Surface meshes are the domain of Surfice
  https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage
Specifically, the Advanced men's  "Convert voxelwise volume to mesh" menu item.

You can use the Preferences window to set your preferred output mesh format: OBJ, GIfTI, MZ3 or PLY. You can find links to tools to convert OBJ or PLY to STL (I like MeshLab for this)
  https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage#Supported_Formats
I believe Blender already supports OBJ and PLY formats, and I provide a plugin for MZ3:
 https://github.com/neurolabusc/surf-ice/tree/master/mz3

You should only use STL as a format of last resort if your tools do not support other formats. STL is inherently inferior to other formats like OBJ and PLY. Specifically, it does not reuses vertices. This results in large file sizes. Further, STL meshes will either appear faceted or require a slow vertex unification stage with an arbitrary tolerance. 
  https://discourse.slicer.org/t/beware-of-the-stl-file-format/7642