Dear Shane, the "topological defect" in FreeSurfer jargon means that the estimated surface contains errors like "holes" or "handles".
See PPT from FreeSurfer course http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.failure_modes.ppt or https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData XL (=extra large?) defect often means large error in previous steps of recon-all, usually skullstrip or white matte segmentation. In some cases the error is automatically corrected, but not always. To see, what is happening, I would suggest to inspect brainmask.mgz or wm.mgz and correct errors. You can also find more information on the forum, there are quite large amount of posts related to topological defects. For example: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30763.html Antonin Skoch Hi Freesurfer Team, I am running recon-all on Freesurfer version 6. A few of my subjects have “XL defect detected …” and their recon-all have been running for more than 20 hours. I hope this is not a silly question, but will this XL defect be corrected eventually…? Another question, what are “defects”? Is there anything I could do to the raw T1 before recon-all? Thanks! Shane
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