ctf_write_mri.m

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function ctf_write_mri(mri, fileName, force)

% ctf_write_mri - write a CTF .mri file
%
% ctf_write_mri(mri,fileName,force)
%
% mri is a data struct returned from ctf_read_mri.  It may contain
% mri.file, in which case, you do not need the fileName input here.  If the
% file exists, you are prompted for a new file name, unless force = 1.
%
% The CTF MRI File format used by MRIViewer consists of a binary file with
% a 1,028 byte header. The MRI data can be in 8-bit (unsigned character) or
% 16-bit (unsigned short integer) format and consists of 256 x 256 pixel
% slices, stored as 256 contiguous sagittal slices from left to right (or
% right to left if head orientation is left-on-right). Each slice is stored
% as individual pixels starting at the left, anterior, superior
% corner and scanning downwards row by row. Therefore the coronal
% position is fastest changing, axial position second fastest
% changing and sagittal position slowest changing value in the
% file, always in the positive direction for each axis (see section
% on Head Coordinate System for axis definitions). By default CTF
% MRI files have the file extension .mri 
%
%      <>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> %
%      <                                                      > %  
%      <                    DISCLAIMER:                       > %
%      <                                                      > %
%      < THIS PROGRAM IS INTENDED FOR RESEARCH PURPOSES ONLY. > %
%      < THIS PROGRAM IS IN NO WAY INTENDED FOR CLINICAL OR   > %
%      <                    OFFICIAL USE.                     > %
%      <                                                      > %
%      <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<> %
%



% $Revision: 1.6 $ $Date: 2004/07/18 06:10:17 $

% Copyright (C) 2003  Darren L. Weber
% 
% This program 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 2
% of the License, or (at your option) any later version.
% 
% This program 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 this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.

% History:  08/2003, Darren.Weber_at_radiology.ucsf.edu
%                    - adapted from an appendex to CTF document
%                    MRIConverter.pdf, which is copied at the end of this
%                    function.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


ver = '[$Revision: 1.6 $]';
fprintf('\nCTF_WRITE_MRI [v%s]\n',ver(12:16));  tic;

if ~exist('mri','var'), error('no input mri data struct'); end
if isempty(mri), error('empty input mri data struct'); end

if ~exist('force','var'), force = 0; end % don't overwrite
if isempty(force), force = 0; end

if ~exist('fileName','var'),
    if isfield(mri,'file'),
        file = mri.file;
    else
        [fileName, filePath, filterIndex] = uigetfile('*.mri', 'Locate CTF .mri file');
        file = fullfile(filePath, fileName);
    end
else
    [filePath, fileName, fileExt] = fileparts(fileName);
    file = fullfile(filePath, [fileName,'.mri']);
end

if isempty(file),
  error('...file is empty\n');
end

if exist(file,'file'),
    if force,
        fprintf('...file already exists, overwriting it.\n');
    else
        fprintf('...file already exists\n');
        [fileName, pathName] = uiputfile('*.mri', 'Specify CTF .mri file to write');
        file = fullfile(filePath, [fileName,'.mri']);
    end
end



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% open the file for writing
%    'ieee-be.l64' or 's' - IEEE floating point with big-endian byte
%                            ordering and 64 bit long data type.
[fid,message] = fopen(file,'wb','s');
if fid < 0, error('cannot open file for writing'); end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% write the file header
fprintf('...writing header ');
Version_2_Header_write(fid, mri.hdr);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% check header size, header should be 1028 bytes
header_bytes = ftell(fid);
fprintf('(wrote %d bytes)\n',header_bytes);
if header_bytes ~= 1028,
  msg = sprintf('failed to write 1028 bytes into the header, wrote %d bytes',header_bytes);
  error(msg);
end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% seek beyond the header, to the beginning of the data matrix
%fseek(fid,1028,'bof');

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% check if the data is 8 or 16 bits
switch mri.hdr.dataSize,
  case 1, % we have 8 bit data
    fprintf('...writing 8 bit image data\n');
    precision = 'uchar';
  case 2, % we have 16 bit data
    fprintf('...writing 16 bit image data\n');
    precision = 'int16';
  otherwise,
    msg = sprintf('unknown mri.hdr.dataSize: %g',mri.hdr.dataSize);
    error(msg);
end


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% now have the data array in a 3D matrix, we have to write it out in the
% correct byte order

% The CTF MRI File format used by MRIViewer consists of a binary file with a
% 1,028 byte header. The MRI data can be in 8-bit (unsigned character) or 16-bit
% (unsigned short integer) format and consists of 256 x 256 pixel slices, stored as
% 256 contiguous sagittal slices from left to right (or right to left if head orientation
% is "left-on-right"). Each slice is stored as individual pixels starting at the
% top left corner and scanning downwards row by row. Therefore the coronal
% position is fastest changing, axial position second fastest changing and sagittal
% position slowest changing value in the file, always in the positive direction for
% each axis (see section on Head Coordinate System for axis definitions). By
% default CTF MRI files have the file extension ".mri"

% MRIViewer uses these cardinal directions as axes in an internal coordinate system
% where sagittal = X, coronal = Y and axial = Z forming an additional
% right-handed coordinate system which is translated and rotated with respect to
% the Head Coordinate System and has its origin at the upper left anterior corner
% of the volume.

PixelDim = 256;
RowDim   = 256;
SliceDim = 256;

% imageOrientation, 0 = left on left, 1 = left on right
switch mri.hdr.imageOrientation,
  case 0,
    fprintf('...sagittal slices are neurological orientation (left is on the left)\n');
    fprintf('...+X left to right, +Y anterior to posterior, +Z superior to inferior\n');
  case 1,
    fprintf('...sagittal slices are radiological orientation (left is on the right)\n');
    fprintf('...+X right to left, +Y anterior to posterior, +Z superior to inferior\n');
  otherwise,
    msg = sprintf('...unknown mri.hdr.imageOrientation: %d\n',mri.hdr.imageOrientation);
    error(msg);
end

% output into sagittal slices, with the fastest moving index being Y,
% from anterior to posterior, then Z, from superior to inferior, then X,
% from left to right (or vice versa; depending on input mri struct).

n = 1;
y = 1:PixelDim; % +Y is from anterior to posterior

for x = 1:SliceDim, % +X is from left to right (or vice versa)
  for z = 1:RowDim, % +Z is from superior to inferior
      
      count = fwrite(fid,mri.img(x,y,z),precision);
      
      if count ~= PixelDim,
          error('failed to output 256 data points');
      end
      
  end
end

fclose(fid);

t=toc; fprintf('...done (%5.2f sec).\n\n',t);

return






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