Re: [Freesurfer] Supplying a mask to recon-all?

Try running it with -xmask yourmask.mgz

On 11/17/2022 10:31 AM, Xinyu Liu wrote:

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Dear experts,

I am trying to use freesurfer with a set of high-resolution images (0.6mm3 isotropic) and I found the brain mask generated by freesurfer is not ideal. In this case, is it possible to supply a mask to recon-all? I've seen in previous communications it has been suggested to run auto-recon1, replace the mask and proceed with auto-recon2 etc, but I was hoping to use recon-all directly if that's possible. Or is it possible to run recon-all with skull-stripped image?

Thank you very much.

Best Xinyu

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