You can draw a region of interest, the wiki provides details
  https://www.nitrc.org/plugins/mwiki/index.php/mricrogl:MainPage#Drawing_Regions_of_Interest
The View/ExtractBrain menu item will run BET to create a Brain Extraction. On some operating systems you may need to install FSL to get BET.

The FSL BET is pretty simple, and may not generate a good result. I tend to use SPM's segmentation for this - my SPM script is here
  https://github.com/rordenlab/spmScripts/blob/master/nii_nii2stl.m