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 mailto: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
Freesurfer mailing list --freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email tofreesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...