Fixing BEM and head surfaces#

Low-resolution head#

For EEG forward modeling, it is possible that outer_skin.surf would be manually edited. In that case, remember to save the fixed version of -head.fif from the edited surface file for coregistration.

# Load the fixed surface
coords, faces = mne.read_surface(bem_dir / 'outer_skin.surf')

# Make sure we are in the correct directory
head_dir = bem_dir.parent

# Remember to backup the original head file in advance!
# Overwrite the original head file
#
# mne.write_head_bem(head_dir / 'sample-head.fif', coords, faces,
#                    overwrite=True)

High-resolution head#

We use mne.read_bem_surfaces() to read the head surface files. After editing, we again output the head file with mne.write_head_bem(). Here we use -head.fif for speed.

# If ``-head-dense.fif`` does not exist, you need to run
# ``mne make_scalp_surfaces`` first.
# [0] because a list of surfaces is returned
surf = mne.read_bem_surfaces(head_dir / 'sample-head.fif')[0]

# For consistency only
coords = surf['rr']
faces = surf['tris']

# Write the head as an .obj file for editing
mne.write_surface(conv_dir / 'sample-head.obj',
                  coords, faces, overwrite=True)

# Usually here you would go and edit your meshes.
#
# Here we just use the same surface as if it were fixed
# Read in the .obj file
coords, faces = mne.read_surface(conv_dir / 'sample-head.obj')

# Remember to backup the original head file in advance!
# Overwrite the original head file
#
# mne.write_head_bem(head_dir / 'sample-head.fif', coords, faces,
#                    overwrite=True)

    1 BEM surfaces found
    Reading a surface...
[done]
    1 BEM surfaces read
Overwriting existing file.

Blender editing tips#

A particularly useful operation is the Shrinkwrap functionality, that will restrict one surface inside another surface (for example the Skull inside the Outer Skin). Here is how to use it:

① Select surface

Select the surface that is creating the problem.

② Select vertices

In Edit Mode, press C to use the circle selection tool to select the vertices that are outside.

③-⑤ Group vertices

In the Object Data Properties tab use the + button to add a Vertex Group and click Assign to assign the current selection to the group.

⑥-⑧ Shrinkwrap

In the Modifiers tab go to Add Modifier add a Shrinkwrap modifier and set it to snap Inside with the outer surface as the Target and the Group that you created before as the Vertex Group. You can then use the Offset parameter to adjust the distance.

⑨ Apply

In Object Mode click on the down-pointing arrow of the Shrinkwrap modifier and click on Apply.

That’s it! You are ready to continue with your analysis pipeline (e.g. running mne.make_bem_model()).

Blender operations#

When editing BEM surfaces/meshes in Blender, make sure to use tools that do not change the number or order of vertices, or the geometry of triangular faces. For example, avoid the extrusion tool, because it duplicates the extruded vertices.

Cleaning up a bad dense head surface by smoothing#

If you get a rough head surfaces when using mne make_scalp_surfaces, consider smoothing your T1 ahead of time with a Gaussian kernel with FreeSurfer using something like the following within the subject’s mri directory:

$ mri_convert --fwhm 3 T1.mgz T1_smoothed_3.mgz

Here the --fwhm argument determines how much smoothing (in mm) to apply. Then delete SUBJECTS_DIR/SUBJECT/surf/lh.seghead, and re-run mne make_scalp_surfaces with the additional arguments --mri="T1_smoothed_3.mgz" --overwrite, and you should get cleaner surfaces.

Topological errors#

MNE-Python requires that meshes satisfy some topological checks to ensure that subsequent processing like BEM solving and electrode projection can work properly.

Below are some examples of errors you might encounter when working with meshes in MNE-Python, and the likely causes of those errors.

1. Cannot decimate to requested ico grade

   This error is caused by having too few or too many vertices. The full error is something like:

   RuntimeError: Cannot decimate to requested ico grade 4. The provided
   BEM surface has 20516 triangles, which cannot be isomorphic with a
   subdivided icosahedron. Consider manually decimating the surface to a
   suitable density and then use ico=None in make_bem_model.
   

2. Surface inner skull has topological defects

   This error can occur when trying to match the original number of triangles by removing vertices. The full error looks like:

   RuntimeError: Surface inner skull has topological defects: 12 / 20484
   vertices have fewer than three neighboring triangles [733, 1014,
    2068, 7732, 8435, 8489, 10181, 11120, 11121, 11122, 11304, 11788]
   

3. Surface inner skull is not complete

   This error (like the previous error) reflects a problem with the surface topology (i.e., the expected pattern of vertices/edges/faces is disrupted).

   RuntimeError: Surface inner skull is not complete (sum of solid
   angles yielded 0.999668, should be 1.)
   

4. Triangle ordering is wrong

   This error reflects a mismatch between how the surface is represented in memory (the order of the vertex/face definitions) and what is expected by MNE-Python. The full error is:

   RuntimeError: The source surface has a matching number of triangles
   but ordering is wrong
   

>>> import pymeshfix
>>> rr, tris = mne.read_surface('lh.seghead')
>>> rr, tris = pymeshfix.clean_from_arrays(rr, tris)
>>> mne.write_surface('lh.seghead', rr, tris)