mne_surf2bem

Overview

mne_surf2bem converts FreeSurfer surfaces and/or ASCII triangle files into BEM FIFF files. It supports multiple surface inputs with separate IDs and conductivities, vertex shifting along normals, surface reordering, and topology checks.

This is a C++ port of the original MNE-C tool by Matti Hämäläinen.

Usage

mne_surf2bem [options]

Options

Option	Description
--surf <name>	Input FreeSurfer binary surface file
--tri <name>	Input ASCII triangle file
--fif <name>	Output FIFF BEM surface file
--id <id>	BEM surface ID: 1 = brain, 3 = skull, 4 = head. Applies to the last --surf or --tri specified.
--swap	Swap vertex winding order (for ASCII files)
--meters	Coordinates are in meters (default: millimeters)
--coordf <no>	Coordinate frame for ASCII vertices
--shift <val>	Shift vertices along normals by specified amount (mm)
--ico <number>	Downsample to icosahedron subdivision level (0–6)
--sigma <val>	Compartment conductivity (S/m)
--force	Load the surface despite topological defects
--check	Perform topology and solid angle checks
--checkmore	Also check skull/skin thicknesses

Description

mne_surf2bem is used to convert surfaces from FreeSurfer binary format or ASCII triangle format into the FIFF BEM format required by the MNE forward solution computation. Multiple surfaces can be combined into a single BEM file by specifying multiple --surf or --tri options with corresponding --id values.

Surface IDs

ID	Surface
1	Brain (inner skull)
3	Skull (outer skull)
4	Head (scalp)

Topology Checks

When --check is specified, the following checks are performed:

• Completeness — The total solid angle subtended by all triangles should be close to $4\pi$
• Surface ordering — Surfaces are verified to be properly nested (inner skull inside outer skull inside scalp)
• Extent — Surface extent must be at least 50 mm (to detect meters/millimeters confusion)

Example

Convert a FreeSurfer inner skull surface to BEM format:

mne_surf2bem --surf inner_skull.surf --id 1 --fif inner_skull-bem.fif --check

Create a three-layer BEM from FreeSurfer surfaces:

mne_surf2bem \
    --surf inner_skull.surf --id 1 --sigma 0.3 \
    --surf outer_skull.surf --id 3 --sigma 0.006 \
    --surf outer_skin.surf --id 4 --sigma 0.3 \
    --fif three-layer-bem.fif --check