How to import data from MNE-Python and FreeSurfer

% This script was made by Mikkel Vinding, based on code that is courtesy of Bushra Riaz Syeda

if ispc
    addpath C:\Users\Mikkel\Documents\MATLAB
    [dirs, sub_info, lh_subs] = PD_proj_setup_WIN('tap');
    fs_subject_dir  = 'Z:\PD_motor\fs_subjects_dir';
    dirs.mriDir     = 'Z:\PD_motor\MRI';
    dirs.transDir   = 'Z:\PD_motor\tap\trans_files';
    src_path        = 'Z:\PD_motor\tap\mri';
else
    addpath /home/mikkel/PD_motor/global_scripts
    [dirs, sub_info, lh_subs] = PD_proj_setup('tap');
    fs_subject_dir  = '/home/mikkel/PD_motor/fs_subjects_dir';
    dirs.mriDir     = '/home/mikkel/PD_motor/MRI'; 
    dirs.transDir   = '/home/mikkel/PD_motor/tap/trans_files';
    src_path        = '/home/mikkel/PD_motor/tap/mri';
end

%% Overwrite old files?
overwrite = 0;

%% Filenames and paths [CLEAN UP]
% [ LOOP HERE ]
sub='0313';

volname = 'Z:\PD_motor\tap\meg_data\0313\vol.fif';

meg_path    = fullfile(dirs.megDir,sub);    % Sub specific path to MEG data
mriDir      = fullfile(dirs.megDir,sub);    % Sub specific path to 

% savemrito='/home/mikkel/PD_motor/tap/mri';
% mkdir (savemrito);

% It is important that you use T1.mgz instead of orig.mgz as T1.mgz is normalized to [255,255,255] dimension
mridata     = fullfile(fs_subject_dir, sub, '/mri/T1.mgz');                 
transfname  = fullfile(dirs.transDir, sub, [sub, '-trans.fif']);
dataset     = fullfile(meg_path, [sub, '_tap_1-ica_raw.fif']);    % for sensor location and definition 
src_fname   = fullfile(src_path,[sub, '-ico4-src.fif']);

% Define outputs
src_outFname = fullfile(meg_path, 'source_surf.mat');
hdm_outFname = fullfile(meg_path, 'headmodel_surf.mat');

% Check if exists
if isfile(src_outFname) && ~overwrite
    continue
end

%% Read transformation (head -> MRI)
trans_orig = fiff_read_coord_trans(transfname);
% In FieldTrip every thing is in head cordinate therefore in next line we are inverting the transformation
trans.trans=inv(trans_orig.trans);                                         

%% Read MRI (does not work on Win PC)
mri_orig = ft_read_mri(mridata );
mri_orig = ft_convert_units(mri_orig, 'cm'); 

%% The following lines are importing MNE coregistration to FieldTrip
trans_orig.trans(1:3,4) = trans_orig.trans(1:3,4)*100;  % translation: meters to cm
ttt= mri_orig.hdr.tkrvox2ras;                           % This is for FS T1.mgz!
ttt(1:3,:)=ttt(1:3,:)/10;

mri_orig.transform = inv(trans_orig.trans)*(ttt);
mri_orig = ft_determine_coordsys(mri_orig, 'interactive', 'no');
mri_orig.coordsys='neuromag';

%% Read sensor and headpoints
grad    = ft_read_sens(dataset,'senstype','meg'); 
grad    = ft_convert_units(grad, 'cm');
%     ft_datatype_sens(grad)
shape   = ft_read_headshape(dataset);
shape   = ft_convert_units(shape, 'cm');

% % Plot for inspection
% h=figure;
% ft_plot_headshape(shape)
% ft_plot_sens(grad, 'style', '*g');
% view([1 0 0])
% title('MEG headshape and sensors', 'FontSize', 13)

%% Read potato
vol = ft_read_vol(volname);
headmodel = vol;
headmodel = ft_convert_units(headmodel,'m'); % Make sure units is in meters for transform

% Transform
headmodel_pos=headmodel.bnd.pos;
temp_vect=headmodel_pos;
temp_vect(:,4)=1;
headmodel_pos=temp_vect*trans.trans';
headmodel.pos=headmodel_pos(:,1:3);
headmodel = ft_convert_units(headmodel, 'cm');

%% Reading Freesurfer Source Space
src = ft_read_headshape(src_fname, 'format', 'mne_source');

% Transform
temp_vect=src.pos;
temp_vect(:,4)=1;
src_pos=temp_vect*trans.trans';
src_pos=src_pos(:,1:3);

% Make source model
sourcemodel = src;
sourcemodel.pos = src_pos;
sourcemodel = ft_convert_units(sourcemodel, 'cm');
sourcemodel.inside = ones(length(sourcemodel.pos),1);

%% Check coregistration
cfg = [];
mri_orig = ft_determine_coordsys(mri_orig, 'interactive', 'no');
hold on; % add the subsequent objects to the same figure
ft_plot_headshape(shape);
ft_plot_mesh(headmodel, 'facealpha',0.25,'edgecolor', 'b','facecolor','b')
ft_plot_sens(grad, 'style', '*g','edgecolor','cyan');
ft_plot_mesh(sourcemodel, 'edgecolor','k')
view ([90 0])
title('MEG coregistration', 'FontSize', 13)

%% Save stuff
disp('Saving...');
save(src_outFname, 'sourcemodel', '-v7.3');
save(hdm_outFname, 'headmodel', '-v7.3');
disp('DONE')