mne_make_morph_maps

Overview

mne_make_morph_maps precomputes surface morphing maps between two FreeSurfer subjects. These maps enable efficient morphing of source estimates from individual subjects to a common template (e.g., fsaverage) for group analysis.

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

Usage

mne_make_morph_maps [options]

Options

Option	Description
--from <subject>	Source subject name
--to <subject>	Destination subject name
--subjects_dir <dir>	Subjects directory (default: $SUBJECTS_DIR)
--out <file>	Output morph map FIFF file
--nearest <n>	Number of nearest neighbors (default: 5)
--help	Print help
--version	Print version

Description

Morphing maps define the correspondence between vertices on two subjects' cortical surfaces using the FreeSurfer spherical registration. By precomputing these maps, repeated morphing operations (e.g., morphing many time points or conditions) can be done efficiently.

The --nearest parameter controls the number of nearest neighbors used for interpolation. More neighbors produce smoother results but may blur fine spatial detail.

Workflow Context

Morph maps are precomputed before group analysis:

1. Compute morph maps → mne_make_morph_maps (for each subject to fsaverage)
2. Compute source estimates → mne_compute_mne
3. Morph source estimates to template using the precomputed maps

Example

# Precompute morph map from sam to fsaverage
mne_make_morph_maps --from sam --to fsaverage --out sam-to-fsaverage-morph.fif

# Use more neighbors for smoother morphing
mne_make_morph_maps --from sam --to fsaverage --nearest 10 --out sam-to-fsaverage-morph.fif