mne_watershed_bem
Overview
mne_watershed_bem creates BEM (Boundary Element Model) surfaces using FreeSurfer's mri_watershed algorithm. It produces brain, inner skull, outer skull, and outer skin surfaces and writes the head surface as a FIFF BEM file.
This is a C++ port of the original MNE shell script by Matti Hämäläinen.
Usage
mne_watershed_bem [options]
Options
| Option | Description |
|---|---|
--subject <name> | Subject name. Defaults to the SUBJECT environment variable. |
--subjects-dir <dir> | Subjects directory. Defaults to SUBJECTS_DIR environment variable. |
--volume <name> | MRI volume name (default: T1) |
--overwrite | Overwrite existing watershed files |
--atlas | Pass --atlas flag to mri_watershed |
--gcaatlas | Use subcortical atlas for mri_watershed |
--preflood <number> | Change preflood height for mri_watershed |
--verbose | Verbose output |
Environment Variables
| Variable | Description |
|---|---|
FREESURFER_HOME | FreeSurfer installation directory (required) |
SUBJECTS_DIR | Directory containing FreeSurfer subject reconstructions |
SUBJECT | Current subject name |
Description
The watershed algorithm segments the MRI volume and creates the following triangulated surfaces:
- Brain surface — The brain-CSF boundary
- Inner skull surface — The inner surface of the skull
- Outer skull surface — The outer surface of the skull
- Outer skin surface — The outer surface of the head
These surfaces are stored in the subject's bem/watershed/ directory and are used by mne_setup_forward_model to create the BEM geometry needed for forward solution computation.
Example
export SUBJECTS_DIR=/path/to/subjects
export SUBJECT=sample
mne_watershed_bem --overwrite --verbose