mne_setup_mri
Overview
mne_setup_mri sets up FreeSurfer MRI data for MNE software by creating the Neuromag directory structure and converting FreeSurfer MRI volumes (COR files or .mgz/.mgh) into COR.fif FIFF files.
This is a C++ port of the original MNE-C tools mne_setup_mri and mne_make_cor_set by Matti Hämäläinen.
Usage
mne_setup_mri [options]
Options
| Option | Description |
|---|---|
--subject <name> | Subject name. Defaults to SUBJECT environment variable. |
--subjects-dir <dir> | Subjects directory. Defaults to SUBJECTS_DIR environment variable. |
--mri <name> | MRI set name to process (can be specified multiple times; default: T1 brain) |
--overwrite | Overwrite existing data |
--verbose | Verbose output |
Description
mne_setup_mri prepares FreeSurfer MRI data for use with MNE tools. It performs the following steps:
- Creates the required Neuromag-style directory structure within the subject's FreeSurfer directory
- Converts FreeSurfer MRI volumes (in COR or MGZ format) to FIFF format (
COR.fif) - Sets up the coordinate transformations needed for MNE processing
This step should be performed after the FreeSurfer cortical reconstruction is complete and before computing the forward solution.
Example
export SUBJECTS_DIR=/path/to/subjects
mne_setup_mri --subject sample --overwrite --verbose
Process a specific MRI set:
mne_setup_mri --subject sample --mri T1 --overwrite