mne_flash_bem
Overview
mne_flash_bem creates BEM (Boundary Element Model) surfaces using multi-echo FLASH MRI sequences. It orchestrates FreeSurfer tools for DICOM conversion, parameter map fitting, flash volume synthesis, registration, and triangulation.
This is a C++ port of the original MNE shell script by Matti Hämäläinen.
Usage
mne_flash_bem [options]
Options
| Option | Description |
|---|---|
--noflash30 | Only 5-degree flash data available; average flash-5 echoes instead of combining with flash-30 |
--noconvert | Skip DICOM-to-MGZ conversion step |
--unwarp <option> | Apply gradient distortion unwarping |
--subject <name> | Subject name. Overrides SUBJECT environment variable. |
--subjects-dir <dir> | Subjects directory. Overrides SUBJECTS_DIR environment variable. |
--flash-dir <dir> | Flash data directory (default: current working directory) |
Environment Variables
| Variable | Description |
|---|---|
FREESURFER_HOME | FreeSurfer installation directory (required) |
SUBJECTS_DIR | Directory containing FreeSurfer subject reconstructions |
SUBJECT | Current subject name |
Description
The FLASH-based BEM surface creation typically provides better results than the watershed approach, especially for the skull surfaces. The method uses multi-echo FLASH MRI sequences acquired at different flip angles (typically 5° and 30°) to estimate tissue parameters and segment the head into different compartments.
The processing pipeline includes:
- DICOM conversion — Converting raw DICOM images to FreeSurfer MGZ format
- Parameter map fitting — Computing parameter maps from multi-echo data
- Flash volume synthesis — Creating a synthetic volume from the parameter maps
- Registration — Aligning flash volumes with the FreeSurfer reconstruction
- Triangulation — Creating triangulated surfaces for each compartment
The resulting surfaces (inner skull, outer skull, and outer skin) are stored in the subject's bem/flash/ directory.
Example
export SUBJECTS_DIR=/path/to/subjects
export SUBJECT=sample
cd /path/to/flash/dicoms
mne_flash_bem --subject sample
If only 5-degree flash data is available:
mne_flash_bem --noflash30 --subject sample