Fixes make_scalp_surfaces

mne/bem.py

@@ -2394,19 +2394,20 @@ def make_scalp_surfaces(
         mri = mri if (subj_path / "mri" / mri).exists() else "T1"
 
     logger.info("1. Creating a dense scalp tessellation with mkheadsurf...")
+    threshold = _ensure_int(threshold, "threshold")
 
-    def check_seghead(surf_path=subj_path / "surf"):
+    def check_seghead(surf_path=subj_path / "surf", overwrite=overwrite):
         surf = None
         for k in ["lh.seghead", "lh.smseghead"]:
             this_surf = surf_path / k
             if this_surf.exists():
                 surf = this_surf
+                _check_file(surf, overwrite)
                 break
         return surf
 
-    my_seghead = check_seghead()
-    threshold = _ensure_int(threshold, "threshold")
-    if my_seghead is None:
+    my_seghead = check_seghead(overwrite=overwrite)
+    if (my_seghead is None) or overwrite:
         this_env = deepcopy(os.environ)
         this_env["SUBJECTS_DIR"] = str(subjects_dir)
         this_env["SUBJECT"] = subject
@@ -2432,7 +2433,7 @@ def check_seghead(surf_path=subj_path / "surf"):
             env=this_env,
         )
 
-    surf = check_seghead()
+    surf = check_seghead(overwrite=False)
     if surf is None:
         raise RuntimeError("mkheadsurf did not produce the standard output file.")
 

mne/tests/test_bem.py

@@ -43,7 +43,7 @@
 from mne.io import read_info
 from mne.surface import _get_ico_surface, read_surface
 from mne.transforms import translation
-from mne.utils import _record_warnings, catch_logging, check_version
+from mne.utils import _record_warnings, catch_logging, check_version, requires_freesurfer
 
 fname_raw = Path(__file__).parents[1] / "io" / "tests" / "data" / "test_raw.fif"
 subjects_dir = testing.data_path(download=False) / "subjects"
@@ -519,11 +519,26 @@ def test_io_head_bem(tmp_path):
     assert np.allclose(head["tris"], head_defect["tris"])
 
 
-@pytest.mark.slowtest  # ~4 s locally
+@pytest.mark.slowtest
+@requires_freesurfer("mkheadsurf")
+@testing.requires_testing_data
 def test_make_scalp_surfaces_topology(tmp_path, monkeypatch):
-    """Test topology checks for make_scalp_surfaces."""
+    """Test make_scalp_surfaces and topology checks."""
     pytest.importorskip("pyvista")
     pytest.importorskip("nibabel")
+
+    # tests on 'sample'
+    subject = 'sample'
+    with pytest.raises(OSError, match="use --overwrite to overwrite it"):
+        make_scalp_surfaces(
+            subject, subjects_dir, force=False, verbose=True, overwrite=False
+        )
+
+    make_scalp_surfaces(
+        subject, subjects_dir, force=False, verbose=True, overwrite=True
+    )
+
+    # tests on custom surface
     subjects_dir = tmp_path
     subject = "test"
     surf_dir = subjects_dir / subject / "surf"
@@ -551,6 +566,7 @@ def _decimate_surface(points, triangles, n_triangles):
         make_scalp_surfaces(
             subject, subjects_dir, force=False, verbose=True, overwrite=True
         )
+
     bem_dir = subjects_dir / subject / "bem"
     sparse_path = bem_dir / f"{subject}-head-sparse.fif"
     assert not sparse_path.is_file()
@@ -570,6 +586,8 @@ def _decimate_surface(points, triangles, n_triangles):
     (surf,) = read_bem_surfaces(sparse_path, on_defects="ignore")
     assert len(surf["tris"]) == 319
 
+
+
 
 @pytest.mark.parametrize("bem_type", ["bem", "sphere"])
 @pytest.mark.parametrize("n_pos", [1, 10])