trk_write.m

function trk_write(header,tracks,savePath)
%TRK_WRITE - Write TrackVis .trk files
%
% Syntax: trk_write(header,tracks,savePath)
%
% Inputs:
%    header   - Header information for .trk file [struc]
%    tracks   - Track data struc array [1 x nTracks]
%      nPoints  - # of points in each track
%      matrix   - XYZ coordinates (in mm) and associated scalars [nPoints x 3+nScalars]
%      props    - Properties of the whole tract
%    savePath - Path where .trk file will be saved [char]
%
% Output files:
%    Saves .trk file to disk at location given by 'savePath'.
%
% Other m-files required: none
% Subfunctions: none
% MAT-files required: none
%
% See also: TRK_READ

% Author: John Colby (johncolby@ucla.edu)
% UCLA Developmental Cognitive Neuroimaging Group (Sowell Lab)
% Apr 2010

fid = fopen(savePath, 'w');

% Write header
fwrite(fid, header.id_string, '*char');
fwrite(fid, header.dim, 'short');
fwrite(fid, header.voxel_size, 'float');
fwrite(fid, header.origin, 'float');
fwrite(fid, header.n_scalars , 'short');
fwrite(fid, header.scalar_name', '*char');
fwrite(fid, header.n_properties, 'short');
fwrite(fid, header.property_name', '*char');
fwrite(fid, header.vox_to_ras', 'float');
fwrite(fid, header.reserved, '*char');
fwrite(fid, header.voxel_order, '*char');
fwrite(fid, header.pad2, '*char');
fwrite(fid, header.image_orientation_patient, 'float');
fwrite(fid, header.pad1, '*char');
fwrite(fid, header.invert_x, 'uchar');
fwrite(fid, header.invert_y, 'uchar');
fwrite(fid, header.invert_z, 'uchar');
fwrite(fid, header.swap_xy, 'uchar');
fwrite(fid, header.swap_yz, 'uchar');
fwrite(fid, header.swap_zx, 'uchar');
fwrite(fid, header.n_count, 'int');
fwrite(fid, header.version, 'int');
fwrite(fid, header.hdr_size, 'int');

% Check orientation
[tmp ix] = max(abs(header.image_orientation_patient(1:3)));
[tmp iy] = max(abs(header.image_orientation_patient(4:6)));
iz = 1:3;
iz([ix iy]) = [];

% Write body
for iTrk = 1:header.n_count
    % Modify orientation back to LPS for display in TrackVis
    header.dim        = header.dim([ix iy iz]);
    header.voxel_size = header.voxel_size([ix iy iz]);
    coords = tracks(iTrk).matrix(:,1:3);
    coords = coords(:,[ix iy iz]);
    if header.image_orientation_patient(ix) < 0
        coords(:,ix) = header.dim(ix)*header.voxel_size(ix) - coords(:,ix);
    end
    if header.image_orientation_patient(3+iy) < 0
        coords(:,iy) = header.dim(iy)*header.voxel_size(iy) - coords(:,iy);
    end
    tracks(iTrk).matrix(:,1:3) = coords;
    
    fwrite(fid, tracks(iTrk).nPoints, 'int');
    fwrite(fid, tracks(iTrk).matrix', 'float');
    if header.n_properties
        fwrite(fid, tracks(iTrk).props, 'float');
    end
end

fclose(fid);