FreeSurferToFieldTrip

The FreeSurfer software provides a good automatic segmentation of T1 images. It includes utilities to generate BEM surfaces that can be used to construct a head model for FieldTrip.

The following assumes you've run FreeSurfer on your T1.

Post-recon steps in the shell

Generate BEM surfaces (brain, inner/outer skull & outer skin)

SUBJECTS_DIR=~/mris-tms/fs SUBJECT=anattms_50 mne_watershed_bem

Convert T1 to nifti

mri_convert fs/anattms_50/mri/T1.mgz fs/anattms_50/mri/T1.mgz.nii

Obtain transform from T1 voxels to BEM surface space

mri_info --vox2raw-tkr fs/anattms_50/mri/T1.mgz > fs/anattms_50/transforms/t1-vox2ras-tkr.xfm

In MATLAB

Read the Nifti

t1 = ft_read_mri('fs/anattms_50/mri/T1.mgz.nii')

Read the BEM surfaces (this function is given below)

bems = read_bem_surfs('fs/', 'anattms_50');

Plot the two together

ft_determine_coordsys(t1, 'interactive', 'no')
hold on
plot_bem_surfs(bems);