Hi Mateus,
Please attach the recon-all.log file for your subject and I will take a look. Best, Emma ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of MATEUS ROZALEM ARANHA <mateus.ara...@hc.fm.usp.br> Sent: Friday, August 11, 2017 9:56 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Skullstriping problems Hi, I had problems with skullstriping. I ran recon-all and part of the skull is being considered as cortex in the segmentation. I tried to fix this using: recon-all -skullstrip -wsthresh 50 -clean-bm -subjid <subject name> and than recon-all -autorecon-pial -subjid <subject name> But nothing changed. Do I need to run recon-all all over? Thanks, Mateus
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