kreilkamp <bakk.hbg@googlemail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, July 6, 2016 at 12:05 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] question about white matter edits

Hi Rito,

I just read this today myself "Select a few control points around your trouble areas, space them out throughout the brain and on different slices. You want to pick points in a region where the wm intensity is lower than it should be (that is, having a voxel value less than 110)." from https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_freeview

Could it be that those control points grasp voxels that already have an intensity of at least 110? 

Best wishes,

Barbara




On 06/07/2016 17:25, Ritobrato Datta wrote:
Hi All,

We have run recon-all on T1 FLASH images have identified regions where the sulci were included inside the white matter boundary. We added controls points around the sulci (please see attached pic) and reran recon-all as follows

recon-all -autorecon2-cp -autorecon3 -subjid <subject>

but on a lot of instances, the specified control points were not incorporated (please see attached image). How do we fix this, now that we have already run the recon-all with -autorecon2-cp and the error persists ?

Can someone please suggest ?

Thank you,

Rito and Jack




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