you can run recon-all with -autorecon1 instead of -all or
you can run mri_synthstrip to get the brainmask
or you can run mri_synthseg and binarize to keep the segments you want
or you can run samseg and binarize to keep the segments you want

mri_synthstrip will probably get you where you want to be the fastest

On 10/13/2022 10:13 PM, priya padma wrote:

External Email - Use Caution

Hello Team,

I am trying to do only Skull stripping for my image and get the output. is there any command of freesurfer, when it executes only the first step- skull stripping. My objective is to get whole brain segmentation where only the brain tissues should remain and all the skull has to be removed.

I searched through the internet but haven't got anything. Does anyone know any solution?

Thank you

--

Best Regards
Padma Priya

AI Developer

PhenoMx, Inc.

priya@phenomx.ai | (+82)10-5405-2685
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