[Freesurfer] run recon-all with already skull-stripped data

External Email - Use Caution Hello,According to the FAQ for earlier version of Freesurfer (maybe 6.x), the instruction is below.First you must run only -autorecon1 like this:recon-all -autorecon1 -noskullstrip -s Then you will have to make a symbolic link or copy T1.mgz to

Re: [Freesurfer] recon-all error

And how  did you create 001.mgz? Sometimes SPM will put NaNs in the image to indicate a mask. On 11/17/2023 10:12 AM, Huang, Yujing wrote: Hi Carlos, Can you attach recon-all.log? Best, Yujing *From:* freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Carlos Alcocer *Sent:*