I believe I already answered this. I don't understand what amplified noise you mean. The brainmask.mgz can be used with mri_mask to apply to any input volume you want.

cheers Bruce On Sun, 7 Jul 2019, Admin wrote:

External Email - Use Caution

Dear Freesurfer group： Now,I want  generated a brain mask including the brain but excluding the amplified noise regions after skull strip, but I can't find the corresponding command line, so I send this email to you, hoping to get your help.  My English is poor, if I make mistakes , I hope you can understand me. Thanks for your help！

Sincerely: Meng Nan Lin                                                                                                                                                                                 Date: 07/04/2019