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Dear Rosalia,
I’d suggest you run recon-all –autorecon1 with you native data. Then you use mri_mask to mask the T1.mgz with your skull stripped volume to get your desired skull stripping. Name the result brainmask.mgz and continue with recon-all –autorecon2 –autorecon3.
Remember that FreeSurfer requires to have the cerebellum attached to the brain. Also inputting the already skull stripped volume in autorecon1 may fail during talairach registration and potentially cause errors during skull stripping (if not skipped anyways).
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Rosalia Dacosta Aguayo Gesendet: Donnerstag, 18. Oktober 2018 06:30 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] autorecon1 with skull stripped image
External Email - Use Caution Dear Free Surfer's team,
I have a doubt. I have a sample of patients in which I already have done the skull stripping using specific options with bet, so the skull stripping has been successful. I wonder if I could feed autorecon1 with the skull stripped image instead of the T1 image with skull. Thank you very much for your time, Rosalia