Slicer3D is an excellent tool with a huge number of features. Here are a couple of other options:

1.) If you want to segment the brain from the head, you may want to try out my Matlab script:
  https://github.com/rordenlab/spmScripts/blob/master/nii_nii2stl.m
this uses SPM for the segmentation. It creates both a traditional STL file, as well as a "hollow" STL file, which is much less expensive to 3D print with companies like ShapeWays where you pay by the volume of material used. The attached image shows the segmented volume as NIfTI format (left, MRIcroGL), and as a STL format mesh (right, Surfice).

2.) The Surfice Advanced/ConvertVoxelwiseDataToMesh can be helpful. It can also be used in combination with my Matlab script, where you can adjust the iso-surface threshold (e.g. to show either white matter or pial surface).

As ever, I urge users to only create surface meshes in STL format as a format of last resort. If the other tools you are using can use ANY other surface format (OBJ, GIfTI, PLY, etc), you should choose the non-STL format. Since STL does not re-use vertices, STL files inherently use a lot of disk space. For the same reason, the files either are slow to load (e.g. Surfice) or have a jagged/faceted appearance (e.g. Slicer3D) when viewed.