This died when trying to do topology correction. Look at the unfixed surface and see if there is something going wrong. Eg, the skull stripping could have left a lot of dura or part of the skull and the initial surface may include some of these things. For example, run
cd yoursubject
freeview mri/brain.finasurfs.manedit.mgz -f surf/lh.smoothwm.nofix surf/rh.smoothwm.nofix
If you see that the skull stripping failed, you can edit the brain.finalsurfs.manedit.mgz to remove the offending voxels and then rerun recon-all

On 8/27/2025 12:11 PM, Reyes, Nicholas wrote:

External Email - Use Caution

Hello! I cannot seem to figure out the problem with this patient. I am newer to using freesurfer, so I am a little lost trying out what I've read in the documentation. Could you help give me some insight on figuring this out?

Thank you in advance,

Nicholas K. Reyes | B.S. in Neuroscience

Neural Signals Processing and Modeling Lab

The University of Alabama at Birmingham

nkreyes@uab.edu || 205-937-3421

Nicholas K. Reyes | UNP Major & BME Minor

College of Arts and Sciences

The University of Alabama at Birmingham

nkreyes@uab.edu || 205-937-3421
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