ge_convertvolumemr.m

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function status = GE_convertVolumeMR(firstfile,outName)
%
% status = GE_convertVolumeMR(firstfile,outName)
%
%GE_convertVolumeMR
%
% Version 1.0
%
% Converts a series of GE slices in the EXXXXSYYYI*.MR format
% into Analyze format for SPM.
% firstfile is the name of the first file in the series.
% e.g. /home/inati/structdata/E12739S3I1.MR
% outName is used for naming the Analyze files
% status = 1 if there is an error.
%
% Uses spm functions
%
% Souheil J. Inati  
% Dartmouth College
% January 2002
% [e-mail]
%

status = 1;

if (nargin < 2)
        error('Not enough input arguments.')
        return
end

% Read the Header from the first file
[su_hdr,ex_hdr,se_hdr,im_hdr,pix_hdr,im_offset] = GE_readHeader(firstfile);

% The image Dimensions
Nx =  im_hdr.imatrix_X; % X Voxels
Ny =  im_hdr.imatrix_Y; % Y Voxels
Nz =  im_hdr.slquant;   % Z Voxels
volSize = [Nx Ny Nz];

% Read in the volume
[imageVol] = GE_readVolumeMR(firstfile, volSize, pix_hdr.img_depth, im_offset);

% Is the first image the first or the last?
if (se_hdr.end_loc - se_hdr.start_loc) > 0
  scandir = 1;
else
  scandir = -1;
end

% Compute the M matrix
M = GE_createSPMmat(im_hdr,scandir);

% Create the SPM volume
V.fname = outName;
V.dim = [volSize spm_type('int16')]; % short ints
V.mat = M;
V.pinfo = [1 0 0]';
V = spm_create_image(V);

% Write out the SPM Volume
% Don't use spm_write_vol because that sets a scale factor.
for i = 1:Nz
  V = spm_write_plane(V,squeeze(imageVol(:,:,i)),i);
end

% Done with vol
fprintf('Wrote %s.img.\n',outName);

% Done
fprintf('\nConversion Finished. \n');

status = 0;

return