MRG, BUG: Fix config (mne-tools#6991)

* BUG: Fix config

* FIX: Overwrite [ci skip]

mne/bem.py

@@ -31,7 +31,7 @@
                       _fast_cross_nd_sum, _get_solids)
 from .transforms import _ensure_trans, apply_trans, Transform
 from .utils import (verbose, logger, run_subprocess, get_subjects_dir, warn,
-                    _pl, _validate_type, _TempDir)
+                    _pl, _validate_type, _TempDir, get_config)
 from .fixes import einsum
 
 
@@ -1153,7 +1153,8 @@ def make_watershed_bem(subject, subjects_dir=None, overwrite=False,
                                                  read_metadata=True)
             volume_info.update(new_info)  # replace volume info, 'head' stays
 
-            write_surface(s, rr, tris, volume_info=volume_info)
+            write_surface(s, rr, tris, volume_info=volume_info,
+                          overwrite=overwrite)
             # Create symbolic links
             surf_out = op.join(bem_dir, '%s.surf' % s)
             if not overwrite and op.exists(surf_out):
@@ -1563,7 +1564,8 @@ def write_bem_solution(fname, bem):
 def _prepare_env(subject, subjects_dir, requires_freesurfer):
     """Prepare an env object for subprocess calls."""
     env = os.environ.copy()
-    if requires_freesurfer and not os.environ.get('FREESURFER_HOME'):
+    fs_home = get_config('FREESURFER_HOME')
+    if fs_home is None:
         raise RuntimeError('I cannot find freesurfer. The FREESURFER_HOME '
                            'environment variable is not set.')
 
@@ -1577,8 +1579,8 @@ def _prepare_env(subject, subjects_dir, requires_freesurfer):
     if not op.isdir(subject_dir):
         raise RuntimeError('Could not find the subject data directory "%s"'
                            % (subject_dir,))
-    env['SUBJECT'] = subject
-    env['SUBJECTS_DIR'] = subjects_dir
+    env.update(SUBJECT=subject, SUBJECTS_DIR=subjects_dir,
+               FREESURFER_HOME=fs_home)
     mri_dir = op.join(subject_dir, 'mri')
     bem_dir = op.join(subject_dir, 'bem')
     return env, mri_dir, bem_dir