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ctf_avw2mri.m
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ctf_avw2mri.m
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function mri = ctf_avw2mri(avw)
% mri = ctf_avw2mri(avw)
%
% The purpose of this function is to convert an Analyze volume into a CTF
% .mri volume. It currently requires that the Analyze volume is
% 256x256x256, 1x1x1 mm voxels. The avw_read function can
% handle various Analyze orientations, so this function assumes that the
% avw.img volume has axial unflipped orientation (it always is when
% returned by avw_read, regardless of the format in the .img file). The
% returned mri struct in the matlab workspace can be saved using
% ctf_write_mri.
%
% This function depends on the avw* functions availabe in the mri_toolbox
% at http://eeg.sf.net/. In particular, the avw_read and associated
% functions for reading an Analyze volume into a matlab avw struct, used as
% input to this function.
%
% <>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> %
% < > %
% < DISCLAIMER: > %
% < > %
% < THIS PROGRAM IS INTENDED FOR RESEARCH PURPOSES ONLY. > %
% < THIS PROGRAM IS IN NO WAY INTENDED FOR CLINICAL OR > %
% < OFFICIAL USE. > %
% < > %
% <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<> %
%
% $Revision: 1.1 $ $Date: 2009-01-30 03:49:26 $
% 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.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
mri = ctf_mri_make;
mri.file = [avw.fileprefix,'.mri'];
ver = '[$Revision: 1.1 $]';
fprintf('\nCTF_AVW2MRI [v%s]\n',ver(12:16)); tic;
% these checks for the volume dims/pixel size could be replaced with an
% interpolation function that could take any Analyze volume and convert it
% to 256x256x256, 1x1x1 mm
if avw.hdr.dime.dim(2) ~= 256,
error('avw.hdr.dime.dim(2) ~= 256');
end
if avw.hdr.dime.dim(3) ~= 256,
error('avw.hdr.dime.dim(3) ~= 256');
end
if avw.hdr.dime.dim(4) ~= 256,
error('avw.hdr.dime.dim(4) ~= 256');
end
if avw.hdr.dime.pixdim(2) ~= 1,
error('avw.hdr.dime.dim(2) ~= 256');
end
if avw.hdr.dime.pixdim(3) ~= 1,
error('avw.hdr.dime.dim(3) ~= 256');
end
if avw.hdr.dime.pixdim(4) ~= 1,
error('avw.hdr.dime.dim(4) ~= 256');
end
% mri.hdr.dataSize = 1 or 2 (bytes), 8 or 16 bits
if avw.hdr.dime.bitpix == 8,
mri.hdr.dataSize = 1;
mri.hdr.clippingRange = 255;
else
mri.hdr.dataSize = 2;
mri.hdr.clippingRange = 65536;
end
% This next step should always work correctly, given that avw_read always
% converts any Analyze orientation into axial unflipped in the matlab
% workspace variable avw.img; the axial unflipped orientation is
% (+X left, +Y anterior, +Z superior); the ctf orientation is
% (+X right, +Y posterior, +Z inferior), the complete opposite.
temp = flipdim(avw.img,1);
temp = flipdim(temp,2);
temp = flipdim(temp,3);
mri.img = temp;
t=toc; fprintf('...done (%5.2f sec).\n\n',t);
return