function [ ret_val ] = write_freesurfer_registration( registration_struct, out_registration_fqn )
%READ_FREESURFER_REGISTRATION read registration matrix into matlab
%   Detailed explanation goes here
% FREESURFER REGISTRATION CONVENTIONS
% 
% For the purposes of FreeSurfer, the registration matrix maps the XYZ
% of the anatomical reference (ie, the subjects brain as found in 
% $SUBJECTS_DIR) to the XYZ of the functional volume. The anatomical
% reference is the 'target' volume (argument of --targ) and the 
% functional volume is the 'movable' volume (argument of --mov).
% The XYZ of a given col, row, and slice is defined
% based on the field-of-view by the following matrix:
% 
%           (-dc 0   0  dc*Nc/2)
%      T =  ( 0  0  ds -ds*Ns/2) 
%           ( 0 -dr  0  dr*Nr/2)
%           ( 0  0   0     1   )
% 
% where dc, dr, and ds are the voxel resolutions in the column, row,
% and slice directions, respectively, and  Nc, Nr, and Ns are the
% number of columns, rows, and slices.  Under this convention, 
% 
%   XYZ = T*[r c s 1]
% 
% The FreeSurfer registration matrix is then defined by:
% 
%    XYZmov = R*XYZtarg
% 
% FREESURFER REGISTRATION FILE FORMAT
% 
% The FreeSurfer registration is stored in an ASCII file with the 
% following format:
% 
%       subjectname
%       in-plane-res-mm
%       between-plane-res-mm
%       intensity
%       m11 m12 m13 m14
%       m21 m22 m23 m24
%       m31 m32 m33 m34
%       0   0   0   1
% 
% The subject name is that as found in the SUBJECTS_DIR. The in-plane-res-mm
% is the in-plane pixels size in mm. The between-plane-res-mm is
% the distance between slices in mm. Intensity only affect the display
% of the movable in the GUI.


% example of freesurfer registration matrix
% subject-unknown
% 0.500000
% 0.500000
% 0.150000
% 9.999794e-01 3.618304e-03 5.413820e-03 -3.438210e-01 
% -3.503619e-03 9.997724e-01 -2.104418e-02 8.644047e+00 
% -5.488733e-03 2.102475e-02 9.997640e-01 8.490714e+00 
% 0 0 0 1
% round

debug = 0;
success = 0;

if nargin < 2
	disp('Not enough arguments. failing...');
	return
end

if (debug)
	disp('DEBUG');
	registration_struct = [];
	out_registration_fqn = fullfile(pwd, '..', '..', 'mri', 'rotate_unconf_2_120227Rocco_raw_rawavg.dat.out');
end

% check existence
if ~isempty(dir(out_registration_fqn))
	disp([out_registration_fqn, ' file exists, will overwrite contents...']);
end

% open the file
reg_fd = fopen(out_registration_fqn,'w+');
if reg_fd == -1
	disp(['Could not open ', out_registration_fqn, ' directory might not be writeable, please check the permissions']);
	return
end

% write the contents of registration_struct
% all lines end n OA == LF line feed, so '\n' should work
if ~isempty(registration_struct)
	fprintf(reg_fd, '%s\n', registration_struct.subjectname);
	fprintf(reg_fd, '%0.7f\n', registration_struct.in_plane_res_mm);
	fprintf(reg_fd, '%0.7f\n', registration_struct.between_plane_res_mm);
	fprintf(reg_fd, '%0.7f\n', registration_struct.intensity);
	% all values are followed by a space, formaed as seen from the example
	fprintf(reg_fd, '%.6e %.6e %.6e %.6e \n', registration_struct.reg_mat(1:3, :)');
	% special case the last line...
	fprintf(reg_fd, '%#1d %#1d %#1d %#1d \n', registration_struct.reg_mat(4, :)');
	fprintf(reg_fd, '%s\n', registration_struct.round);
	
	success = 1;
else
	disp([]);
	return
end

% clean up
fclose(reg_fd);

% TODO? check inputs for sanity???

return
end