function elec = bis2fieldtrip(mgridfile, mrifile)

% BIS2FIELDTRIP reads BioImage Suite .mgrid files and converts them

% into a FieldTrip-compatible elec datatype structure and converts electrode

% positions from BioImage Suite mgrid that are in 'xyz' to head coordinates

% of the corresponding MRI volume

%

% Use as

% elec = bis2fieldtrip('Subject_grid.mgrid', 'Subject_MR.nii')

%

% See also FIELDTRIP2BIS, FT_READ_SENS, READ_BIOIMAGE_MGRID

% Copyright (C) 2017, Arjen Stolk & Sandon Griffin

%

% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org

% for the documentation and details.

%

% FieldTrip is free software: you can redistribute it and/or modify

% it under the terms of the GNU General Public License as published by

% the Free Software Foundation, either version 3 of the License, or

% (at your option) any later version.

%

% FieldTrip is distributed in the hope that it will be useful,

% but WITHOUT ANY WARRANTY; without even the implied warranty of

% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

% GNU General Public License for more details.

%

% You should have received a copy of the GNU General Public License

% along with FieldTrip. If not, see <http://www.gnu.org/licenses/>.

%

% $Id$

% import .mgrid electrode positions

elec_xyz = ft_read_sens(mgridfile, 'senstype', 'eeg');

% convert xyz coordinates to ijk coordinates

mri = ft_read_mri(mrifile);

elec_ijk.elecpos(:, 1) = elec_xyz.elecpos(:, 1)/mri.hdr.xsize;

elec_ijk.elecpos(:, 2) = elec_xyz.elecpos(:, 2)/mri.hdr.ysize;

elec_ijk.elecpos(:, 3) = elec_xyz.elecpos(:, 3)/mri.hdr.zsize;

% adjust for bioimage suite indexing first voxel at [0 0 0] instead of [1 1 1]

elec_ijk.elecpos = elec_ijk.elecpos+1;

% convert ijk coordinates to mri head coordinates

elec = keepfields(mri, {'unit', 'coordsys'});

elec.label = elec_xyz.label;

elec.elecpos = ft_warp_apply(mri.transform, elec_ijk.elecpos);

% ensure that the elec description is up-to-date

elec = ft_datatype_sens(elec);