mne_setup_forward_model
Overview
mne_setup_forward_model sets up the BEM for forward modeling. It reads triangulated surface files (inner skull, outer skull, scalp), creates a BEM geometry FIFF file with conductivity assignments, exports .pnt and .surf files, and optionally computes the BEM solution matrix.
This is a C++ port of the original MNE shell script by Matti Hämäläinen.
Usage
mne_setup_forward_model [options]
Options
| Option | Description |
|---|---|
--subject <name> | Subject name. Defaults to SUBJECT environment variable. |
--subjects-dir <dir> | Subjects directory. Defaults to SUBJECTS_DIR environment variable. |
--scalpc <value> | Scalp conductivity in S/m (default: 0.3) |
--skullc <value> | Skull conductivity in S/m (default: 0.006) |
--brainc <value> | Brain conductivity in S/m (default: 0.3) |
--model <name> | BEM model name (auto-generated if omitted) |
--homog | Use a single-compartment (homogeneous) model |
--surf | Use FreeSurfer .surf files instead of ASCII .tri files |
--ico <number> | Downsample surfaces to icosahedron subdivision level (0–6) |
--nosol | Skip BEM solution preparation |
--noswap | Don't swap triangle winding order |
--meters | Coordinates are in meters (for ASCII .tri files) |
--innershift <mm> | Shift inner skull surface outward by specified amount |
--outershift <mm> | Shift outer skull surface outward by specified amount |
--scalpshift <mm> | Shift scalp surface outward by specified amount |
--overwrite | Overwrite existing output files |
Description
This tool is a critical step in the MEG/EEG source localization pipeline. It takes the triangulated BEM surfaces (created by mne_watershed_bem or mne_flash_bem) and sets up the boundary element model with appropriate conductivity values for each compartment.
Conductivity Values
The default conductivity values are:
| Compartment | Default (S/m) | Typical ratio |
|---|---|---|
| Scalp | 0.3 | 1 |
| Brain | 0.3 | 1 |
| Skull | 0.006 | 1/50 |
The skull conductivity ratio has been a subject of considerable discussion in the literature. Recent publications report values ranging from 1:15 to 1:50 relative to brain/scalp conductivity.
Single-Compartment Model
For MEG-only analyses, a single-compartment (homogeneous) BEM model using only the inner skull surface is often sufficient. Use the --homog flag for this:
mne_setup_forward_model --homog --subject sample
Surface Shifting
The --innershift, --outershift, and --scalpshift options allow shifting surfaces outward along their normals. This can be useful when surfaces are too close together or intersecting.
Example
Set up a three-layer BEM model:
export SUBJECTS_DIR=/path/to/subjects
mne_setup_forward_model --subject sample --surf --overwrite
Set up with custom conductivities:
mne_setup_forward_model --subject sample --surf \
--scalpc 0.33 --skullc 0.0132 --brainc 0.33