Try running it with -xmask yourmask.mgz
On 11/17/2022 10:31 AM, Xinyu Liu wrote:
External Email - Use Caution
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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