mne_make_cor_set

Overview

mne_make_cor_set creates a FIFF MRI description file from FreeSurfer COR slices or mgh/mgz volume data.

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

Usage

mne_make_cor_set [options]

Options

Option	Description
--dir <directory>	FreeSurfer COR directory
--mgh <file>	FreeSurfer mgh/mgz volume file
--out <file>	Output FIFF file (required)
--help	Print help
--version	Print version

Either --dir or --mgh must be specified.

Description

This utility converts FreeSurfer MRI data to the FIFF format used by MNE tools. It reads either a directory of COR slice files or an mgh/mgz volume file, and writes a FIFF file containing the MRI data with proper coordinate transforms and voxel metadata.

Workflow Context

Use this tool as part of MRI setup when mne_setup_mri does not handle your specific data layout. The output FIFF file can be used by mne_setup_forward_model and other MNE tools that require MRI information.

Example

# From COR slices
mne_make_cor_set --dir subjects/sam/mri/T1-neuromag/sets/COR-sam --out sam-mri.fif

# From mgh/mgz volume
mne_make_cor_set --mgh subjects/sam/mri/T1.mgz --out sam-mri.fif