Hi Dr. Kevin Aquino - could you please upload the entire subject directory? At first glance, it looks like fs is incorrectly including gm in the wm.mgz just superior to the surface errors you're seeing - the cluster of voxels w/ intensity 250 around the coordinate 87 178 97 in the wm.mgz.

Try editing the wm.mgz (look at the opposite hemi as a reference) and running the following command:

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

This wiki page may also be helpful: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview

Bram

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Kevin Aquino <aquino@physics.usyd.edu.au>
Sent: Tuesday, May 15, 2018 2:05:56 AM
To: Freesurfer support list
Subject: [Freesurfer] Pial surface running into white surface

External Email - Use Caution

Hi free surfer mailing list!

I am having a problem with some subjects where the pial surface is running into the white surface (and terminating at some points terminating within white matter). Apologies if the solution is in the mailing list (all I could find is that this could be fixed with FS v6). The build stamp is:

freesurfer-Linux-centos6_x86_64-dev-20170915-

what kind of edits should I be doing?

I have added the necessary files to https://github.com/KevinAquino/errorPial if you could be so kind to have a look!

Cheers,

Dr Kevin Aquino

Research fellow,

School of Psychology, Monash University, Australia.

Hon. Research Fellow

Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham.

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The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office.
-
Robert Frost