my guess is that it is a topological defect that was fixed incorrectly. Try looking at this tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...

You can also run defect-seg to create a segmenttation of the defects and see whether a defect is in that area. run it with --help to get more info

One more thing: just check the skull strip to make sure it was not too aggressive.

On 5/27/2020 12:34 PM, Isaac Adanyeguh wrote:

External Email - Use Caution

Dear Freesurfer Development Team,

I am having some issues with recon-all where it misses a huge chunk of the occipital cortex in several of my subjects. I have searched the archive and have not found any report of similar issues. Could you please help me figure out how to solve this issue. I have attached a screenshot showing the missing occipital cortex segmentation and a copy of the recon-all.log.

I performed the analysis using:

• Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20150828
• Platform: Linux 3.10.0-1127.el7.x86_64

Thank you and hope you will be able to help me resolve the issue.

Isaac

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