you can apply the brainmask to any volume using mri_mask, including the orig if you want. The skull stripping shouldn't amplify noise though. What amplified noise regions do you mean? Maybe you can send a picture?

cheers Bruce

On Thu, 4 Jul 2019, Admin wrote:

External Email - Use Caution

Dear Freesurfer： I am a graduate student of Northeastern University in China, and I do brain image analysis . 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. Thank for your kind consideration of this request. Looking forward to receiving your reply. Thank you very much again. My Email address is:15140248156@163.com.

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