Try mri_binarize --i aseg.mgz --match 7 8 46 47 --o cerebellum.nii.gz Those numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt

On 7/23/2020 9:47 PM, Camargo, Aldo wrote:

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Hi Freesurfer experts,

I am trying to extract only the cerebellum and then save it to nii file. How can I do it with freesurfer ?

Thanks a lot and have a nice day,

Aldo

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