I am trying to run 'recon-all' and then do some QC on the output. With 7.3.2 for skull stripping, I can fairly fix the brain mask with adjusting thresholds. But after fixing it, when I ran "recon-all -autorecon2 -autorecon3 -subjid <subject name>", the surface didn't change noticeably. However, I obtained noticeable changes with version 7.2.0.

I am attaching a screenshot to make it understandable. Should there be output differences between 7.2.0 and 7.3.2? 

I was wondering if anyone has comments about which version one should rely on. 

Any help will be highly appreciated. Thank you. 

Regards,

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Mahfuz